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Palumbo, Fabio. « Exploiting genomics and molecular markers for plant genetics and breeding ». Doctoral thesis, Università degli studi di Padova, 2018. http://hdl.handle.net/11577/3422297.
Texte intégralRésumé :
Co-dominant molecular markers, such as Microsatellites (or Simple Sequence Repeats, SSRs), are powerful tools for basic and applied research programs in crop plant species. Among the possible applications, they are frequently adopted for genetic traceability of food products, for assessing the genetic diversity of local varieties as well as the genetic identity of modern varieties, and also for marker-assisted breeding purposes. In fact, SSR markers are known to be highly polymorphic and discriminant, well distributed throughout the genome, not affected by environmental factors, more efficient and robust than phenotype-based field trials to detect and predict large numbers of distinct differences/traits among genotypes. However, a review of 90 original articles concerning the varietal characterization of some economically relevant crops in Italy, pointed out a lack of wider consensus among the authors regarding the strategy to design and to adopt for genotyping plant varieties with SSR markers. This study emphasized the urgent need to establish a common procedure concerning: i) the criteria adopted for selecting the marker loci and ii) the genetic parameters to be employed for varietal genotyping.
In order to demonstrate the potentials of these molecular markers, two case studies are presented. A study performed in Agordino, a very old local Venetian landrace of barley (Hordeum vulgare L.), stressed the concrete possibility to use SSR markers for genetic traceability of local varieties and, in particular, of their food derivatives. The genetic characterization of four main corn (Zea mays L.) landraces grown in Veneto (Italy), namely Sponcio, Marano, Biancoperla and Rosso Piave, by means of SSR markers, has shown great utility for monitoring and preventing further genetic erosion, thus preserving their gene pools, phenotypic identities and qualitative traits.
Despite the economic relevance of some crop species, it is common for researchers to deal with the complete lack of SSR data and, more in general, of genomic information. Fennel (Foeniculum vulgare Mill., 2n=2x=22) represents a brilliant example. To overcome this shortage, an Illumina HiSeq 2500 sequencing was carried out in this species, enabling the assembly of the first genome draft in 300,408 scaffolds. The subsequent annotation, permitted to detect and to characterize 103,306 SSR regions. Of these 40 were randomly chosen to design specific primer pairs, preliminary tested and 14 were successfully validated using a core collection of 118 fennel individuals potentially useful for F1 hybrid development. Moreover, the first fennel leaf transcriptome was produced overlapping two transcriptomes, one assembled de novo, the other with an in silico genome-guided approach. A total of 47,775 out of the 79,263 assembled transcripts were annotated and, among them, 11,853 loci contained a putative full-length CDS. Detailed analysis revealed 1,011 transcripts encoding for transcription factors (TFs), 6,411 EST-SSRs, 43,237 SNPs and 3,955 In/Dels. Assembled transcripts were also used to conduct the identification of loci related to the t-anethole biosynthesis, the major component of the fennel essential oils, well-known for its capability in reducing mild spasmodic gastro-intestinal pains as well as for its antithrombotic and hypotensive activity. Finally, detailed analysis revealed 1,011 transcripts encoding for transcription factors (TFs), 6,411 EST-SSRs, 3,955 In/Dels and 43,237 SNPs.
Single nucleotide polymorphisms (SNPs) represent another class of co-dominant markers heavily exploited for the discovery of Mendelian inheritance genes and for the analysis of polygenes or QTLs (quantitative trait loci). Adopting a Genotyping By Sequencing (GBS) approach, the first SNP-based genetic linkage map of leaf chicory (Cichorium intybus L. subsp. intybus var. foliosum, 2n=2x=18) was built using a BC1 population segregating 1:1 for the male sterility (ms) trait. This study enabled the genetic localization of the nuclear ms gene, termed Cims1, within linkage group 9 and the identification of four SNPs that proved to fully co-segregate with the target gene. Considering that this form of male-sterility, controlled by a single recessive nuclear gene, is one of the most effective methods to develop F1 hybrids, our data will be exploitable for marker-assisted selection purposes.I marcatori co-dominanti, tra cui i Microsatelliti (o SSR), sono strumenti molecolari ampiamente utilizzati nell’ambito della ricerca di base e applicata in specie di interesse alimentare. Tra le possibili applicazioni ricordiamo il loro impiego per studi di tracciabilità genetica di prodotti alimentari, per analisi di diversità genetica di varietà locali e identità genetica di varietà moderne e per il miglioramento genetico. Infatti gli SSR sono noti per essere altamente polimorfici e discriminanti, ben distribuiti all’interno del genoma, non influenzati da fattori ambientali, più efficienti e robusti dei marcatori fenotipici nelle analisi di diversità tra genotipi. Tuttavia, un’indagine condotta su 90 articoli scientifici basati sull’identificazione varietale delle specie economicamente più rilevanti in Italia, ha messo in luce la mancanza di un approccio comune tra gli autori in relazione alle strategie da utilizzare per questo tipo di studi. Inoltre lo studio ha evidenziato il bisogno improrogabile di stabilire procedure comuni riguardanti: i) i criteri da adottare per la scelta dei marcatori SSR ii) i parametri genetici più utili a questo scopo. Per dimostrare il potenziale di questa classe di marcatori, vengono presentati due casi studio. Il primo, che ha come oggetto Agordino, un’antica varietà locale veneta di orzo (Hordeum vulgare L.), ha permesso di enfatizzare la possibilità concreta di utilizzare i microsatelliti per la tracciabilità genetica di varietà locali ed, in particolare, di prodotti alimentari derivati. La caratterizzazione delle quattro principali varietà di mais (Zea mays L.) in Veneto -Sponcio, Marano, Biancoperla e Rosso Piave- attraverso marcatori SSR si è dimostrata invece estremamente utile per monitorare e prevenire fenomeni di erosione genetica, consentendo così di preservare la ricchezza genetica che le caratterizza, la loro identità fenotipica e i tratti qualitativi. Nonostante l’interesse economico di alcune specie, non è così raro per i ricercatori doversi interfacciare con la totale mancanza di dati SSR e, più in generale, di informazioni genomiche. Finocchio (Foeniculum vulgare Mill., 2n=2x=22), a tal proposito, rappresenta un esempio calzante. Per sopperire a questa carenza di dati, è stato condotto un sequenziamento su piattaforma Illumina Hiseq 2500, permettendo così l’assemblaggio del prima bozza del genoma di finocchio in 300408 sequenze. La successiva annotazione ha consentito quindi di individuare e caratterizzare 103306 regioni altamente ripetute. Di queste, 40 scelte in modo casuale per il disegno di primer specifici, sono state testate e 14 sono state validate su una popolazione commerciale di 118 individui potenzialmente fruibili per lo sviluppo di ibridi F1. Inoltre, il primo trascrittoma di foglia di finocchio è stato prodotto sovrapponendo due trascrittomi uno assemblato de novo e l’altro in silico, tramite allineamento sul genoma. 47775 dei 79263 trascritti totali sono stati annotati e 11853 risultano contenere una sequenza codificante completa. L’assemblaggio ha quindi consentito l’identificazione di loci coinvolti nella via biosintetica dei trans-anetolo, componente preponderante degli oli essenziali di finocchio e noto per le sue abilità nel ridurre dolori gastro-intestinali nonché per la sua attività antitrombotica e ipotensiva. Analisi dettagliate hanno infine messo in luce 1011 trascritti codificanti per fattori di trascrizione (FT), 6411 microsatelliti (EST-SSR), 3955 inserzioni/delezioni e 43237 polimorfismi a singolo nucleotide (SNP). I marcatori di tipo SNP costituiscono un’altra classe di marcatori codominanti largamente sfruttati per la caratterizzazione di geni ad eredità Mendeliana e per l’analisi di poligeni o loci codificanti tratti quantitativi (QTL). Attraverso un approccio di genotipizzazione tramite sequenziamento (GBS) è stata costruita la prima mappa genetica in radicchio (Cichorium intybus L. subsp. intybus var. foliosum, 2n=2x=18) utilizzando una popolazione BC1 (ottenuta tramite tecniche di reincrocio) segregante 1:1 per il tratto “maschio sterilità”. Questo studio ha permesso di localizzare finemente il gene nucleare della maschio sterilità Cims1 all’interno del gruppo di associazione 9 e ha consentito l’identificazione di 4 SNP co-segreganti a 0 cM con il suddetto gene. Considerato che questa forma di maschio-sterilità, controllata da un singolo allele recessivo nucleare, è uno dei metodi più efficaci per produrre ibridi F1, questi risultati saranno di estrema utilità per studi di miglioramento genetico.
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Marconi, Thiago Gibbin. « Mapa funcional em cana-de-açúcar utilizando marcadores moleculares baseados em SSR e SNP ». [s.n.], 2011. http://repositorio.unicamp.br/jspui/handle/REPOSIP/316492.
Texte intégralRésumé :
Orientadores: Anete Pereira de Souza, Antonio Augusto Franco GarciaTese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
Made available in DSpace on 2018-08-19T06:27:16Z (GMT). No. of bitstreams: 1 Marconi_ThiagoGibbin_D.pdf: 16468359 bytes, checksum: 01e191ac164eff1d269733328f5be31e (MD5) Previous issue date: 2011
Resumo: A utilização dos marcadores moleculares em estudos de mapeamento genético e de QTLs (Quantitative Trait Loci) tem proporcionado um importante progresso no conhecimento da genética e da estrutura genômica da cana-de-açúcar. O projeto de sequenciamento de ESTs (Expressed Sequence Tags) do programa Genoma da FAPESP (SUCEST) identificou aproximadamente 43 mil clusters que representam os genes de cana-de-açúcar. Sabe-se que os ESTs apresentam grande potencial para serem utilizados no desenvolvimento de marcadores genético-moleculares. Tendo em vista os avanços possíveis no melhoramento genético da cana-de-açúcar com a construção de um mapa genético funcional a partir de ESTs de interesse, este trabalho teve como objetivos o mapeamento genético em uma população F1 de cana-de-açúcar utilizando marcadores moleculares do tipo EST-SSRs (Expressed Sequence Tags - Simple Sequence Repeats) e SNP (Single Nucleotide Polymorphism), desenvolvidos a partir de seqüências ESTs homólogas a genes de interesse. Os SNPs desenvolvidos e mapeados demonstraram novos tipos de segregações possíveis de serem incorporadas ao mapeamento genético em cana-de-açúcar, representando avanços para a análise genética de poliplóides e possibilitando a saturação do mapa genético com marcadores completamente informativos. Os marcadores moleculares EST-SSRs e SNPs desenvolvidos e integrados ao mapa genético da cana-de-açúcar aumentaram sua resolução e também as possibilidades de mapeamento dos QTLs com maior precisão
Abstract: The use of molecular markers in genetic mapping studies and QTL (Quantitative Trait Loci) has provided an important advance in knowledge of genetics and genomic structure of sugarcane. The sequencing project of ESTs (Expressed Sequence Tags) form FAPESP's Genome Program (SUCEST) identified approximately 43 000 clusters representing the sugarcane genes. It is known that the ESTs have great potential for use in the development of genetic molecular markers. Given the possible advances in genetic breeding of sugarcane with the construction of a functional genetic map from ESTs of interest, the aim of this study was the construction of a genetic map in a F1 population of sugarcane using molecular markers EST-SSR (Expressed Sequence Tags - Simple Sequence Repeats) and SNP (Single Nucleotide Polymorphism) derived from ESTs sequences homologous to genes of interest. The developed and mapped SNPs demonstrated new types of segregation ratio that could be incorporated in the genetic mapping of sugarcane, representing advances for the genetic analysis of polyploid and allowing the saturation of the genetic map with fully informative markers. The EST-SSR markers and SNPs developed and integrated into the genetic map of sugarcane increased the resolution, coverage of the genome and also the possibilities of mapping QTLs with greater precision
Doutorado
Genetica Vegetal e Melhoramento
Doutor em Genetica e Biologia Molecular
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Costa, Zirlane Portugal da. « Desenvolvimento de marcadores SSR e SNP em maracujá-doce a partir de uma biblioteca enriquecida com genes de resposta à Xanthomonas axonopodis ». Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-12082014-082213/.
Texte intégralRésumé :
Um dos desafios atuais da pesquisa em frutíferas tropicais é incorporar abordagens baseadas em marcadores moleculares nos programas convencionais de melhoramento. O maracujá-doce (Passiflora alata) é uma espécie diploide, de fecundação cruzada e pouco explorada. Recentemente, nosso grupo construiu um mapa de ligação de P. alata composto de diferentes tipos de marcadores moleculares. Além disso, dispõe-se de um conjunto de transcritos de Passiflora edulis, obtidos a partir de duas bibliotecas de expressão: forward e reverse onde foram isolados transcritos diferencialmente expressos na planta inoculada com Xanthomonas axonopodis (Xap) (672) e na planta controle, não inoculada (310), respectivamente. Assim, neste estudo, este conjunto de transcritos foi explorado visando ao desenvolvimento de marcadores SSR e SNP com o intuito de enriquecer, posteriormente, o mapa de ligação de P. alata com marcadores funcionais putativos. Para o desenvolvimento dos marcadores SSRs, as 672 sequências da biblioteca forward foram investigadas e em 91 delas foram encontrados 115 SSRs. Como esperado, a classe de repetições trinucleotídicas foi a mais abundante, sendo o motivo (AG)n o mais comum entre as repetições dinucleotídicas. Desenhou-se primers para amplificar 42 desses SSRs. Dois acessos de P. edulis e seis indivíduos da população de mapeamento de P. alata foram usados nos testes de transferibilidade e avaliação do polimorfismo. Trinta e quatro pares de primers apresentaram bom padrão de amplificação, porém apenas 10 deles revelaram polimorfismo em P. alata. Para o desenvolvimento dos marcadores SNPs, 118 sequências selecionadas das bibliotecas de expressão forward e reverse foram usadas para o desenho de primers; 37 delas foram usadas para avaliar o polimorfismo no mesmo set de indivíduos de P. alata. Foram encontrados 34 locos contendo SNPs bialélicos em 16 fragmentos gênicos, cujas sequencias variaram em tamanho de 332 a 872 pb. Considerando todos os fragmentos gênicos (16), foi analisado um total de 10.003 pb; a frequência de SNPs foi estimada como sendo 1 a cada 294 pb. Observou-se a mesma ocorrência de SNPs (50%, 17/34) em regiões codantes e não-codantes. Uma função putativa pôde ser atribuída a todos os fragmentos gênicos de P. alata, sendo que 82% mostraram homologia com as mesmas proteínas das sequências de origem, isoladas de P. edulis. No geral, os locos marcadores apresentaram baixo nível de polimorfismo molecular. Este é o primeiro trabalho sobre o desenvolvimento de locos marcadores funcionais putativos em Passiflora usando transcritos expressos em resposta à Xap.One of the current challenges of tropical fruit research is to incorporate molecular marker-based approaches into conventional breeding programs. The sweet passion fruit (Passiflora alata) is a diploid, outcrossing and underexploited species. Recently, our group has constructed a P. alata linkage map consisted of different types of molecular markers. Moreover, we have a set of transcripts of Passiflora edulis obtained from two expression libraries: the forward and the reverse where differentially expressed transcripts were isolated from a plant inoculated with Xanthomonas axonopodis (Xap) (672), and from the control plant, uninoculated (310), respectively. Thus, in this study, this set of transcripts were exploited aiming at the development of SNP and SSR markers for future enrichment of the P. alata linkage map with putative functional markers. For the development of SSR markers, the 672 sequences from the forward library were investigated and 91 of them were found to have 115 SSRs. As expected, the trinucleotide class of repeats was the most abundant, and the (AG)n motif was the most common among the dinucleotide repeats. Primers were designed to amplify 42 of these SSRs. Transferability tests and polymorphism investigation were carried out using two accessions of P. edulis and six individuals of the mapping population of P. alata. Thirty-four primer pairs showed a good amplification pattern but only 10 loci revealed polymorphism in P. alata. For the development of SNP markers, 118 sequences selected from forward and reverse expression libraries were used for designing primers; 37 were used to assess the polymorphism in the same set of individuals of P. alata. Thirty-four biallelic SNPs were found in 16 gene fragment sequences that ranged in size from 332 to 872 bp. Considering all gene fragments, a total of 10,003 bp was obtained; the frequency of SNPs was estimated to be 1 every 294 bp. The same prevalence of SNPs (50%, 17/34) was observed within coding and non-coding regions. A putative function was assigned to all gene fragments of P. alata; 82% of them have shown homology to the original protein sequences isolated from P. edulis. Overall, the marker loci showed a low level of molecular polymorphism. This is the first report on the development of putative functional marker loci in Pasiflora using transcripts induced in response to Xap.
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Pereira, Guilherme da Silva. « Desenvolvimento de marcadores SSR, M-AFLP e SNP visando à integração de mapas genético-moleculares de Passiflora alata Curtis ». Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-17032011-105123/.
Texte intégralRésumé :
Embora não exista uma variedade comercial de maracujazeiro-doce (Passiflora alata Curtis), a fruta vem ganhando espaço no mercado brasileiro, justificando o uso de técnicas convencionais e moleculares no melhoramento da cultura. Nas espécies em que ocorre autoincompatibilidade e o cruzamento entre indivíduos é obrigatório, como nos maracujazeiros, não é possível a obtenção de populações convencionais de mapeamento. Por isso, utiliza-se a técnica two-way pseudo-testcross para a geração de mapas genéticos, usando uma população F1 segregante e marcas dominantes, o que resulta na geração de mapas individuais, sendo um por genitor. A inconveniência desta estratégia tem sido superada pelo uso de marcadores codominantes e estatísticas mais robustas. Marcadores baseados em SSRs (ou microssatélites) e em SNPs são úteis para promover a integração dos mapas, pois são codominantes e abundantes no genoma de plantas. O presente trabalho objetivou gerar um mapa integrado de P. alata, usando novos marcadores SSR, além de M-AFLP e SNP. Os locos SSR foram desenvolvidos a partir de uma biblioteca genômica enriquecida, previamente construída. Dentre os motivos, prevaleceram os dinucleotídicos perfeitos de (AC)n e (AG)n. Neste trabalho, mais 175 primers de SSR foram desenhados e avaliados juntamente com 111 previamente obtidos, observando-se uma taxa de polimorfismo entre os genitores de 31,9%. Ainda com esse conjunto de primers, foi possível recuperar polimorfismos de conformação de fita simples (SSR-SSCP) em 23 locos. A genotipagem de 26 SSRs na população segregante resultou em 40 locos, os quais, associados a um SSR-SSCP, resultaram em seis locos com segregações mais informativas do tipo 1:1:1:1 e 1:2:1. M-AFLPs apresentaram 34,0% de polimorfismo, acrescendo mais seis locos informativos ao mapa de ligação. Os SNPs revelados pelo alinhamento das sequências de AFLP e de genes putativos revelaram uma mutação a cada 110 pb, em média. Foi possível a genotipagem de SNP para um dos genes, e conjuntos de primers para outros locos são propostos. Mapas individuais para ambos os genitores foram obtidos com 175 e 229 marcadores de segregação 1:1, respectivamente, ao passo que o mapa integrado incluiu, além desses, 12, 7 e 40 marcas de segregação 1:1:1:1, 1:2:1 e 3:1, respectivamente. Foi possível estabelecer a correspondência para a maioria dos grupos de ligação individuais e integrados. Observou-se a ampla distribuição de marcadores baseados em microssatélites, com a eventual formação de clusters. Este mapa, embora preliminar, pode ser útil no mapeamento de caracteres agronômicos e em estudos comparativos com o mapa integrado de P. edulis f. flavicarpa.Although there is no a commercial variety of sweet passion fruit (Passiflora alata Curtis) the crop has gained importance in the Brazilian market. This justifies the use of conventional and molecular techniques for breeding the crop. In species where self-incompatibility occurs and crossing between plants is necessarily required, as in passion fruits, conventional mapping populations are not possible to be produced. Therefore, the two-way pseudo-testcross approach is used for the generation of genetic maps, employing an F1 segregating population and dominant markers, resulting in individual maps, one for each parent. The drawback of this strategy has been overcome by the use of codominant markers and more robust statistics. Markers based on SSRs (or microsatellites) and SNPs are useful for integrating the maps, because of their codominant inheritance and abundance in plant genomes. This study aimed to generate an integrated map of P. alata using new SSR, M-AFLP and SNP markers. The SSR loci were developed from an enriched genomic library previously constructed. Among the motifs, the most frequent were perfect di-nucleotides, (AC)n and (AG)n rich. In this study, 175 SSR primers were designed and evaluated along with 111 previously obtained. A polymorphism rate of 31.9% was observed between the parents. Using these primer sets, it was possible to recover single-stranded conformation polymorphisms (SSR-SSCP) at 23 loci. The genotyping of the segregating population using the 26 SSRs resulted in 40 loci; adding a SSR-SSCP, the result was six informative loci showing segregation rations of 1:1:1:1 and 1:2:1. M-AFLPs showed 34.0% of polymorphism, providing six informative loci to the map. The alignment of parental AFLP and putative gene sequences revealed one SNP per 110 bp on average. It was possible to genotype one gene-derived SNP, and primer sets for other loci are proposed. Individual maps of both parents were obtained with 175 and 229 markers segregating in 1:1 ratio, respectively, while in the integrated map were included 12, 7 and 40 markers segregating in 1:1:1:1, 1:2:1 and 3:1 rations, respectively. It was possible to establish the correspondence for most of the individual linkage groups and the integrated groups. Microsatellite-based markers showed a wide genome distribution, with eventual cluster formation. Although preliminary, this map may be useful for mapping agronomic traits and in comparison studies with the integrated map of P. edulis f. flavicarpa.
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Ortega, Maria Andrea. « Identification of Molecular Markers Associated with the Rps8 locus in Soybean and Evaluation of Microsporogenesis in Rps8/rps8 Heterozygous Lines ». The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1259772038.
Texte intégral
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Gettings, Katherine Butler. « Forensic Ancestry and Phenotype SNP Analysis and Integration with Established Forensic Markers ». Thesis, The George Washington University, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=3590467.
Texte intégralRésumé :
When an evidential DNA profile does not match identified suspects or profiles from available databases, further DNA analyses targeted at inferring the possible ancestral origin and phenotypic characteristics of the perpetrator could yield valuable information. Single Nucleotide Polymorphisms (SNPs), the most common form of genetic polymorphisms, have alleles associated with specific populations and/or correlated to physical characteristics. With this research, single base primer extension (SBE) technology was used to develop a 50 SNP assay designed to predict ancestry among the primary U.S. populations (African American, East Asian, European, and Hispanic/Native American), as well as pigmentation phenotype. The assay has been optimized to a sensitivity level comparable to current forensic DNA analyses, and has shown robust performance on forensic-type samples. In addition, three prediction models were developed and evaluated for ancestry in the U.S. population, and two models were compared for eye color prediction, with the best models and interpretation guidelines yielding correct information for 98% and 100% of samples, respectively. Also, because data from additional DNA markers (STR, mitochondrial and/or Y chromosome DNA) may be available for a forensic evidence sample, the possibility of including this data in the ancestry prediction was evaluated, resulting in an improved prediction with the inclusion of STR data and decreased performance when including mitochondrial or Y chromosome data. Lastly, the possibility of using next-generation sequencing (NGS) to genotype forensic STRs (and thus, the possibility of a multimarker multiplex incorporating all forensic markers) was evaluated on a new platform, with results showing the technology incapable of meeting the needs of the forensic community at this time.
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Nsabiyera, Vallence. « Genetic analysis and development of molecular markers linked with rust resistance in wheat ». Thesis, The University of Sydney, 2017. http://hdl.handle.net/2123/17847.
Texte intégralRésumé :
The main aim of this study was to develop closely linked markers for rust resistance genes Lr48, Lr49 and Sr48. In addition, mapping of adult plant stripe rust resistance in a landrace Aus27284 was also performed. Close SNP-Lr48 associations were identified using the iSelect 90K Infinium Array. Five SNP markers co-segregated with Lr48 and IWB70147 mapped 0.3 cM proximal. Kompetitive allele-specific PCR (KASP) assays were developed for linked SNP. In contrast, the KASP markers developed from the iSelect 90K Infinium SNP array for Lr49 did not result in close marker-trait association. Sequence comparison of flow sorted chromosome 4B from parents VL404 (Lr49) and WL711 (lr49) resulted in close association of sunKASP_21 (0.4 cM) with Lr49. The Arina/Cezanne RIL population was used to develop markers linked with Sr48 using the DArTseq platform and the iSelect 90K Infinium SNP Array. DArTseq based linkage map located Sr48 on the short arm of chromosome 2D. Marker sun590 derived from a DArTseq marker mapped 0.4 cM distal to Sr48. Sr48 was earlier mapped in the long arm of chromosome 2A in the Arina/Forno RIL population based on repulsion linkage with Yr1. The detection of 2AL-2DS translocation in Forno through genomic in-situ hybridisation (GISH) appears to have resulted in pseudo-linkage to locate Sr48 in chromosome 2AL. Aus27284 was susceptible to stripe rust at the seedling stage and exhibited resistance in field experiments. Genetic analysis showed monogenic segregation and the resistance gene was temporarily designated YrAW11. YrAW11 was located on chromosome 3BS near the centromere and KASP¬_65624/KASP_58449 and KASP_53113 flanked this locus. The closely linked markers identified in this study were tested on a set of Australian and Nordic wheat genotypes to validate their suitability for marker assisted selection (MAS). The results indicated that IWB70147, sunKASP_21, sun590 and KASP-53113 can be used for MAS of Lr48, Lr49, Sr48 and YrAW11, respectively.
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Moreira, Ricardo Franco Cunha. « Estrutura genética de populações de Crinipellis perniciosa e Moniliophthora roreri utilizando marcadores RAPD e SSR / ». Jaboticabal : [s.n.], 2006. http://hdl.handle.net/11449/102837.
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Resumo: Vassoura-de-bruxa e podridão de Moniliophthora, causadas pelos fungos Crinipellis perniciosa e Moniliophthora roreri, respectivamente, são as doenças de maior impacto econômico da cultura do cacau e estão presentes na maioria dos países produtores do Continente Americano. Evidências biológicas e moleculares comprovam que estes fitopatógenos estão intimamente relacionados. O uso de resistência genética através de dones resistentes de cacaueiro, é a medida mais eficiente no controle destas doenças. O conhecimento sobre as populações destes fungos é importante na geração de informações para o programa de melhoramento genético do cacau visando resistência. Marcadores moleculares RAPO e SSR foram usados para analisar a estrutura genética de populações destes fitopatógenos. No geral, as populações do Brasil, Equador, Peru e Trinidad agruparam-se de acordo com o país de origem, apresentando maior variabilidade dentro e não entre países, com presença de subpopulações. A população do Brasil apresentou maior diversidade genotípica em comparação com as demais. A transferibilidade de pares de primers SSR de C. perniciosa para M. roreri foi satisfatório. Populações de M. roreri do Equador e Peru apresentaram alta diferenciação genética interpopulacional, sendo que a do Peru apresentou maior variabilidade.Abstract: Witches' broom and fresty pod hot, caused by Crinipellis perniciosa and Moniliophthora roreri, are the most important disease of cacao in the American Continent. Biological and molecular data have shown that these pathogen are closely related. Resistance is the most efficient method to control these diseases. Therefore, information about the population structure of these cacao pathogen are important to support the breeding programo Molecular markers such as RAPD and SSR were used to analyzed the genetic structure of C. perniciosa and M. roreri frem the American Continent. Populations of C. perniciosa clustered according to their country of origin, with more variability within than between countries, revealing the presence of subpopulations. C. perniciosa Brazilian populations presented higher genotypic diversity than C. perniciosa from other countries. The transferability of C. perniciosa-SSR to M. roreri was positive. On the contrary, high interpopulation variability was observed between Ecuador and Peru, being M. roreri from Peru much more diverse than Ecuador.
Orientador: Carlos Ruggiero
Coorientador: Karina Peres Gramacho
Banca: João Carlos de Oliveira
Banca: Antonio de Goes
Banca: Maria Lúcia Carneiro Vieira
Banca: João Alexio Scarpare Filho
Doutor
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Soattin, Marica. « The use of molecular markers for analyzing genes and genomes of livestock ». Doctoral thesis, Università degli studi di Padova, 2008. http://hdl.handle.net/11577/3425494.
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The present thesis has been developed considering three different livestock species such as chicken, cattle and sheep. The aim of the study was the evaluation of the application of molecular makers in order to assay the genetic population structure on seven local breeds of chicken, to evaluate the applicability of candidate genes as support of conventional breeding on Piedmontese cattle breed and to detect new SNPs on a sheep population. The first two researchs were carried out at Department of Animal Science of University of Padova while the last one at Reprogen (Faculty of Veterinary Science, University of Sydney, NSW, AUS).
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Fazenda, Pedro Miguel Jesus. « Identificação de marcadores SSR e de SNPs em medronheiro (Arbutus unedo L.) por sequenciação massiva paralela ». Master's thesis, ISA, 2013. http://hdl.handle.net/10400.5/6487.
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Mestrado em Engenharia Agronómica - Instituto Superior de AgronomiaThe strawberry tree (Arbutus unedo L.) is native to the Mediterranean region. The use of molecular markers in this species has been limited to the use of RAPDs, ISSRs as well to the cross-amplification of SSRs from other Ericaceae. In this work, we developed a protocol for extracting nuclear DNA from the strawberry tree and performed partial next-generation sequencing of the Arbutus unedo L. genome using the "Ion Torrent" (Life Technologies) platform. The next-generation sequencing resulted in 198,856 sequences ("raw data") with an average size of 123 bp, which were uploaded to the NCBI database "Sequence Read Archive" (SRA) with the accession number: SRX341237. Data analysis led to the identification of 1085 microsatellite-containing sequences, which were also uploaded with accession numbers: from KF023636 to KF024720 to the NCBI databases. Primers were designed for 18 microsatellite loci of which only three have proved to be polymorphic in a panel of 16 samples. Based on identified 25 SNPs one CAPS marker was developed, which despite being heterozygous revealed to be monomorphic among the 16 analyzed samples.
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Priori, Daniela. « Caracterização molecular de recursos genéticos de Cucurbita argyrosperma, Cucurbita ficifolia e Cucurbita pepo ». Universidade Federal de Pelotas, 2011. http://repositorio.ufpel.edu.br/handle/ri/2068.
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Previous issue date: 2011-02-25Genetic resources conserved in genebanks have a great value in terms of conservation of rare types, when they are threatened by abandonment of farming or as a unique resource for plant breeding programs. Among the accessions conserved in genebanks important sources of genetic variability can be found for obtaining more productive genotypes tolerant to biotic and abiotic stresses and improved nutritional quality. To have success in that demand is necessary that the accessions contained in genebanks are characterized and evaluated in terms of both qualitative and quantitative characters. The characterization and evaluation of accessions conserved in genebanks must be priorities in the strategy for management of genetic resources, as they provide better knowledge of the germplasm available, is essential for use in breeding programs. In Brazil, there is little information on genetic resources of Cucurbits, especially as regards Cucurbita ficifolia, Cucurbita argyrosperma. Large number of Cucurbita landraces grown in the country could be better exploited as sources of genes for breeding programs, after genetic characterization. Much of the genetic diversity of different Cucurbita landraces grown in southern Brazil has been lost due to neglect of cultivation or its replacement by commercial hybrid varieties. This work was carried in order to contribute to general knowledge related to genetic resources of Cucurbita argyrosperma, Cucurbita ficifolia and Cucurbita pepo, and with specific objectives to assess the transferability of primers designed to C. pepo in C. argyrosperma and C. ficifolia and to evaluate the genetic variability within and among landraces of C. pepo grown in Rio Grande do Sul through analysis of microsatellite markers. Ten accessions of C. pepo, nine of C. argyrosperma and five of C. ficifolia belonging to the Active Germplasm Bank of Cucurbitaceae from Embrapa Temperate Agriculture were submitted to molecular characterization. The genetic distance between these accessions was determined. The transferability of SSR loci from C. pepo to C. argyrosperma and C. ficifolia was 85% and 80% respectively. The analysis of these 24 accessions with 35 loci generated a total of 105 SSR markers, ranging from one to four alleles per locus, of which 56 (53,33%) were polymorphic, showing that there is genetic diversity in the accessions analyzed. The presence and absence of markers allowed to find 100 loci, varying from one to five alleles per locus, with overall average of three alleles per marker analyzed. Among the 34 loci tested, 29 (85.2%) were polymorphic, showing that there is genetic variability among the accessions of C. pepo analyzed. Data evaluation was done by molecular analysis of molecular variance (AMOVA). It was observed that 54.60% of genetic variability is attributable to variation between accessions and 45.39% is attributed to differences within accessions. A comparative analysis was made between the ten accessions studied, analyzed two by two by AMOVA. From 45 comparisons between the ten accessions significant differences there were detected between 35 comparisons, with average of 57.10% of molecular variation attributed to differences between accessions. Genetic variation among counties where the accessions were collected was not significant, indicating that there is not population subdivision according to geographic region. Results indicate that the microsatellites were efficient for the characterization and molecular analysis of genetic divergence. These studies contributed to increase the knowledge related to these genetic resources. SSR primers developed for Cucurbita pepo can be used for molecular characterization of C. argyrosperma and C. ficifolia. Landraces of C. argyrosperma and C. ficifolia showed low genetic variation, while C. pepo shows great variability. The largest proportion of variability in C. pepo is distributed between accessions and not within accessions.
Os recursos genéticos conservados em bancos de germoplasma apresentam grande valor do ponto de vista da conservação de tipos raros, quando os mesmos são ameaçados pelo abandono do cultivo ou como recurso insubstituível para programas de melhoramento genético vegetal. Dentre os acessos contidos nos bancos de germoplasma podem ser encontradas importantes fontes de variabilidade genética para a obtenção de genótipos mais produtivos, tolerantes a estresses bióticos e abióticos e com melhor qualidade nutricional. Para que haja sucesso nessa demanda é necessário que os acessos contidos nos bancos de germoplasma sejam caracterizados e avaliados, tanto em termos de caracteres qualitativos quanto quantitativos. No Brasil, há pouca informação sobre os recursos genéticos de Cucurbitáceas, de modo especial no que se refere à Cucurbita argyrosperma e Cucurbita ficifolia. Grande número de variedades locais de Cucurbita cultivadas no país poderiam ser melhor exploradas como fontes de genes para programas de melhoramento, após a devida caracterização. Muito da diversidade genética das variedades locais de diferentes espécies de Cucurbita cultivadas no Sul do Brasil vem sendo perdida devido ao abandono do cultivo ou à sua substituição por variedades híbridas comerciais. Este trabalho foi realizado com o objetivo geral de contribuir para o conhecimento relacionado aos recursos genéticos de Cucurbita argyrosperma, C. ficifolia e C. pepo, e objetivos específicos de avaliar a transferibilidade de loci de microssatélites de C. pepo para C. argyrosperma e C. ficifolia; e avaliar a variabilidade genética entre e dentro de variedades locais de C. pepo cultivadas no Rio Grande do Sul por meio da análise de marcadores microssatélites. Foram analisados dez acessos de C. pepo, nove de C. argyrosperma e cinco de C. ficifolia do acervo do Banco Ativo de Germoplasma de Cucurbitáceas da Embrapa Clima Temperado. A distância genética entre esses acessos foi determinada. A transferibilidade de locos SSR de C. pepo para C. argyrosperma e C. ficifolia foi de 85% e 80%, respectivamente. A análise dos 24 acessos de Cucurbita por meio de 35 loci SSR gerou um total de 105 marcadores SSR, com variação de um a quatro alelos por loco, dos quais 56 (53,33%) foram polimórficos, evidenciando que há diversidade genética entre os acessos analisados. Através dos dados de presença e ausência de marcadores obtidos com 34 combinações de primers, foram encontrados 100 locos com variação de um a cinco alelos por loco, com média geral de três alelos por marcador analisado. Dentre os 40 locos analisados, 29 (85,3%) foram polimórficos, evidenciando que há variabilidade genética entre os acessos de C. pepo analisados. A avaliação dos dados moleculares foi feita pela análise molecular da variância (AMOVA). Deste modo, foi possível verificar que 54,60% da variabilidade genética é atribuída à variação entre acessos e 45,39% é atribuída a diferenças dentro dos acessos. Foi feita a análise comparativa entre os dez acessos estudados, analisados dois a dois, pela análise AMOVA. Das 45 comparações entre os dez acessos, foram significativas as diferenças entre 35 delas, com média de 57,10% da variação molecular atribuída às diferenças entre acessos. A variação genética entre os municípios onde os acessos foram coletados não foi significativa, indicando que não ocorre subdivisão de populações em função da região geográfica. Os resultados obtidos indicam que os microssatélites foram eficientes para a caracterização molecular e a análise da divergência genética. É possível utilizar primers de microssatélites desenvolvidos para C. pepo na caracterização molecular de C. argyrosperma e C. ficifolia. Variedades locais de C. argyrosperma e C. ficifolia apresentam pouca variabilidade genética, enquanto que C. pepo evidencia grande variabilidade genética. A maior proporção da variabilidade em C. pepo encontra-se distribuída entre os acessos, e não dentro dos acessos.
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Roldan, Montes Valentina [UNESP]. « Estudo de polimorfismos do gene TLR4 e suas associações com características de importância econômica em búfalas leiteiras ». Universidade Estadual Paulista (UNESP), 2016. http://hdl.handle.net/11449/144661.
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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
Considerando a importância das doenças que afetam o desempenho produtivo dos animais na indústria leiteira em todo o mundo é necessário implementar ferramentas moleculares que auxiliem na identificação e controle destas doenças. Quando ocorre alguma infecção em um organismo superior, existe aumento do número de células de defesa e o sistema imune inato proporciona uma linha de defesa contra os patógenos. Os “Toll Like Receptors” (TLR) são proteínas da membrana que desempenham um papel chave na imunidade, reconhecendo patógenos e, posteriormente, ativando as respostas. O presente estudo foi realizado para identificar SNPs no gene TLR4 bubalino e analisar suas associações com características de importância produtiva, incluindo a contagem de células somáticas (CCS). Foram utilizadas amostras de DNA de 130 búfalas da raça Murrah. A região codificante do gene TLR4 foi amplificada através de reações de PCR e posteriormente sequenciada. Os polimorfismos encontrados tiveram suas frequências alélicas e genotípicas calculadas e verificadas quanto ao equilíbrio de Hardy-Weinberg, além de serem utilizados para os estudos de associação. Foram identificados 13 polimorfismos do tipo SNP para as regiões sequenciadas do gene TLR4, sendo que a maioria encontra-se em região codificante. Encontrou-se associação significativa, com porcentagem de gordura dos Snps g514>C/T (P=0,0040) e g536>A/T (P=0,0035). As associações para CCS demostrou-se altamente significantes (p=<0,001) para todos os Snps (g322>G/A, g514>C/T, g536>A/T, g8338>A/C, g8341>A/G, g8342>T/G, g8343>G/A, g8345>A/G, g8413>A/G, g8428>G/A, g8438>A/C, g8578>G/T e g8582>A/C). Sugere-se que os Snp do gene TLR4 possam ser utilizados como marcadores moleculares em búfalos, já que foram verificadas suas associações com características como porcentagem de gordura e proteína, e contagem de células somáticas.
Molecular markers might be developed to investigate genetic variants associated to the disease and assist selection process in order to identify resistant animals. When the mammary gland is infected, there is an increase in the defense cells, also called somatic cells. It is a defense line of the immune system against pathogens. The “tool like receptors” TLR are membrane proteins that have an important role in the immunity, recognizing pathogens and activating adequate responses. The present study aimed to investigate the association of TLR4 gene SNPs with productive characteristics and SCC in buffaloes. The DNA was extracted from hair follicules of 130 Murrah buffaloes. The fragments were amplified by Polymerase Chain Reaction (PCR) and sequenced. Thirteen SNPs were found. Allelic and genotypic frequencies were calculated as well as the adhesion to Hardy-Weinberg equilibrium and the linkage disequilibrium (r2) and the association to the characteristic. For SCC was tested methodology linear generalized mixed model, assuming Poisson distribution. Bonferroni correction was applied for the number of SNPs. Thirteen SNP polymorphisms were identified in coding region of the TLR4 (g322>G/A, g514>C/T, g536>A/T, g8338>A/C, g8341>A/G, g8342>T/G, g8343>G/A, g8345>A/G, g8413>A/G, g8428>G/A, g8438>A/C, g8578>G/T, g8582>A/C). The SNPs g514>C/T and g536>A/T had significant association whit %G. All the SNPs were associated (p=0.001) whit the CCS. Other authors also reported the association of TRL4 SNPs to the trait. The results show that the SNPs of TLR4 gene can be used as molecular markers in buffaloes.
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Alves, Milena Ferreira. « caracteriza??o in situ e estrutura gen?tica de popula??es de Gossypium mustelinum ». Universidade Federal do Rio Grande do Norte, 2009. http://repositorio.ufrn.br:8080/jspui/handle/123456789/16769.
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Previous issue date: 2009-02-27Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior
Gossypium mustelinum Miers ex Watt is the only cotton species native from Brazil. It is endemic of the semi-arid region from North-east of the country, where it occur near from resilient water sources. The threats to the in situ conservation of the populations are caused by human interference in its habitat, mainly by excessive cattle graze and deforestation. Establish efficient strategies of in situ conservation depend on the accomplishment of a diagnosis of how the specie is found in its natural environment, and the knowledge about the genetic structure of the populations. The objectives of this work were i) to determine the in situ conditions of two populations present in rivers from basin of Rio Paragua?u at the Bahia State, ii) to evaluate the structure and genetic variability presented in both populations, iii) to establish in situ and ex situ conservation strategies. It were realized collection in november 2007, when was realized in situ characterization of G. mustelinum. SSR markers were used for analyze 218 genotypes deriving from two populations of the G. mustelinum, localized at Toc? river and the Capivara river. The allelic frequencies, the heterozigosity and the F statics were estimated. All the plants were classified as wild and natives, and there was no evidence of the use the plants or its parts. The populations showed different conservation conditions in situ. Few plantlets were found in sites with excessive cattle feed, an indication that the damages in young plants should be high enough to compromise the renovation of the populations. On the other hand, populations were well preserved when the anthropic damages was low or inexistent. The 14 SSR primer pairs amplified 17 loci with a medium number of 5 alleles per locus (a total of 85 alleles). The high level of endogamy estimated (FIS=0,808) and the low observed heterozygosity (H0=0,093) were indicatives that the populations reproduce mainly by selfing, geitonogamy and crosses between related individuals. The genetic diversity was high (HE=0,482) and the differentiation between the populations was very high (FST=0,328). At least two sites from both populations of G. mustelinum must be preserved to achieve suitable in situ conservation. Actions that preserve the gallery forest and keep the cattle away should implemented, and could be as simple as erecting a fence. It is not possible anticipated if the in situ preservation will be possible. Therefore collections and ex situ preservation of representative specimens are essential to conserve the genetic diversity of native G. mustelinum
Gossypium mustelinum Miers ex Watt ? a ?nica esp?cie de algod?o nativa do Brasil. ? uma esp?cie end?mica do semi-?rido nordestino do pa?s, ocorrendo pr?ximo a fontes de ?gua mais duradouras. Os riscos para conserva??o in situ das popula??es est?o associados a interfer?ncia humana em seu habitat, principalmente devido ao excessivo pastejo por bovinos e caprinos, al?m do desmatamento em matas ciliares. Estabelecer estrat?gias eficazes de conserva??o in situ depende da realiza??o de um diagn?stico da esp?cie em seu ambiente natural, e do conhecimento acerca da estrutura gen?tica das popula??es. Os objetivos deste trabalho foram: i) determinar as condi??es in situ de duas popula??es presentes em rios da bacia do Rio Paragua?u no estado da Bahia, ii) avaliar a estrutura e variabilidade gen?tica presente em ambas as popula??es, iii) e estabelecer estrat?gias de conserva??o in situ e ex situ. Foram realizadas coletas em novembro de 2007, quando foi realizada a caracteriza??o in situ de G. mustelinum. Marcadores SSR foram usados para analisar 218 gen?tipos de duas popula??es, localizadas nos rios Toc? e Capivara. As freq??ncias al?licas, a heterozigozidade e as estat?sticas F foram estimadas. Todas as plantas foram classificadas como selvagens e nativas, e nenhuma evidencia de explora??o antr?pica foi observada. As popula??es apresentavam diferentes condi??es de conserva??o in situ. Poucas plantas foram encontradas em locais onde havia pr?tica de pecu?ria extensiva, um ind?cio de que os danos causados a plantas jovens sejam maiores, comprometendo a renova??o das popula??es. Em contraste, popula??es foram encontradas em adequadas condi??es de preserva??o quando os danos causados pela a??o antr?pica eram pequenos ou inexistentes. Os 14 pares de primers SSR amplificaram 17 locos com n?mero m?dio de 5 alelos por loco (85 alelos no total). O alto ?ndice de endogamia estimado (FIS=0,808) e a baixa quantidade de heterozigotos (Ho=0,093) indicam que as popula??es propagam-se preferencialmente por autofecunda??o, geitonogamia e cruzamentos entre indiv?duos aparentados. A diversidade gen?tica total foi alta (HE=0,482) e a diferencia??o entre as popula??es foi muito elevada (FST=0,328). No m?nimo duas sub-popula??es devem ser preservadas em cada rio para uma adequada conserva??o in situ. A??es de preserva??o das matas ciliares e que impe?am o acesso do gado ?s popula??es devem ser implementadas, erguendo cercas pr?ximas as plantas. N?o ? poss?vel prever se as sugest?es propostas para preserva??o in situ ser?o implementadas. Coletas devem ser intensificadas e a??es para preserva??o ex situ devem ser realizadas para conserva??o da diversidade gen?tica presente nesta esp?cie nativa do Brasil
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Nucci, Stella Maris. « Diversidade genética em germoplasma de pinhão-manso (Jatropha curcas L.) identificada por marcadores SSR e ISSR ». Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-13092011-111035/.
Texte intégralRésumé :
O pinhão-manso (Jatropha curcas) é uma espécie arbórea de ampla distribuição geográfica e com qualidades que a tornam importante do ponto de vista natural, ecológico e principalmente sócio-econômico, pois seus frutos são uma valiosa fonte de óleo vegetal com potencial para produção de biodiesel, proporcionando vantagens ambientais, econômicas e sociais. Este trabalho teve como objetivo avaliar a diversidade genética no germoplasma de pinhão-manso e para isto foram utilizados marcadores moleculares microssatélites e ISSR. A partir de uma biblioteca enriquecida com locos microssatélites foram desenvolvidos 18 pares de primers para a espécie, sendo estes utilizados, juntamente com 30 pares de primers SSR desenvolvidos no CBMEG, visando à caracterização e estudo da estrutura genética populacional. Os acessos dos bancos de germoplasma do CPQBA (Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas) da UNICAMP e da UFS (Universidade Federal de Sergipe) foram avaliados. O germoplasma pertencente ao CPQBA está organizado em 12 populações e o da UFS representado por 17 acessos únicos. Não foi observado polimorfismo entre as populações inviabilizando o estudo populacional. A caracterização dos grupos formados pelos acessos dos bancos de germoplasma foi realizada utilizando 14 marcadores ISSR, revelando que 86,64% da variação genética encontram-se dentro dos grupos e 13,36% entre eles. O número médio total de alelos (na) foi de 1,99 alelos por loco e o número efetivo de alelos (ne) foi de 1,42 alelos por loco. A diversidade genética de Nei (1973) indicou uma baixa diversidade genética dentro dos grupos (0,26), assim como o Índice de Shannon (I) para os acessos (0,41), considerado um baixo valor de diversidade genética. A análise bayesiana alocou todos os acessos avaliados em quatro grupos, todos os acessos apresentaram Q > 0,8. Os grupos formados não apresentaram nenhuma relação com a origem dos acessos. O índice médio de similaridade de Jaccard indicou que existem 30% de similaridade entre os grupos e a amplitude de similaridade variou de 0,23 a 0,94. O dendrograma formou os mesmos quatro grupos de acessos que o formado pela análise bayesiana, tornando ainda mais consistente os resultados obtidos na presente análise. O estudo revela a necessidade e importância de reunir o maior número possível de acessos de diferentes regiões e países para formar o banco de germoplasma da espécie viabilizando a conservação e programas de melhoramento da espécie, haja vista seu promissor potencial para produção de bicombustível.Physic nut (Jatropha curcas) is a geographically widespread perennial plant species. It is ecologically important in natural communities and economically due to the oil extracted from its fruits that exhibit high potential for biodiesel production, thus, providing environmental, economical and social advantages. The current work aimed to evaluate the genetic diversity in physic nut germplasm using microsatellites and ISSR molecular markers. From a microsatelliteenriched library, 18 primer pairs were developed for the species and were used along with 30 SSR primer pairs developed at CBMEG to characterize and study the population genetic structure. Acessions from the germplasm banks at CPQBA (Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas) from UNICAMP and from UFS (Universidade Federal de Sergipe) were evaluated. The germplasm from CPQBA is organized in 12 populations whereas the accessions from UFS represent 17 soloist accessions. The polymorphism observed between the populations does not impair population genetic studies. The clusters of accessions from the germplasm Banks were characterized using 14 ISSR markers, revealing 86.64% of the genetic diversity are found within the clusters whereas between them, it corresponds to 13.36%. The total average number of alleles per locus (na) corresponded to 1.99 and the effective number of alleles (ne) was of 1.42 alleles per locus. The genetic diversity, investigated as in Nei (1973), indicated a low genetic diversity within the groups (0.26). Shannon index (I) for the accessions evidenced a low value of genetic diversity (0.41). Bayesian analyses of all investigated accessions in four groups demonstrated that all the accessions exhibit Q > 0.8. The clustering patterns did not indicated origin relationships among the accessions. Jaccard average index indicated 30% of similarity between the groups and the amplitude of similarity ranged from 0.23 to 0.94. The dendrogram analysis grouped the four clusters generated by the Bayesian analysis, confirming the consistency of the results. The current study reveals the necessity and importance of gathering as many germplasm accession as possible for the species in order to allow the establishment of conservation and breeding program strategies, considering the potential of the species for biofuel production.
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Manca, A. « CHARACTERIZATION OF CAMELINA SATIVA GENOME, AN OILSEED PLANT, THROUGH A COMBINED APPROACH BASED ON THE Β-TUBULIN GENE FAMILY AND MICROSATELLITE MOLECULAR MARKERS ». Doctoral thesis, Università degli Studi di Milano, 2012. http://hdl.handle.net/2434/168717.
Texte intégralRésumé :
ABSTRACT
The study reported in this thesis was performed in order to increase our knowledge on Camelina sativa genome and on the degree of the genetic polymorphism and relatedness present within a collection of camelina accessions.
This aim has been pursued trough the characterization of the β-tubulin gene
family and the use of novel and specific SSR markers.
The β-tubulin gene family of C. sativa has been isolated, cloned and
characterized using the h-TBP method. This technique allows the rapid cloning of
the β-tubulin genomic sequences that encompass the two introns, invariantly
present at fixed positions within the coding region of the vast majority of the plant
species. We have found that in C. sativa this family was composed of at least 20
different β–tubulin isotypes, named CsTUB1 through CsTUB20. This large
number of β–tubulin is an indication that C. sativa (chromosome number 2n = 40)
might be a polyploid species. The phylogenetic tree obtained from the β-tubulin
coding sequences of C. sativa and A. thaliana has shown a distribution of
CsTUBs that is spread throughout the clusters without distinction between A.
thaliana and C. sativa.
Then, we reported the isolation and characterization of specific camelina
microsatellite markers by using one C. sativa (GA)-SSR-enriched library. All
SSR markers utilised in this study produced clear and unambiguous amplification
fragments permitting the detection of a large number of alleles per locus. A total
of 134 alleles were generated at 15 SSR loci in the germplasm analysed with a
mean of 8.93 alleles per locus. The high discriminatory capacity of the SSR
markers, as observed in other plant species, have also been confirmed in our
study, in fact in our camelina collection thirty-eight out of forty accessions are
clearly distinguished by the 15 polymorphic microsatellites used. In addition, a
certain degree of association among the SSR camelina sub-groups and some of
the evaluated agronomic/biochemical traits has been observed.
In conclusion, knowledge of genetic variation and the genetic relationship
between genotypes is important for an efficient utilisation of C. sativa germplasm
resources. Beside of providing a useful tool for germplasm identification and
genetic diversity, these 15 newly developed SSR polymorphic markers will prove
very useful in genetic mapping and in assisting plant breeders in early progeny
selection.
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Silva, Renato Rodrigues. « Estudo da estrutura populacional em cana-de-açúcar usando marcadores do tipo SNP ». Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-29042013-094035/.
Texte intégralRésumé :
Embora já existam estudos anteriores a respeito da estrutura de população em cana-deaçúcar, até o momento nenhum estudo foi feito usando marcadores SNPs gerados a partir de plataformas de genotipagem de larga escala, como por exemplo, Sequenom iPLEX MassARRAY. No presente trabalho, foi investigada a estrutura populacional no painel brasileiro de variedades de cana-de-açúcar. Esse painel é formado por materiais elites, ancestrais importantes e cultivares utilizados em programa de melhoramento. Um total de 1033 marcadores SNPs foram utilizados para genotipar os acessos do painel. A classificação dos dados feita usando o software SuperMASSA. A estrutura de população foi analisada por meio de análise de componentes principais (ACP), análise de agrupamentos e usando o software STRUCTURE. Devido ao fato que no software STRUCTURE não é possível dados de marcadores moleculares provenientes de espécies poliploides com aneuplodia frequente, o conjunto de dados foi separado e analisado de acordo com nível de ploidias dos SNPs. Com a finalidade de comparar os resultados, foi feita uma análise de coordenadas principais na matriz de distância, com os elementos definidos por 1 - coeficiente de parentesco. A análise de componentes principais revelou presença de estrutura de população. O primeiro componente separou o acesso IN84-58 (S. spontaneum) dos outros acessos que por sua vez estão separados em três grupos: o primeiro grupo formado pelos acessos que são S. sinense, o segundo grupo formado pelos cultivares modernos de cana-de-açúcar e o terceiro grupo formado por acessos que são espécies S. officinarum. Resultados da análise de agrupamento usando distância de alelos compartilhados são condizentes com resultados da ACP. Por outro lado, análise de coordenadas principais e método de agrupamento UPGMA usando o coeficiente de parentesco mostraram uma maior dissimilaridade genética entre os acessos separando as progênies do cultivar RB72454 do grupo formado pelos genitores e ou progenies do cultivar NA56-79. A diferença entre os resultados da análise de componentes principais e de coordenadas principais é devido principalmente a pressuposições nas estimativas do coeficiente de parentesco que são irrealísticas. Com relação a análise feita com o software STRUCTURE, o número de subpopulações e a matriz Q estimada variou de acordo com nível de ploidia dos marcadores. De um modo geral, as análises de estrutura de população mostrou que há evidências de estreitamento da base genética dos acessos devido a cruzamentos recorrentes de indivíduos aparentados. Espera-se que estas informações sejam importantes para o mapeamento associativo e melhoramento genético da espécie.Although there are several studies inferring population structure in sugarcane, none of them have yet used SNP markers generated from high-throughput platforms, such as, Sequenom iPLEX MassARRAY platform. In this study, it was investigated the population structure in a Brazilian panel of sugarcane varieties. This panel is comprised by elite breeding materials, important ancestors, and cultivars mostly used by breeding programs. 1,033 SNP markers were scored. SNP genotype calling was made using software SuperMASSA. The population structure was analyzed via principal components analysis (PCA), cluster analysis and using the software STRUCTURE. Due to the fact that STRUCTURE is not possible to analyze molecular markers data scored on species withmixed ploidy level, the dataset was separated and analyzed according to SNPs level ploidy estimates. With purpose of comparing the results, it was made a principal coordinate analysis (PCO) of distance matrix, with elements defined by 1 - kinship coefficient. The principal components analysis revealed some structure. The first component separated out IN84-58 (Saccharum spontaneum) from the others acessions, whereby these others acessions were allocated in three groups, comprised by S. sinense species, sugarcane modern cultivars and S. officinarum species. Results from cluster analysis using allele shared distance are in agreement with PCA results. On the other hand, principal coordinates analysis and UPGMA hierarchical clustering method based on kinship coefficient showed a broader genetic dissimilarity between acessions, allocating RB72454 progenies apart from its parents and/or progenies of NA56-79. The difference of results between PCA and PCO are mainly due to irrealistics assumptions in the calculation of kinship. Regarding analysis from the STRUCTURE, the number of subpopulations and Q matrix estimated varied with level ploidy. In general, the study of population structure showed some evidence of narrow genetic distances between accessions, due to recurrent crosses between related individuals. The information presented hereby could be important for association mapping and sugarcane breeding program.
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Dernaika, Maher. « Molecular Characterization Of Strawberry By Applying Dna Fingerprinting Technique Using Simple Sequence Repeats (ssrs) Markers ». Master's thesis, METU, 2009. http://etd.lib.metu.edu.tr/upload/2/12611258/index.pdf.
Texte intégralRésumé :
In this study, strawberry fruit was taken as the studied model. An attempt was carried on trying to identify a unique DNA fingerprint in each of the selected different strawberry cultivars of Fragaria x ananassa Duch species available in Turkey. The basis of the study was to examine the fruit characteristics at the molecular level rather than at the morphological level. It is of great importance to differentiate and trace the origin of any variety by examining its DNA by using a very sophisticated molecular technique. In this case, DNA fingerprinting technique depending on the Simple Sequence Repeats (SSRs) markers which are also called Microsatellite markers were used. DNA fingerprinting technique reveals the specific DNA profile which is unique as a fingerprint for a fruit specimen and this DNA profile is the same and constant throughout different parts of the fruit as well as its developmental stages. In this thesis work, nine primers flanking the SSR markers already available in the online databases were designed hoping to detect SSRs that could differentiate among the five selected cultivars of strawberry.
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Moreira, Ricardo Franco Cunha [UNESP]. « Estrutura genética de populações de Crinipellis perniciosa e Moniliophthora roreri utilizando marcadores RAPD e SSR ». Universidade Estadual Paulista (UNESP), 2006. http://hdl.handle.net/11449/102837.
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moreira_rfc_dr_jabo.pdf: 545090 bytes, checksum: 6b6b5062d2bd5f7bc8ff1ca523e6a689 (MD5)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
Fundação de Amparo à Pesquisa do Estado da Bahia (FAPESB)
Comon Fund For Comidities, International Cocoa Organization
Vassoura-de-bruxa e podridão de Moniliophthora, causadas pelos fungos Crinipellis perniciosa e Moniliophthora roreri, respectivamente, são as doenças de maior impacto econômico da cultura do cacau e estão presentes na maioria dos países produtores do Continente Americano. Evidências biológicas e moleculares comprovam que estes fitopatógenos estão intimamente relacionados. O uso de resistência genética através de dones resistentes de cacaueiro, é a medida mais eficiente no controle destas doenças. O conhecimento sobre as populações destes fungos é importante na geração de informações para o programa de melhoramento genético do cacau visando resistência. Marcadores moleculares RAPO e SSR foram usados para analisar a estrutura genética de populações destes fitopatógenos. No geral, as populações do Brasil, Equador, Peru e Trinidad agruparam-se de acordo com o país de origem, apresentando maior variabilidade dentro e não entre países, com presença de subpopulações. A população do Brasil apresentou maior diversidade genotípica em comparação com as demais. A transferibilidade de pares de primers SSR de C. perniciosa para M. roreri foi satisfatório. Populações de M. roreri do Equador e Peru apresentaram alta diferenciação genética interpopulacional, sendo que a do Peru apresentou maior variabilidade.
Witches' broom and fresty pod hot, caused by Crinipellis perniciosa and Moniliophthora roreri, are the most important disease of cacao in the American Continent. Biological and molecular data have shown that these pathogen are closely related. Resistance is the most efficient method to control these diseases. Therefore, information about the population structure of these cacao pathogen are important to support the breeding programo Molecular markers such as RAPD and SSR were used to analyzed the genetic structure of C. perniciosa and M. roreri frem the American Continent. Populations of C. perniciosa clustered according to their country of origin, with more variability within than between countries, revealing the presence of subpopulations. C. perniciosa Brazilian populations presented higher genotypic diversity than C. perniciosa from other countries. The transferability of C. perniciosa-SSR to M. roreri was positive. On the contrary, high interpopulation variability was observed between Ecuador and Peru, being M. roreri from Peru much more diverse than Ecuador.
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Matteis, Rafael de [UNESP]. « Variantes da região cromossômica do gene da miostatina e suas relações com linhagens, desempenho e medidas corporais na raça Quarto de Milha ». Universidade Estadual Paulista (UNESP), 2017. http://hdl.handle.net/11449/152119.
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Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
Ao longo de várias décadas a raça Quarto de Milha foi selecionada para diferentes objetivos, formando grupos com aptidões ou habilidades distintas, como a linhagem de corrida, que apresenta melhor desempenho que qualquer outra linhagem ou raça em corridas de curta distância e a linhagem de trabalho, utilizada no manejo de bovinos a campo e em provas de caráter funcional. Considerando as diferenças nas medidas corporais e na musculatura que ocorrem entre as linhagens de corrida e de trabalho da raça Quarto de Milha, o objetivo deste trabalho foi analisar a ocorrência de relações entre alelos de polimorfismos da região cromossômica do gene da miostatina MSTN (ECA18), um regulador negativo do desenvolvimento muscular, e as duas linhagens da raça. Outro objetivo foi realizar análises de associação de polimorfismos dessa região cromossômica com valor genético estimado (EBV) do desempenho em corridas, dado pelo índice de velocidade máximo (IV max), e EBVs da altura à cernelha (AC), perímetro torácico (PT) e comprimento corporal (CC) na linhagem de corrida, e com EBVs da AC, PT e CC na linhagem de trabalho. Foram utilizadas informações genômicas, fenotípicas e de pedigree de 420 equinos, de ambos os sexos, registrados na associação Brasileira de criadores (ABQM), sendo 352 da linhagem de corrida e 68 da de trabalho. Na região genômica estudada (gene MSTN ± 2Mb), foram identificados 46 SNPs e 1 SINE – ERE1 comuns às linhagens de trabalho e de corrida, dos quais 32 SNPs e 1 SINE apresentaram alelos com frequências significativamente diferentes entre às mesmas. Também foi constatado que a porção dessa região mais próxima ao gene MSTN (± 1Mb) é menos polimórfica na linhagem de corrida em relação à de trabalho, o que pode ser consequência de maior pressão de seleção sobre essa região na linhagem de corrida e/ou em função do uso de animais da raça Puro Sangue Inglês na mesma. Em relação aos polimorfismos associados à fenótipos (p não ajustado < 0,05), destacaram-se os relacionados à altura de cernelha na linhagem de corrida devido ao seu grande número (p não ajustado < 0,05) e alto desequilíbrio de ligação. Ademais estes marcadores apresentaram frequências do alelo favorável significativamente maiores em relação à linhagem de trabalho. Tendo se em vista a possibilidade de associação genética entre características morfológicas e desempenho em equinos, esse resultado é de grande importância, fornecendo informações para futuros estudos de melhoramento genético animal.
For several decades the Quarter Horse breed was selected for different purposes, forming groups with different abilities, such as the racing line, which performs better than any other lineage or breed in short distance races and the lineage of work, used in the management of field cattle and in functional tests. Considering the differences in body measurements and musculature that occur between racing and working strains of the Quarter-Mile breed, the objective of this study was to analyse the occurrence of relations between polymorphic alleles of the chromosomal region of the myostatin (MSTN) gene (ECA18), a negative regulator of muscle development, and the two lineages of the breed. Other objective was to perform association analyses of these polymorphisms with estimated genetic value (EBV) of the performance in lineages, given by the maximum velocity index (IV max), and EBVs of height at withers (HW), heart girth (HG) and body length (BL) in the racing line, and with EBVs of AC, PT and CC in the working line. We used genomic, phenotypic and pedigree information from 420 horses of both sexes, recorded in the Brazilian breeders' association (ABQM), 352 and 68 of the racing and working line, respectively. In the studied genomic region (MSTN gene ± 2Mb), 46 SNPs and 1 SINE - ERE1 were identified, common to the working and running strains, of which 32 SNPs and one SINE presented alleles with significantly different frequencies between them. It has also been found that the portion of this region closest to the MSTN gene (± 1Mb) is less polymorphic in the racing versus the working strain, which may be a consequence of higher selection pressure on that region in the racing line and / or due to the use of purebred English animals in it. In relation to the polymorphisms associated with the phenotypes (p not adjusted <0.05), those related to the height of the withers in the race line due to their large number (p not adjusted <0.05) and high linkage disequilibrium were the most prominent. In addition, these markers presented frequencies of the favorable allele significantly higher in relation to the working lineage. Considering the possibility of genetic association between morphological characteristics and performance in equines, this is a result of great importance, providing information for future animal breeding studies.
CNPq: 134521/2015-3
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Alonso, Rodrigo Vitorio. « Diagnóstico genético pré-implantacional de embriões bovinos utilizando plataformas de genotipagem de marcadores moleculares do tipo SNP ». Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/10/10131/tde-23072013-154403/.
Texte intégralRésumé :
Apesar do grande desenvolvimento das biotecnologias da reprodução animal, como a produção in vitro de embriões (PIV), o diagnóstico genético pré-implantacional (PGD) ainda é aplicado com restrição na rotina da transferência de embriões em animais. Os recentes avanços da genômica têm permitido associar características fenotípicas com informações moleculares, possibilitando a realização da seleção assistida por marcadores moleculares. O objetivo do presente estudo foi de realizar o PGD de embriões bovinos em plataforma de alta densidade de SNP (BeadChip/6.909 SNP). A pequena quantidade de DNA genômico (gDNA) obtida na biópsia embrionária é a principal limitação para a análise de grande número de SNP. Dessa forma, a metodologia de amplificação total do genoma (WGA) (Repli-g Mini Kit, Qiagen, Hilden, Alemanha) foi utilizada para aumentar a quantidade de gDNA da biópsia e permitir a análise de milhares de SNP simultaneamente. Foram utilizados 88 embriões bovinos PIV, submetidos à micromanipulação pela técnica de microaspiração, possibilitando a formação de 3 grupos com diferentes números de células biopsiadas: G1) 5-10 (n=28); G2) 10-20 (n=37); G3) >100 - blastocisto eclodido (n=23). Todas as amostras foram submetidas ao mesmo protocolo de WGA e 4µL de cada amostra foram utilizados para a genotipagem em plataforma iScan/Illumina. A qualidade dos genótipos foi avaliada pela análise do Call Rate (CR), 10o percentil do GCScore (GC10), Alelle Drop In (ADI) e Alelle Drop Out (ADO). O teste de Kruskal-Wallis foi utilizado para investigar diferenças na distribuição das variáveis entre os grupos. O coeficiente de correlação de postos de Spearman revelou correlação significativa entre todas as variáveis. Os resultados apresentaram correlação positiva entre o CR e GC10 (0,99/P<0,001), enquanto as taxas de ADI e ADO apresentaram correlação negativa com o CR e CG10 (ADI/CR: - 0,87; ADI/GC10:-0,88; ADO/CR:-0,87; ADO/GC10:-0,86), com P<0,001 para todas as variáveis. O teste de Kruskal-Wallis apontou para diferença significativa em todas as variáveis analisadas (CR, GC10, ADI e ADO) entre os 3 grupos de biópsias (G1, G2 e G3). O CR médio foi de 59,26%, 78,47% e 95,97%, para G1, G2 e G3, respectivamente. Foi desenvolvido programa computacional (mendelFix) baseado na Lei da Segregação, para inferência dos genótipos não determinados baseado no genótipo do progenitores, aumentando o CR dos grupos 1, 2 e 3 para 79,69%, 88,20% e 97,28%, respectivamente. Os resultados do presente estudo permitem concluir que é possível realizar a genotipagem de embriões bovinos em plataforma de alta densidade de SNP com amostras submetidas ao protocolo WGA/MDA, mas o número de células obtidas na biópsia embrionária afeta a qualidade da genotipagem. A associação das biotecnologias descritas no presente trabalho permite a aplicação da seleção assistida por marcadores moleculares em embriões bovinos, contribuindo para acelerar ainda mais o processo de melhoramento genético animal.Despite the great development of animal reproduction biotechnology, such as embryo in vitro production (IVP), preimplantation genetic diagnosis (PGD) is still applied with restraint in animals embryo transfer. Recent advances in genomics have associated phenotypic characteristics with molecular information, allowing the development of marker assisted selection. The aim of this study was to perform PGD in bovine embryos using high-throughput SNP platform (BeadChip/6,909 SNP). The small amount of genomic DNA (gDNA) obtained from embryo biopsy is the main limitation for the high-density SNP analysis. Thus, the Whole Genome Amplification (WGA) (Repli-g Mini Kit, Qiagen, Hilden, Germany) was used to increase the amount of gDNA from embryo biopsy and allow the analysis of thousands SNP simultaneously. Eighty-eight IVP bovine embryos were subjected to micromanipulation by microaspiration, allowing the formation of three groups with different numbers of biopsied cells: G1) 5-10 (n=28); G2) 10-20 (n=37); G3) > 100 - hatched blastocyst (n = 23). All samples were subjected to the same WGA protocol, and 4µL of each sample were used for genotyping on iScan/Illumina platform. The genotyping quality was assessed using the Call Rate (CR), 10th percentile GCScore (GC10), Alelle Drop In (ADI) and Alelle Drop Out (ADO). Kruskal-Wallis test was applied to investigate differences in the distribution of variables among groups. Spearman`s rank correlation coefficient revealed a significant correlation between all variables. The results showed a positive correlation between CR and GC10 (0.99/P <0.001), while ADI and ADO rates were negatively correlated with CR and CG10 (ADI/CR: -0.87; ADI/GC10: - 0.88; ADO/CR: -0.87; ADO/GC10: -0.86), P<0.001 for all variables. Kruskal Wallis pointed to significant differences in all variables (CR, GC10, ADO and ADI) among the 3 groups of biopsies (G1, G2 and G3). The CR average was 59.26%, 78.47% and 95.97% for G1, G2 and G3, respectively. Was developed a script (mendellFix) based on the \"Law of Segregation\", for inference of not determined genotypes based on the parents genotypes, thus increasing the CR of group 1, 2 and 3 to 79.69%, 88.20% and 97 28%, respectively. The results of this study show that it is possible to perform the genotyping of bovine embryos in highthroughput SNP platform with samples subjected to WGA/MDA protocol, but the number of cells obtained by embryo biopsy affects the quality of genotyping. The association of biotechnologies described in this work allows the application of marker-assisted selection in bovine embryo, contributing to further accelerate the process of animal breeding.
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MOTA, Monalize Salete. « Caracterização molecular de alelos-S e de locos microssatélites em Prunus salicina (Lindl.) ». Universidade Federal de Pelotas, 2008. http://repositorio.ufpel.edu.br/handle/ri/2028.
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Previous issue date: 2008-07-31The production of plum is an important commodity around the world. In Brazil, the state of Rio Grande do Sul is the major producer. However, despite the great potential for cultivation, some factors are limiting for increasing the production, such as: a) climate variability; b) use of inadequate stocks; c) pollination of most cultivar is self-incompatible d) doubtful genetic history of the plant material. Considering these problems, the aim of this work was to identify allele-S related to gametophytic self- incompatibility in Prunus salicina (Lindl.) and to perform the molecular characterization of cultivars by means of microsatellites locus. For these purposes eleven cultivars of Japanese plum [Santa Rosa, Santa Rita, Reubennel, Pluma 7, América, Rosa Mineira, Amarelinha, The First, Gulfblaze (Clone São Paulo), Gulfblaze (Clone Guaíba) e Harry Pickstone] were analysed by Polymerase Chain Reaction (PCR) using three pairs of primers specific for amplifying the alleles-S and primers for five microsatellite locus. The experiments were performed in the Laboratório de Cultura de Tecidos de Plantas Caracterização Molecular, of the Departamento de Botânica da Universidade Federal de Pelotas. In the amplification of alleles-S was observed that the reaction mix for PCR, the PCR conditions, and primers combination, allowed an effective characterization of alleles-S in the cultivars of P. salicina and the identification of pollinators more compatible to commercial cultivars. Sequencing analysis of some amplified alleles-S revealed high similarity to sequences of nucleotides already identified in other studies with Prunus spp. In the analysis of five microsatellite locus thirty polymorphisms were obtained allowing a clear identification of Japanese plum genotypes, elucidating the homonymy between the cultivars Gulfblaze (Clone São Paulo) and Gulfblaze (Clone Guaíba). However, the polymorphisms were not sufficient for obtaining a reasonable estimation of the genetic variability and grouping analysis of the Japanese plums evaluated.
A cultura de ameixeira tem papel de destaque na fruticultura mundial. No Brasil, o Estado do Rio Grande do Sul se destaca como maior produtor. Porém, mesmo apresentando elevado potencial de cultivo, alguns fatores têm limitado o aumento da produção, entre eles: a) a variabilidade de clima; b) o uso de porta- enxertos inadequados; c) a incapacidade de autopolinização da maioria das cultivares d) e a idoneidade genética do material vegetal. Diante disso, o objetivo deste trabalho foi identificar alelos-S relacionados à auto-incompatibilidade gametofítica em Prunus salicina (Lindl.) e caracterizar molecularmente as cultivares por meio de locos microssatélites. Para tal fim foram analisadas 11 cultivares de ameixeira japonesa [Santa Rosa, Santa Rita, Reubennel, Pluma 7, América, Rosa Mineira, Amarelinha, The First, Gulfblaze (Clone São Paulo), Gulfblaze (Clone Guaíba) e Harry Pickstone], por meio de Reação em Cadeia da Polimerase (PCR) com três pares de primers específicos para amplificação de alelos-S e primers para cinco locos de microssatélites. Os experimentos foram desenvolvidos no Laboratório de Cultura de Tecidos de Plantas Caracterização Molecular, do Departamento de Botânica da Universidade Federal de Pelotas. Na amplificação de alelos-S, constatou-se que as concentrações e condições de PCR utilizadas, bem como às combinações de primers, permitiram a efetiva caracterização de alelos-S nas cultivares de P. salicina estudadas, bem como, a escolha das polinizadoras mais compatíveis com as cultivares produtoras. O seqüenciamento de alguns dos alelos-S amplificados revelou elevada similaridade com seqüências de nucleotídeos já identificados em outros trabalhos com Prunus spp.. Na análise de cinco locos de microssatélites obteve-se um total de 30 polimorfismos possibilitando uma clara identificação dos genótipos de ameixeira japonesa, esclarecendo caso de homonímia entre as cultivares Gulfblaze (Clone São Paulo) e Gulfblaze (Clone Guaíba), no entanto, os polimorfismos não foram suficientes para obter uma boa estimativa da variabilidade genética e análise de agrupamento dos genótipos de ameixeira japonesa avaliados.
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Merrill, Keith R. « Usage and Development of Molecular Markers for Investigation of the Population and Ecological Genetics of Bromus tectorum L ». BYU ScholarsArchive, 2011. https://scholarsarchive.byu.edu/etd/2955.
Texte intégralRésumé :
This thesis includes two studies: The first examined patterns of neutral genetic diversity within Bromus tectorum L. across the IMW region, and uses patterns of microsatellite (SSR) genotype distribution to make inferences about the respective roles of adaptively significant genetic variation, adaptive phenotypic plasticity, and facultative outcrossing in the ongoing invasion and recent range expansion of B. tectorum. It has been previously demonstrated that, due to extremely low outcrossing rates, it is possible to characterize individual genotypes of this species using four SSR loci. We sampled 20 individuals from each of 96 B. tectorum populations (classified by region and habitat) from throughout the IMW and used these SSR markers to characterize each individual. We found 131 four-locus SSR genotypes; however, the 14 most common genotypes collectively accounted for 79.2% of the individuals sampled. Individuals with certain SSR genotypes sorted strongly into warm or salt desert habitats (stringent habitats) and flowered earlier than individuals with genotypes from more mesic habitats, providing evidence of adaptively significant genetic variation associated with these genotypes. Other SSR genotypes were found across a wide range of habitats though they tended to be less prevalent in stringent habitats, providing evidence that adaptive phenotypic plasticity may be important for the distribution of some common genotypes. We observed very few heterozygous individuals, consistent with the highly inbreeding reproductive strategy of B. tectorum. Because specialist genotypes dominating recently invaded areas within the IMW region contained unique alleles, they are not likely to have resulted from recombination, leading us to doubt the role of facultative outcrossing as a significant mechanism facilitating the current range expansion of B. tectorum in the IMW.Previous research investigating the population and ecological genetics of Bromus tectorum L. in the North American invaded range has relied on either allozyme or microsatellite (SSR) genetic analyses, both of which have proven to have shortcomings. In order to overcome the issues associated with these other marker types, in the second study of this thesis we developed single nucleotide polymorphism (SNP) markers for B. tectorum by 1) obtaining normalized cDNA, 2) sequencing normalized cDNA using 454 sequencing, 3) aligning resultant contigs and looking for SNPs, 4) designing assays for SNP validation and genotyping using KASPar, 5) converting working KASPar assays for use with the Fluidigm EP1 platform using the 96.96 Dynamic ArrayTM IFC. Sequencing resulted in 1258041 reads, which assembled into 65486 contigs (20782 large contigs exceeding 500 base pairs). Using selection criteria of at least 10x coverage and 30% of the minor allele, 3333 putative SNPs were identified. We developed KASP assays for 255 putative SNPs, which resulted in 101 working polymorphic assays. Ninety-six assays were then successfully converted for use with KASP on the Fluidigm EP1 genotyping platform using 96.96 dynamic arrays.
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Gabier, Hawwa. « Development of microsatellite (SSR) marker multiplexes for future construction of a genetic linkage map for pear (Pyrus communis L.) ». Thesis, University of the Western Cape, 2012. http://hdl.handle.net/11394/4013.
Texte intégralRésumé :
>Magister Scientiae - MScRecent advances in the field of plant genetics and application of molecular technologies has lead to greater understanding of various crop genomes and their organization.The applications of these techniques include molecular markers which have been used to examine DNA variation within crop species. This allows for the creation of further genetic variation for new and favourable traits.Molecular markers or DNA markers are short fragments of DNA that can be used to locate desirable genetic traits in the genome or show specific genetic differences. The Maloideae subfamily includes fruit species such as pear. Pears (Pyrus communis L.) are large edible fruit that are grown in cool climates, native to coastal regions in Africa, Asia and Europe. The external appearance of this fruit plays a vital role on its rate of sale potential. Thus it is important for the appearances of the pear to meet the expectations of the consumer.External factors affecting the appearance of fruit, such as shape and colour, can have a large influence on the consumer’s first impression and opinion of what the fruit may taste like(Jaeger and MacFie, et al., 2001). The South African pear industry is the fourth largest in the fruit industry after apple, citrus and grape, exporting 3.8% to Europe (Ferrandi, et al., 2005).Increase in production and export of the pear is dependant on the variety of cultivars with desired traits. New cultivars, especially ranges of new cultivars, with harvest dates from early to late in the season, can fill gaps in the marketing strategy of exporters and in the local markets (Human, et al., 2005) Therefore, development of molecular markers allows for their possible use in maker-assisted selection and for the construction of a genetic linkage map thus leading to the location of favourable traits and ultimately the improvement of the quality of the pear.In this study high throughput genomic DNA extractions were performed. The Cetyltrimethyl ammonium bromide (CTAB) method was employed as the results proved to be most promising. Furthermore the screenings of molecular markers were conducted in order to obtain DNA variation. Molecular markers were used to locate specific genetic differences.Multiplexing PCR was conducted using fluorescent primers for further screening and results proved to be useful as many variations could be observed.
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Pollock, Stephanie. « A study of genetic diversity and genome organization of Brassica napus using EST (expressed sequence tags) of Arabidopsis and SSR (simple sequence repeat) markers of B. napus / ». Thesis, McGill University, 2001. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=33023.
Texte intégralRésumé :
Arabidopsis expressed sequence tags (ESTs) and microsatellites of Brassica napus have been developed and used as PCR-based markers for both mapping and genetic diversity studies in B. napus . Out of 300 random Arabidopsis ESTs screened, 43 markers were mapped onto a genetic map of B. napus and then used in a diversity study involving 48 B. napus cultivars. A second set of EST markers were developed from chromosome 1 of Arabidopsis and used in genetic mapping studies of B. napus. From 192 primer pairs developed, 50 markers were added onto the B. napus reference map. Microsatellite markers were developed using a "GA" enriched genomic library from B. napus. From 152 designed primer pairs, 23 markers were added onto the B. napus reference map. Microsatellite markers were also used in genetic diversity studies of B. napus, where, from the 152 primer pairs, 40 revealed polymorphism between the 48 B. napus cultivars.
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Küpper, Anita, Harish K. Manmathan, Darci Giacomini, Eric L. Patterson, William B. McCloskey et Todd A. Gaines. « Population Genetic Structure in Glyphosate-Resistant and -Susceptible Palmer Amaranth (Amaranthus palmeri) Populations Using Genotyping-by-sequencing (GBS) ». FRONTIERS MEDIA SA, 2018. http://hdl.handle.net/10150/627054.
Texte intégralRésumé :
Palmer amaranth (Amaranthus palmeri) is a major weed in United States cotton and soybean production systems. Originally native to the Southwest, the species has spread throughout the country. In 2004 a population of A. palmeri was identified with resistance to glyphosate, a herbicide heavily relied on in modern no-tillage and transgenic glyphosate-resistant (GR) crop systems. This project aims to determine the degree of genetic relatedness among eight different populations of GR and glyphosate-susceptible (GS) A. palmeri from various geographic regions in the United States by analyzing patterns of phylogeography and diversity to ascertain whether resistance evolved independently or spread from outside to an Arizona locality (AZ-R). Shikimic acid accumulation and EPSPS genomic copy assays confirmed resistance or susceptibility. With a set of 1,351 single nucleotide polymorphisms (SNPs), discovered by genotyping-by-sequencing (GBS), UPGMA phylogenetic analysis, principal component analysis, Bayesian model-based clustering, and pairwise comparisons of genetic distances were conducted. A GR population from Tennessee and two GS populations from Georgia and Arizona were identified as genetically distinct while the remaining GS populations from Kansas, Arizona, and Nebraska clustered together with two GR populations from Arizona and Georgia. Within the latter group, AZ-R was most closely related to the GS populations from Kansas and Arizona followed by the GR population from Georgia. GR populations from Georgia and Tennessee were genetically distinct from each other. No isolation by distance was detected and A. palmeri was revealed to be a species with high genetic diversity. The data suggest the following two possible scenarios: either glyphosate resistance was introduced to the Arizona locality from the east, or resistance evolved independently in Arizona. Glyphosate resistance in the Georgia and Tennessee localities most likely evolved separately. Thus, modern farmers need to continue to diversify weed management practices and prevent seed dispersal to mitigate herbicide resistance evolution in A. palmeri.
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ALMEIDA, Clébia Maria Alves de. « Diversidade genética em populações de Aechmea fulgens Brongn. (Bromeliaceae) em fragmentos de Mata Atlântica em Pernambuco ». Universidade Federal Rural de Pernambuco, 2006. http://www.tede2.ufrpe.br:8080/tede2/handle/tede2/6204.
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Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq
Habitats fragmentation is the greatest cause of biodiversity erosion in tropical forests among the anthropic action. Due to the high degree of fragmentation and the isolation of the remaining Atlantic forest, many populations are being extinguished locally while others are suffering losses of its genetic variability. The Bromeliaceae family has a great variety of tropical ornamental species. Eleven species of the Aechmea genus occur in the State of Pernambuco, and although it is of great economic and ecological importance, there has been few studies on its genetic diversity. Aechmea fulgens is a native Atlantic forest species, which natural populations may be suffering losses on the genetic variability. Plants genetic diversity may be estimated in many ways. Modern techniques on molecular biology allow observing the polymorphism directly on the organism genic sequence. Molecular markers broaden the horizons on researches for the conservation of species and have been widely used to monitor the genetic variability. Among many molecular markers available, SSR and ISSR are relevant. With the of aim evaluating the degree of genic diversity on Aechmea fulgens populations, providing from three different fragments of Atlantic forest in Pernambuco, SSR and ISSR markers were used. Twelve pairs of microsatellites oligonucleotides developed for Tillandsia, Guzmania and Pictairnia bromeliad genera were tested. From these, only five pairs had polymorphism, showing transference of these primers to the Aechmea gender. Twenty ISSR oligonucleotides were used to amplify Aechmea fulgens sample, from which eight primers that had the most consistent polymorphism. The analysis on variance results revealed greater differences inside populations than among them. The results suggest that both markers may be used for genetic variability evaluation, contributing for the success of future studies and species conservation programs.
A fragmentação de habitats é a maior causa da erosão da biodiversidade nas florestas tropicais junto com a ação antrópica. Devido ao alto grau de fragmentação e ao isolamento dos remanescentes atuais da floresta atlântica, várias populações estão se extinguindo localmente e outras sofrendo perda de sua variabilidade genética. A família Bromeliaceae inclui uma grande variedade de espécies ornamentais tropicais. O gênero Aechmea tem significativa representatividade no Estado de Pernambuco, onde ocorrem onze espécies e, apesar de sua grande importância ecológica e econômica, existem poucos estudos sobre sua diversidade genética. Aechmea fulgens é uma especie nativa da Mata Atlântica, cujas populações naturais podem estar sofrendo perda de sua variabilidade genética. A diversidade genética em plantas pode ser estimada de várias maneiras. As modernas técnicas de biologia molecular permitem a observação de polimorfismo diretamente na seqüência gênica de organismos. Os marcadores moleculares abriram novas perspectivas para pesquisas em conservação de espécies e têm sido amplamente utilizados no monitoramento da variabilidade genética. Dentre os diversos marcadores moleculares disponíveis atualmente, destacam-se as seqüências simples repetidas (SSR) e repetições entre seqüências simples (ISSR). Com o objetivo de avaliar o nível de diversidade genética de populações de Aechmea fulgens (Brongn.) provenientes de três fragmentos distintos da mata atlântica de Pernambuco, foram utilizados marcadores SSR e ISSR. Um total de 12 pares de oligonucleotídeos de microssatélites, desenvolvidos para bromeliáceas dos gêneros Tillandsia, Guzmania e Pitcairnia foram testados. Desse total apenas cinco pares apresentaram polimorfismo demonstrando a transferência desses primers para o gênero Aechmea. Adicionalmente, 20 oligonucleotídeos ISSR foram utilizados para amplificar as amostras de A. fulgens, tendo sido selecionados oito primers por apresentarem polimorfismo mais consistente. Os resultados das análises de variância revelaram que a maior divergência esteve presente dentro das populações do que entre elas. Os resultados sugerem que os dois tipos de marcadores são adequados para a avaliação da variabilidade genética, colaborando para o sucesso de futuros estudos e programas de conservação dessa espécie.
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Oliveira, Priscila Silva. « Estudo da diversidade genética e análise de associações de polimorfismo de nucleotídeo (SNP) com resistência às parasitoses gastrintestinais e prolificidade em ovinos da raça Santa Inês ». Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/74/74131/tde-28012015-145254/.
Texte intégralRésumé :
O principal objetivo deste trabalho foi avaliar a presença de polimorfismos e de possíveis associações com características relacionadas com a resistência às parasitoses gastrintestinais e a prolificidade em ovinos da raça Santa Inês. Para avaliação da resistência às parasitoses gastrintestinais, amostras de fezes e de sangue de aproximadamente 700 animais, infectados naturalmente e oriundos de quatro propriedades diferentes, foram coletadas entre os meses de outubro e novembro de 2011, para avaliação das características condição corporal, grau de anemia avaliado pelo cartão FAMACHA, as características dos pelos dos animais, consistência das fezes, contagem de ovos por grama de fezes, hematócrito, contagem de células brancas, contagem de células vermelhas, hemoglobina e plaquetas. Para a avaliação da prolificidade, 340 ovelhas foram avaliadas quanto ao número total de cordeiros nascidos, divididos pelo número de partos de cada ovelha, assim como a correlação dessa característica com o peso médio ao nascimento de seus cordeiros e a eficiência produtiva da mãe ao parto. Foram selecionados 28 polimorfismos de base única (SNP) para o desenvolvimento deste estudo os quais foram genotipados por meio da plataforma Sequenom MassARRAY iPLEX. Foram analisadas as freqüências alélicas e genotípicas, o equilíbrio de Hardy-Weinberg, os efeitos de substituição alélica, de aditividade e de desvio de dominância. Os resultados obtidos demonstraram variabilidade considerável das características avaliadas na população e da maioria dos polimorfismos estudados. Foi verificado também efeito significativo (p≤0,05) ou sugestivo (0,05>p≤0,10) de substituição alélica de pelo menos um SNP para cada uma das características avaliadas, indicando que esses polimorfismos podem auxiliar nos processos de seleção das características relacionadas com a resistência às parasitoses gastrintestinais e com a prolificidade.The aim of this work was to evaluate the presence of polymorphisms and possible associations with characteristics associated with resistance to gastrointestinal parasites and prolificacy in Santa Ines sheep. To evaluate the resistance to gastrointestinal parasites, feces and blood samples of approximately 700 animals infected naturally and from four different properties, were collected between the months of October and November, 2011 to assess characteristics body condition, degree of anemia measured by FAMACHA card, the characteristics of the hair of sheep, feces consistency, egg counts per gram of feces, hematocrit, white blood cell count, red blood cell count, hemoglobin and platelets count. For the evaluation of prolificacy, 340 sheep were evaluated for the total number of lambs born, divided by the number of births from each dam, as well as the correlation of this feature with the average birth weight of their lambs and productive efficiency of dam. 28 single nucleotide polymorphisms (SNPs) were selected for the development of this study and were genotyped by Sequenom MassARRAY iPLEX platform. Allele and genotype frequencies, the Hardy-Weinberg equilibrium, the effects of allelic substitution, additivity and dominance deviation were analyzed. The results showed considerable variability of the characteristics evaluated in the population in study and in most of the polymorphisms. Significant effect was observed (p ≤ 0.05) or suggestive (0.05> p ≤ 0.10) for allelic substitution of at least one SNP for each of the evaluated traits, indicating that these polymorphisms may help in the selection processes of characteristics related to resistance to gastrointestinal parasites and prolificacy.
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Nascimento, Wellington Ferreira do. « Diversidade genética de inhame (Dioscorea trifida L.) avaliada por marcadores morfológicos, SSR e ISSR ». Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/11/11137/tde-10102013-083032/.
Texte intégralRésumé :
Dioscorea trifida L. é uma espécie de inhame comestível originária da América do Sul, que em conjunto com outras espécies importantes economicamente do gênero Dioscorea é mantida por pequenos agricultores tradicionais. Assim, observa-se que as comunidades tradicionais exercem um papel fundamental na manutenção e geração da diversidade genética de inhame.O objetivo deste trabalho foi obter informações a respeito da distribuição, manejo e diversidade genética de D. trifida no Brasil. Para tanto, foram visitados e entrevistados agricultores dos Estados de São Paulo, Santa Catarina e Mato Grosso. Durante as visitas, foram coletados 51 acessos, os quais, juntamente com dois acessos adquiridos em feiras livres no Estado do Amazonas, foram caracterizados por meio de 16 descritores morfológicos, 16 ISSR e oito SSR.Observou-se que o cultivo de D. trifida ocorre na maioria das vezes em roças com menos de dois hectares (92%) mantidas por agricultores tradicionais, com a produção ocorrendo em baixa escala, visando principalmente a subsistência das pessoas envolvidas com o cultivo e manutenção da espécie. Dentre as denominações encontradas para a espécie, as mais citadas foram \"cará roxo\", em 43,4% das unidades amostrais, \"cará\" e \"cará branco\", ambos observados em 9,4%, e \"cará mimoso\", com 7,6%. Observou-se também uma regionalização dessas denominações, onde \"cará roxo\" e \"cará branco\" foram atribuídos à espécie pelos agricultores dos Estados de São Paulo e Mato Grosso, sendo que \"cará\" e \"cará mimoso\" foram atribuídos pelos agricultores de Santa Catarina. Os nomes \"cará roxo\" e \"cará\" foram também atribuídos aos dois acessos da Amazônia. Além dessas, várias outras denominações para a espécie foram encontradas, porém com baixa frequência. Na caracterização morfológica observou-se que as cores da casca e da polpa foram os caracteres morfológicos mais relevantes para a distinção dos acessos. O nível de polimorfismo entre os acessos foi elevado, 95% para SSR e 76% para ISSR. O coeficiente de similaridade de Jaccard, bem como os resultados obtidos com as análises de agrupamento, coordenadas principais e bayesiana para os marcadores SSR e ISSR, separaram os acessos em três grupos principais: I - acessos de Ubatuba-SP; II - acessos de Iguape-SP e SantaCatarina; III - acessos de Mato Grosso. Os dois acessos do Amazonas variaram de posição de acordo com a região genômica analisada. A maior parte da diversidade genética foi observada dentro dos grupos formados (66,5% e 60,6% para ISSR and SSR, respectivamente), embora a diversidade entre grupos tenha sido de considerável magnitude, mostrando a estruturação dos acessos de acordo com sua origem, o que foi comprovado pela correlação baixa, mas significativa entre as distâncias genéticas e geográficas dos acessos. Portanto, os resultados obtidos para os marcadores SSR e ISSR demonstraram que a diversidade genética dos acessos de D. trifida mantidos por pequenos agricultores tradicionais do Brasil está levemente estruturada no espaço geográfico amostrado. Estes resultados poderão auxiliar na elaboração de estratégias de conservação para a espécie, tanto ex situ como in situ, dentro da visão de conservação on farm.Dioscorea trifida L. is a species of edible yams originated in South America, which together with other economically important species of the genus Dioscorea is cultivated by small traditional farmers. Thus, it is observed that traditional communities play a key role in the generation and maintenance of yams genetic diversity. The aim of this study was to obtain information about the distribution, management and genetic diversity of D. trifida in Brazil. So, were visited and interviewed farmers in the states of São Paulo, Santa Catarina and Mato Grosso. During the visits, we collected 51 accessions, which, together with two accessions purchased at fairs in the state of Amazonas, were characterized using 16 morphological descriptors, 16 ISSR and eight SSR markers.We observed that D. trifida occurs most often in swidden fields with less than two hectares (92%) maintained by traditional farmers, with production occurring on a small scale, mainly targeting the livelihood of the people involved with the cultivation and maintenance of the species. Among the names found for the species, the most cited were \"cará roxo\" in 43.4% of the sample units, \"cará\" and \"cará branco\", both observed in 9.4% and \"cará mimoso\" with 7.6%. There is also a regionalization of these denominations, where \"inhame roxo\" and \"inhame branco\" were assigned by farmers to the species in the states of São Paulo and Mato Grosso, where \"cará\" and \"cará mimoso\" were allocated to farmers of Santa Catarina. The names \"cará roxo\" and \"cará\" were also awarded to two accessions from the Amazon. Besides these, several other names for the species were found, but with low frequency. In the morphological characterization, the skin and flesh color were the most relevant traits for the distinction of accessions. The polymorphism level between the accessions was high, 95% for SSR and 76% for ISSR. The Jaccard similarity coefficient and the results obtained in the cluster analysis, principal coordinates and Bayesian analyses for ISSR and SSR markers, separated the accessions into three main groups: I - accessions from Ubatuba-SP; II - accessions from Iguape-SP and Santa Catarina; III - accessions from Mato Grosso. The accessions from Amazonas ranged their position according to the genomic region analyzed. The majority of genetic diversity was observed within groups (66.5% and 60.6% for ISSR and SSR, respectively), although differences between groups was of considerable magnitude, showing the structure of the accessions according to their origin, which was confirmed by correlation between genetic and geographic distances of accessions. Therefore, the results obtained for the SSR and ISSR markers showed that the genetic diversity of accessions of D. trifida maintained by small traditional farmers in Brazil is slightly structured in the geographic area sampled. These results may help in developing conservation strategies for the species, both ex situ and in situ, within the vision of on farm conservation.
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Almeida, Vanessa Cavalcante de. « Caracteriza??o gen?tica e in situ de Gossypium barbadense na regi?o norte do Brasil ». Universidade Federal do Rio Grande do Norte, 2007. http://repositorio.ufrn.br:8080/jspui/handle/123456789/16772.
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Previous issue date: 2007-02-27Brazil has been considered one of the diversity centers of Gossypium barbadense species. It is believed that a relatively big erosion genetic process occurs with the species, due to economic, cultural and agricultural problems. A local diagnostic about species situation is the first step for reducing the diversity loss and establishing conservation strategies in situ. This research aimed the identification of the presence of Gossypium populations, characterization, determination of the main risks and collection of the accesses to store in germoplam banks, in Para and Amapa States. Expeditions were conducted in November 2004. An interview was carried out with the plant proprietor for characterizing in situ of G. barbadense species and of the environment where the plants were inserted. On hundred seventy nine plants in 22 municipal districts were collected in Para State and 117 plants in nine municipal districts in Amapa State. The majority of plants belong to G. barbadense species (98% in Amapa and 94% in Para). Plants occur in back yards, beside roads and spontaneously. That ones from back yards were more abundant (97% in Amapa and 95% in Para) and maintained as medicinal plants as the principal reason. Plants in natural environments in both states evaluated were not found, therefore, the creation of reserves and the application of others conventional methods of maintenance in situ are not applicable. The plant proprietors do not use to store or process seeds. Seed storage was reported as a practice by only 1% of the plant proprietors from Para and 11% from Amapa. The most plants collected were from two to three years of age (58% in Amapa and 93% in Para). As conclusions G. barbadense is the species most spread in the two studied states and are found in back yards. In Amapa State the botanical variety barbadense or Quebradinho is predominant, whereas in Para State the predominant variety is brasiliense or Rim-de-boi. Adequate conservation of thestudied species must be carried out in germoplasm collections maintained ex situ
O Brasil ? considerado um dos centros de diversidade da esp?cie Gossypium barbadense. Acredita-se que grande parte da variabilidade gen?tica de G. barbadense esteja sendo perdida, em virtude de problemas econ?micos, culturais e agr?colas. O primeiro passo para reduzir a perda de diversidade e estabelecer estrat?gias de conserva??o in situ ? realizar um diagn?stico de como a esp?cie se encontra nos locais em que ocorre. Os objetivos deste trabalho foram identificar popula??es de Gossypium presentes no estado do Par? e Amap?, caracteriz?-Ias, determinar os principais riscos e coletar acessos para armazenamento em bancos de germoplasma. Foram realizadas expedi??es em Novembro de 2004, e a caracteriza??o in situ de G. barbadense foi realizada por entrevista do propriet?rio da planta e da an?lise do ambiente em que as plantas estavam inseridas. Foram coletadas 179 plantas em 22 munic?pios no estado do Par? e 117 plantas em nove munic?pios no estado do Amap?. A maioria das plantas pertence ? esp?cie G. barbadense (98% no Amap? e 94% no Par?). As plantas ocorrem em fundo de quintal, beira de estrada e de modo espont?neo, sendo as de fundo de quintal bem mais abundantes (97% no Amap? e 95% no Par?) e mantidas com a finalidade principal de serem usadas como plantas medicinais. Os moradores n?o possuem o h?bito de armazenar e beneficiar as sementes, no Par? apenas 1 % dos propriet?rios relatou armazenar as sementes e no Amap? esse ?ndice foi de 11 %. A maioria das plantas coletadas tinha de dois a tr?s anos de idade (58% no Amap? e 93% no Par?). Conclui-se ent?o que G. barbadense ? a esp?cie mais difundida nos dois estados e que s?o encontradas em fundo de quintal. No estado do Amap? predomina a variedade bot?nica barbadense ou Quebradinho, enquanto que no Par? predomina a variedade brasiliense ou Rim-de-boi. N?o foram encontradas plantas em ambientes naturais nos dois estados, portanto a cria??o de reservase o emprego de outros m?todos convencionais de manuten??o in situ n?o parecem ser aplic?veis a G. barbadense em ambos os estados. A adequada conserva??o dessas esp?cies deve ser realizada em cole??es de germoplasma mantidas ex situ
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Beyene, Yoseph Aydagn. « Genetic analysis of traditional Ethiopian Highland Maize (Zea Mays L.) using molecular markers and morphological traits : implication for breeding and conservation ». Thesis, University of Pretoria, 2005. http://hdl.handle.net/2263/30529.
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Knowledge of the genetic variation of crop collections is essential for their efficient use in plant breeding programs. The Ethiopian Highland Maize Germplasm Collection Mission was launched throughout the highlands of Ethiopia in 1998 and 287 traditional maize accessions were collected from farmers’ fields. To date, no information was available on the morphological and genetic diversity in this important collection. Various molecular marker techniques and quantitative genetics approaches were applied to accurately unravel the extent of phenotypic and genetic diversity, to study patterns of morphological and molecular variation and to determine association of molecular markers with quantitative trait variation, with the view of designing a sound breeding program and management strategy for maize in the highlands of Ethiopia. The morphological study confirmed that traditional Ethiopian highland maize accessions contain large amounts of variation for agro-morphological traits. The broad trait diversity observed among the accessions suggested ample opportunities for the genetic improvement of the crop through selection directly from the accessions and/ or the development of inbred lines for a future hybrid program. Selection practices followed by local farmers are mostly consistent within agroecology and gave rise to morphologically distinct maize accessions in different agroecologies. This underscores the importance of considering farmers’ knowledge of diversity in the collection and evaluation of local accessions. The results of amplified fragment length polymorphism (AFLP) and microsatellite or simple sequence repeat (SSR) marker analyses showed that bulking leaf samples from 15 individual plants per out-bred accession is an effective means of producing representative profiles of individual plants, thereby reducing the cost of DNA extraction and subsequent marker analysis of open-pollinated varieties. Cluster analyses based on AFLP and SSR data showed that most of the accessions collected from the Northern agroecology were genetically distinct from the Western and Southern accessions suggesting that differentiation for adaptive traits for drought conditions may have occurred in the Northern accessions. However, there was very little genetic differentiation between the Western and Southern accessions suggesting gene flow between the two agroecologies and recent introduction of similar improved varieties in these agroecoogies . In both marker systems, high mean genetic diversity was observed among the traditional Ethiopian highland maize accessions. This is possibly due to (i) the continuous introduction of maize from abroad by different organizations; (ii) genetic variation generated through farmers management practices; and (iii) the presence of different environmental conditions in the highlands of Ethiopia to which local landraces may have been adapted. The correlation between the morphological dissimilarity matrix and the matrices of genetic dissimilarity based on SSR and AFLP markers were 0.43 and 0.39, respectively (p = 0.001 in both cases). The correlation between SSR and AFLP dissimilarity matrices was 0.67 (p = 0.001). These significant correlations indicate that the three independent sets of data likely reflect the same pattern of genetic diversity, and validate the use of the data to calculate the different diversity statistics for Ethiopian highland maize accessions. From this study, three groups of maize accessions with distinctive genetic profiles and morphological traits were identified that will be useful for future collection, conservation and breeding programs of maize for the highlands of Ethiopia. A pilot association study using SSR markers and quantitative trait variation indicated that molecular markers could be useful to identify genetic factors controlling earliness, tallness, grain yield and associated traits, which could be exploited by various breeding schemes. The analytical tools outlined in this dissertation can be a useful tool in managing genetic variation of open-pollinated crops and will aid in the conservation of unique genetic diversity. Production stability and global food security are linked to the conservation and exploitation of worldwide genetic resources and this research attempts to add to that body of knowledge. Copyright 2005, University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. Please cite as follows: Beyene, YA 2005, Genetic analysis of traditional Ethiopian Highland Maize (Zea Mays l.) using molecular markers and morphological traits : implication for breeding and conservation, PhD thesis, University of Pretoria, Pretoria, viewed yymmdd < http://upetd.up.ac.za/thesis/available/etd-02212006-112610 / >Thesis (PhD (Genetics))--University of Pretoria, 2005.
Genetics
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Passos, Ana Laura Pereira. « Mapeamento de locos de resistência ao crestamento bacteriano comum do feijoeiro (Phaseolus vulgaris L.) ». Universidade Federal de Goiás, 2016. http://repositorio.bc.ufg.br/tede/handle/tede/7319.
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Fundação de Amparo à Pesquisa do Estado de Goiás - FAPEG
The common bean (Phaseolus vulgaris) is grown in Brazil in various locations, soil and climatic conditions. The diseases are among the leading causes of losses in productivity of this legume, and the common bacterial blight (CBB) is the most important bacterioses that affects the culture. The resistance of CBB in common bean is a complex quantitative trait that results from the interaction of several genes. Genetic maps are tools that optimize the search for loci associated with this type of feature, and the most commonly used molecular markers available for this type of study are the SNPs (Single Nucleotide Polymorphism). In this sense, this study aimed to: (i) develop a robust genetic map for common bean using SNP markers and the RIL (Recombinant Inbreed Lines) mapping population derived from Ruda × AND 277; (ii) characterize this RIL population and their parents about the reaction to common bacterial blight in field and greenhouse; and (iii) identifying genomic regions (major genes and/or QTL) that control the bacterial blight in this population. We used 393 individuals of the Ruda × AND 277 RIL population, evaluated for reaction to CBB in two field trials in Ponta Grossa - PR, in the rain growing season of 2012 and 2014 and in an inoculation test at the greenhouse, in Santo Antônio de Goiás - GO. The population was genotyped with 5,398 SNP markers and mapping was performed using the R-OneMap and MapDisto programs. Statistical analyzes were performed in the Genes program, and the Scott-Knott method was used for averages groupingin R platform. The QTL analysis was conducted in QTLCartographer program. Using the chi-square test (1:1), 2,062 markers were selected for mapping. Three genetic maps with high strengt, saturation and resolution were built. Statistical analysis showed that there is genetic variability for the CBB resistance in the population of RILs. The QTL analysis identified 10 QTLs linked to resistance of CBB in the Ruda × AND 277 RIL mapping population, in the chromosomes PV01, PV02, Pv07, Pv09 and PV11, based on results from evaluations carried out in the field and greenhouse. The maps constructed for this population have high strength and resolution and may be used for future work on integrative mapping. The statistical analysis evidenced the quantitative character of resistance to CBB in common bean and showed that the parent Rudá has the CBB resistance alleles. It is expected that the markers linked to these QTLs identified can be used in future studies of marker assisted selection.
O feijoeiro-comum (Phaseolus vulgaris) é cultivado no Brasil em vários locais e diversas condições edafoclimáticas. As doenças estão entre as principais causas de prejuízos na produtividade dessa leguminosa, sendo o crestamento bacteriano comum (CBC) a principal bacteriose que afeta essa cultura. A resistência ao CBC no feijoeiro-comum é uma característica complexa, quantitativa, que resulta da interação de vários genes. Os mapas Genéticos são ferramentas que otimizam a busca de locos associados a esse tipo de característica, e os marcadores moleculares mais utilizados disponíveis para esse tipo de estudo são os SNPs (Single Nucleotide Polymorphism). Neste sentido, o presente trabalho teve como objetivos: (i) construir um mapa genético robusto para o feijoeiro-comum, utilizando marcadores SNP e a população de RILs (Recombinant Inbred Lines, ou linhagens endogâmicas recombinantes) derivada do cruzamento Rudá × AND 277; (ii) caracterizar esta população de RILs e seus genitores quanto à reação ao crestamento bacteriano comum, em campo e em casa de vegetação; e (iii) identificar regiões genômicas (genes de efeito principal e/ou QTLs) que controlam a reação ao crestamento bacteriano comum nesta população. Foram utilizados 393 indivíduos da população de RILs Rudá × AND 277, avaliados quanto à reação ao CBC em dois ensaios de campo em Ponta Grossa – PR, nas águas de 2012 e 2014, e em um ensaio de inoculação em casa de vegetação, em Santo Antônio de Goiás - GO. A população foi genotipada com 5.398 marcadores SNP e o mapeamento das RILs foi realizado utilizando os programas R-OneMap e MapDisto. As análises estatísticas foram realizadas no programa Genes, sendo o agrupamento de médias de Scott-knott realizado na plataforma R. A análise de QTL foi realizada no programa QTLCartographer. Por meio do teste de quiquadrado (1:1) foram selecionados 2.062 marcadores para o mapeamento. Foram construídos três mapas genéticos com elevada robustez, saturação e resolução. As análises estatísticas evidenciaram que há variabilidade genética para a característica de resistência ao CBC na população de RILs. A análise de QTL identificou 10 QTLs ligados à resistência ao CBC na população de RILs Rudá × AND 277 nos cromossomos Pv01, Pv02, Pv07, Pv09 e PV11 com base em dados obtidos a partir de avaliações em campo e casa de vegetação. Os mapas construídos para essa população apresentam elevada robustez e resolução e poderão ser utilizados para futuros trabalhos de mapeamento integrativo. As análises estatísticas evidenciaram o caráter quantitativo da resistência ao CBC em feijoeiro-comum e mostraram que o genitor Rudá possui alelos de resistência ao CBC. Espera-se que os marcadores ligados a esses QTLs identificados possam ser utilizados em futuros trabalhos de seleção assistida por marcadores.
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Ferreira, Carlos Eduardo Ranquetat. « Contribuição de machos suínos para paternidade de leitões gerados por inseminação artificial heterospérmica ». Universidade Federal de Pelotas, 2013. http://repositorio.ufpel.edu.br/handle/ri/2491.
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Previous issue date: 2013-03-26The common use of pooled sperm doses (composed of sperm of two or more boars) in artificial insemination (AI) in swine limits the precise evaluation of individual boar fertility. Thus, marginal differences in potential fertility among boars are clouded by the use of heterospermic AI. This study had the objective of identifying the contribution of individual boars for the paternity of progeny generated by heterospermic AI. Four boars were used as sperm donors (A, B, C and D). After collection, ejaculates from those boars were used to compose homospermic and heterospermic doses (AB, AC, AD, BC, BD and CD), all including 3.0 x 109 spermatozoa in 80 ml. A total of 511 females were inseminated. The paternity of 4.119 piglets was determined through the use of SNP (Single nucleotide polymorphism) markers : 3.558 from heterospermic AI; and 461 from homospermic AI. The comparison of paternity per pool showed that the pool AC was the only one in which each boar contributed similarly for paternity (P > 0.05), whereas differences between boars occurred in all other pools (P < 0.05). The greatest contribution for paternity of piglets occurred for boar D, which sired nearly 60% of all piglets boar in the pools in which that boar took part. These results indicate that in most of the heterospermic AI, individual boars contribute distinctly for the paternity of the piglets, even though each boar contributes with the same sperm concentration in the pooled sperm doses. Key
O uso generalizado de pool de sêmen (dois ou mais machos compondo a dose) em inseminações artificiais comerciais limita a análise dos dados de fertilidade dos reprodutores. Pequenas diferenças no potencial fecundante dos machos doadores são ocultadas pelo uso de doses heterospérmicas. Este trabalho teve por objetivo identificar a contribuição individual de reprodutores suínos para a composição da progênie gerada por inseminação artificial heterospérmica. Foram utilizados quatro reprodutores suínos. Após a coleta dos ejaculados foram elaboradas doses inseminantes (DI) homospérmicas (A, B, C e D) e DI heterospérmicas, formando os pools (AB, AC, AD, BC, BD e CD) contendo 3,0 x 109 espermatozoides em 80 ml. Foram inseminadas 511 fêmeas. A determinação da paternidade foi através de marcadores SNP (Single nucleotide polymorphism). Foram genotipadas amostras de um total de 4.019 leitões, 3.558 provenientes de IA heterospérmicas e 461 provenientes de IA homospérmicas. Durante a análise do percentual de paternidade por pool, constatou-se que AC foi o único grupo em cada macho contribuiu igualmente para o tamanho das leitegadas (P > 0,05), nos demais pools foi observada diferença estatística significativa (P<0,05). A avaliação das doses heterospérmicas revelou que as médias mais elevadas foram de pools formados pelo reprodutor D, que contribuiu com aproximadamente 60% do total de nascidos (TN) em seus pools. Conforme os resultados obtidos, na maioria dos casos estudados não há contribuição semelhante na quantidade de leitões nascidos, ainda que a concentração de células espermáticas de cada um dos machos seja idêntica na formação das DIs.
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Carvalho, Alexandre Zanardo de. « Transferabilidade de microssatélites de arroz para trigo na busca por marcadores ligados à resistência à fusariose ». Universidade Federal de Pelotas, 2007. http://guaiaca.ufpel.edu.br/handle/123456789/1255.
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Previous issue date: 2007-12-29Fusarium head blight (FHB) is one of the most important diseases known to affect wheat crop. FHB, caused mainly by Fusarium graminearum, results in severe losses of productivity and grain quality besides its harmful effects to human and animal health due to the accumulation of mycotoxins in infected grains. Genetic resistance is the best way to control FHB which affects crops in several parts of the world. FHB resistance shows a quantitative heritage, hence are QTLs (quantitativetrait- loci) that have a weak effect on character. Studies with microsatellite markers have generated a great number of information related to the position of those QTLs in the genome, in addition to the development of new varieties to be used in breeding programs. The microsatellites are short sequence repeats, spread thoroughly in the organism s genome. For amplification of those sequences it is used specific primers to each loco. Due to the genetic relation between species, information generated from the study in one species can be used successfully when studying related species. Therefore, primers designed for microsatellites in one species can be used to detect markers in related species and to associating those markers with characteristics of interest. Here, the main objective of my work was to verify the transferability of microsatellites from rice to wheat in search of markers related to FHB resistance. It was tested different wheat genotypes showing different levels of resistance to Fusarium and was verified the existence of polymorphism among those genotypes. A number of 55 primer pairs of microsatellites isolated from the rice genome were tested in 13 wheat cultivars classified as susceptible, moderately susceptible, moderately resistant and resistant. In my results, the rate of microsatellite transferability was of 76.4%, where from these, 23.8% showed polymorphism and 76.2% showed monomorphism. In spite of the high rate of the microsatellite transferability observed in my results, the analysis of polymorphism did not allow the identification of markers that could be possibly associated with resistance to Fusarium head blight in wheat.
A fusariose do trigo, causada principalmente pelo fungo Fusarium graminearum, é uma das principais doenças nessa cultura, ocasionando perda de produtividade e de qualidade de grãos, além dos efeitos nocivos à saúde do homem e de animais devido ao acúmulo de micotoxinas nos grãos infectados. A resistência genética é a melhor forma para o controle dessa patologia que atinge a cultura em várias regiões do mundo. Ela exibe herança quantitativa, ou seja, são QTLs que tem um pequeno efeito sobre o caráter. Estudos com marcadores de microssatélites têm gerado um grande número de informações a respeito da posição desses QTLs no genoma e no desenvolvimento de novas variedades para cultivo em programas de melhoramento. Os microssatélites são pequenas seqüências de bases repetidas, posicionadas adjacentemente e distribuídas amplamente no genoma dos organismos. Para sua amplificação são utilizados primers específicos para cada loco. As relações genéticas entre espécies permitem que informações geradas a partir do estudo de uma delas sejam utilizadas para o estudo de espécies relacionadas. Dessa forma, primers desenhados para locos de microssatélites em uma espécie podem ser utilizados para detectar marcadores em espécies afins e serem associados a características de interesse. Sendo assim, o objetivo deste trabalho foi verificar a transferabilidade de locos de microssatélites de arroz para genótipos de trigo com diferentes níveis de resistência à fusariose e verificar a existência de polimorfismo entre os genótipos contrastantes que pudessem ser associados à característica de resistência. Foram testados 55 pares de primers de locos de microssatélites, isolados do genoma do arroz, em 13 cultivares de trigo, classificadas como suscetíveis, moderadamente suscetíveis, moderadamente resistentes e resistentes. Houve a transferabilidade de 76,4% desses locos de microssatélites. Destes, 23,8% apresentaram polimorfismo e o restante, 76,2%, apresentaram-se monomórficos. A análise do polimorfismo não permitiu a identificação de marcadores que pudessem ser associados à resistência para fusariose do trigo.
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BUENO, Luíce Gomes. « Caracterização agronômica e molecular da coleção nuclear de arroz da Embrapa ». Universidade Federal de Goiás, 2010. http://repositorio.bc.ufg.br/tede/handle/tde/432.
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Previous issue date: 2010-08-31The plant genetic resources stored ex situ are considered as a genetic repository, and are raw material for the development of the world agriculture. In rice, despite its high genetic variability, the lack of information of accessions to compose a databank prevents its use to help the choice of genitors for the breeding programs. The Embrapa Rice Core Collection (ERiCC) was developed from 10,000 accessions from Embrapa GeneBank, and it was set up by 550 accessions, divided in three subsets: 1) 94 lines and cultivars from Brazil (LCB); 2) 148 lines and cultivars from abroad (LCI); and 3) 308 traditional varieties (VT), obtained from germplasm collection expeditions in Brazil. This work aimed: 1) to evaluate the extension of genetic variability of 550 accessions from ERiCC by means of agronomic traits characterization using mixed models and multivariate statistics; 2) to perform a comparative analysis of the genetic divergence considering the agronomical and SSR markers characterizations; and 3) to identify the genotypes with higher genetic diversity and with the best agronomic performances, aiming to promote the most efficient use of such germplasm in breeding programs. The agronomic characterization of 550 accessions was performed in nine field experiments, evaluating 18 phenological-agronomic traits. The data were analyzed using the mixed linear and AMMI models. There was wide variation range of genotypical values for most evaluated traits. In different environments, it was observed VT accessions among the high-yielding materials, demonstrating the potential of this group of germplasm, particularly important due to its high genetic variability, to contribute to the development of cultivars regionally adapted. The AMMI approach allowed a good discrimination of ERiCC rice genotypes in relation to the adaptive performance, identifying the accessions CA880078, CA990001, CA870071 (subset VT), and CNA0009113 (LCI) as having good yield and broad adaptation to distinct environments. The comparative analysis of genetic diversity between agronomic and molecular data was performed using the 242 lines and cultivars accessions from ERiCC, which were characterized by 86 fluorescent SSR markers, and five agronomic traits with genotypic values predicted (values without from the effects of interaction genotypes x environment, from a joint analysis of nine experiments. The genetic divergence among accessions was estimated by the average Euclidian distance for phenotypical data, and by the Rogers modified by Wright (RW) genetic distance. The datasets were jointly analyzed by descriptive and multivariate statistics, using correlation analyses from hierarchical grouping of Ward and UPGMA methods. The phenotypical and molecular data showed a broad distribution of dissimilarity indexes, despite they showed different patterns of variation between them. Low molecular distances were associated to low phenotypical distances, however to high molecular distances, occurred a high broad range of phenotypical variation. The correlation between genetical and phenotypical dissimilarities was significant for both lowland and upland accessions, despite with different values (r=0.156 and r=0.409, respectively). Due to the low relation between phenotypical and molecular data, the analysis of genotypes to be used in breeding programs must include both evaluations to a better accession characterization. Considering the high yielding accessions, the higher molecular distances were identified among the accessions from lowland system of cultivation, among which BR IRGA 413 and CNA0005014, BR IRGA 413 and CNA0005853, and CNA0004552 and CNA0005014. Considering the upland accessions, maximum genetic distances were identified in CNA0000482 and CNA0006422, CNA0001006 and CNA0006422, and CNA0001006 and CNA0003490. The molecular analysis was able to identify accessions with reduced genetic relationship, that if used as genitors, will result in a progeny with a high probability to find new allelic combinations. On the other hand, the phenotypical characterization is important to identify accessions not just genetically divergent, but with superior agronomic trait performances for breeding programs. The results of this work will permit to increase the activities related to the characterization of accessions from rice Genebank, giving support of breeding programs to choose the best accessions to obtain new cultivars, with favorable traits, and broad genetic basis. In addition, a continuous program of phenotypical and molecular characterization of germplasm will be able to identify accessions to increase the genetic variability of ERiCC.
Os recursos genéticos vegetais armazenados ex situ são considerados reservatórios de genes e funcionam como matéria-prima para o desenvolvimento da agricultura mundial. Na cultura do arroz, apesar da extensa variabilidade genética existente, a deficiência de informações que integrem dados que possam efetivamente auxiliar na escolha de genótipos importantes para os programas de melhoramento constitui o principal fator que limita a utilização mais ampla dos acessos armazenados nos bancos de germoplasma. A Coleção Nuclear de Arroz da Embrapa (CNAE) representa a variabilidade genética de mais de 10 mil acessos constituintes do Banco Ativo de Germoplasma (BAG) da Embrapa Arroz e Feijão, e é composta por 550 acessos subdivididos em três estratos: 1) 94 Linhagens e Cultivares Brasileiras (LCB), provenientes de programas de melhoramento de instituições brasileiras; 2) 148 Linhagens e Cultivares Introduzidas (LCI), provenientes de programas de melhoramento de outros países; e 3) 308 Variedades Tradicionais (VT), que reúne acessos obtidos por expedições de coleta de germoplasma realizadas em vários estados do Brasil. Este trabalho teve como principais objetivos: 1) avaliar a extensão da variabilidade genética dos 550 acessos pertencentes à CNAE por meio da caracterização agronômica via metodologias de modelos mistos e estatísticas multivariadas; 2) realizar a análise comparativa da divergência genética entre acessos, determinada pela avaliação de caracteres agronômicos e marcadores moleculares SSR; e 3) identificar os genótipos com maior diversidade genética e com melhores atributos agronômicos, a fim de indicar uma melhor utilização destes recursos genéticos em programas de melhoramento. Na caracterização agronômica foram avaliados 550 acessos em experimentos conduzidos em nove locais no Brasil, envolvendo um total de 18 caracteres fenológico-agronômicos. Os dados foram analisados empregando-se a abordagem de modelos lineares mistos e modelo AMMI de análise. Verificou-se grande amplitude de variação dos valores genotípicos para a maioria dos caracteres avaliados. Nos diferentes ambientes, houve ocorrência de genótipos do estrato VT entre os mais produtivos, o que demonstra o potencial deste grupo de germoplasma, particularmente importante por sua grande variabilidade genética, em contribuir para o desenvolvimento de cultivares regionalmente adaptadas. A abordagem AMMI permitiu uma boa discriminação dos genótipos de arroz da CNAE quanto ao seu comportamento adaptativo, identificando os acessos CA880078, CA990001, CA870071 (do estrato VT), e CNA0009113 (LCI) com estabilidade, produtividade satisfatória e ampla adaptação à diferentes ambientes. Para a análise comparativa da diversidade genética entre dados agronômicos e moleculares foram considerados 242 acessos da CNAE, os quais foram caracterizados utilizando-se 86 marcadores SSR fluorescentes, sendo que para os dados agronômicos, foram realizadas análises conjuntas dos experimentos e considerados os valores genotípicos preditos de cinco caracteres (valores livres dos efeitos de interação genótipos x ambientes). A divergência genética entre os acessos foi estimada pelo procedimento de distância Euclidiana média para os dados fenotípicos, e por meio da distância de Rogers modificada por Wright (RW) para os dados moleculares, analisando-se os conjuntos de dados por meio de estatísticas descritivas e multivariadas, empregando-se análises de correlação entre matrizes de dissimilaridade e análises de agrupamento hierárquico de Ward e UPGMA. Os dados fenotípicos e moleculares apresentaram uma ampla distribuição dos índices de dissimilaridade, embora tenham apresentado diferentes padrões dessa variação. Baixas distâncias moleculares estiveram associadas a baixas distâncias baseada nos valores genotípicos, no entanto para elevadas distâncias moleculares houve ocorrência de ampla escala de variação fenotípica. A correlação entre as dissimilaridades genéticas e valores genotípicos foi significativa tanto no conjunto de acessos irrigados quanto no de sequeiro, porém, com diferentes magnitudes (r=0,156 e r=0,409, respectivamente). Devido esta baixa relação entre os dados fenotípicos e moleculares, o estudo de genótipos para fins de uso no melhoramento genético deve incluir ambas avaliações para a melhor caracterização dos acessos. Entre os materiais mais produtivos, as maiores distâncias moleculares foram identificadas entre os genótipos do sistema de cultivo irrigado, dentre eles BR IRGA 413 e CNA0005014, BR IRGA 413 e CNA0005853, e CNA0004552 e CNA0005014. Entre os materiais de sequeiro, máximas distâncias genéticas foram identificadas entre os acessos CNA0000482 e CNA0006422, CNA0001006 e CNA0006422, e CNA0001006 e CNA0003490. A análise molecular permitiu que fossem identificados genótipos de vínculo genético reduzido, que quando utilizados como parentais em cruzamentos, possibilitarão que as progênies obtidas apresentem maiores chances de combinações alélicas inéditas. Por sua vez, a caracterização fenotípica tem papel fundamental na identificação de materiais que além de divergentes, apresentem desempenho agronômico superior para os programas de melhoramento. Os resultados deste trabalho permitirão aumentar eficazmente as atividades relacionadas à caracterização de acessos do Banco Ativo de Germoplasma de arroz, subsidiando os programas de melhoramento na escolha de genótipos a serem utilizados para a obtenção de novas cultivares, com características favoráveis, de ampla base genética. Em adição, um programa contínuo de caracterização fenotípica e molecular de germoplasma permitirá ainda a escolha de acessos para a ampliação da variabilidade genética da CNAE.
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Rezende, Fernanda Marcondes de. « Prospecção da influência de marcadores genéticos sobre características de crescimento, carcaça e qualidade de carne em bovinos da raça Nelore ». Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/74/74131/tde-03062009-094616/.
Texte intégralRésumé :
Dados de desenvolvimento ponderal de 3.844 bovinos da raça Nelore, criados em pastagens em duas fazendas do sudoeste do Brasil, dos quais 1.889 tiveram suas carcaças avaliadas por ultra-sonografia e 674 foram confinados por 90 a 120 dias e abatidos por volta dos 24 meses de idade tiveram análises de associação com dezenas de marcadores genéticos realizadas, visando detectar a associação desses marcadores com características economicamente relevantes. Foram analisadas as características de crescimento, peso ao nascer (PNAS), peso a desmama (PDES), peso ao sobreano (PSOB), ganho de peso pós-desmama (GP345), escores visuais de conformação frigorífica (CONF), precocidade de acabamento (PREC), musculosidade (MUSC) e de carcaça área de olho de lombo medida por ultra-sonografia (AOL_US), espessuras de gorduras medida por ultra-som na região lombar (EGS_US) e na picanha (EGP8). Adicionalmente, foram analisadas as características medidas post-mortem, relacionadas a qualidade de carcaça, peso de carcaça quente (PCQ), área de olho de lombo (AOL), espessura de gordura no músculo Longissimus dorsi (EGS) e as características ligadas à qualidade de carne, perdas por exsudação após 7, 14 ou 21 dias de maturação da carne (PEX7, PEX14, PEX21), perdas por cocção e maciez após os mesmos períodos de maturação (PCO7, PCO14 e PCO21, MAC7, MAC14 e MAC21), além de teor de lipídeos totais e colesterol em amostras após 7 dias de maturação. Os genótipos dos polimorfismos de base única (SNP) foram obtidos em laboratórios licenciados por empresa parceira, com uso de placas de micro-arranjos dessa empresa. Foram analisados os efeitos de substituição em análises de marcador único e multi-polimorfismos e os efeitos de aditividade e desvio de dominância de cada marcador genético. Vários dos polimorfismos de DNA analisados apresentaram ou fixação ou freqüências muito altas, maiores que 99%, de um dos alelos impossibilitando as análises de associação. No entanto, muitos outros polimorfismos apresentaram freqüências gênicas adequadas às análises de associação. Cada uma das características avaliadas apresentou, no mínimo, dois marcadores com efeitos significativos (P≤0,05) ou sugestivos (0,05<P≤0,20), o que indica que polimorfismos de DNA podem ser critérios adicionais e auxiliares nos processos seletivos ligados às 24 características de desenvolvimento ponderal, qualidade de carcaça e carne na raça Nelore. Como os efeitos de substituição alélica são responsáveis apenas por parte da determinação de cada característica, em geral uma pequena parte, recomenda-se que as previsões de efeitos de marcadores sejam feitas com análise conjunta dos mesmos.Data on of 3,844 Nellore cattle, reared under pasture conditions on two different farms in southwestern Brazil, 1,889 of them measured by ultra-sound for carcass traits and 674 bulls finished in a feedlot for 90 to 120 days and slaughtered around 24 month of age were analyzed to verify the association with genetic markers (DNA Single nucleotide polymorphism or SNP) with the objective of detecting association of those markers with traits economically important relevant for Brazilian beef business. Growth traits considered were birth weight (PNAS), weaning weight (PDES), yearling weight, measured at 18 mo (PSOB), weight gain after weaning (GP345), visual scores for carcass conformation (CONF), finishing (PREC) and muscle (MUSC). Carcass traits, measured by ultra-sound were ribeye area (AOL_US), backfat (EGS_US) and fat depth at rump (EGP8). Additionally, carcass traits measured after slaughter were hot carcass weight (PCQ), ribeye area (AOL), fat depth on Longissimus muscle (EGS). Meat quality traits were measured after 7, 14 and 21 days of ageing: weep loss (PEX7, PEX14 and PEX21), shrink loss (PCO7, PCO14 and PCO21) and tenderness (MAC7, MAC14 and MAC21). Total lipids and cholesterol content on samples aged for 7 days, were, also, included on the analysis. The genotypes of DNA markers were carried out in laboratories licensed by a private company using its micro-array panels. Allele substitution effects were estimated in single or multi-polymorphism analysis. Additive and dominance effects were also estimated. Many DNA polymorphisms analyzed showed to be fixed or the frequencies for one of the alleles were too high, more than 99 %. In those cases, analysis could not be performed. However, for many others polymorphisms there was observed variability on allele frequencies what make possible to do the association analysis. All traits analyzed were influenced by, at least, two polymorphisms with statistically significant (P≤0,05) or suggestive (0,05<P≤0,20) effects, thus DNA polymorphisms can be used as additional and auxiliary criteria on selection process of those 24 traits related to animal growth, carcass and meat quality in Nellore cattle. As allele substitution effects explain only a small part of the phenotype, the results of this paper suggest that the effect of those markers should be considered together.
36
Silvestrov, Pavel. « Computational Investigation of DNA Repair Enzymes : Determination and Characterization of Cancer Biomarkers and Structural Features ». Thesis, University of North Texas, 2018. https://digital.library.unt.edu/ark:/67531/metadc1157566/.
Texte intégralRésumé :
Genomic integrity is important for living cells' correct functioning and propagation. Deoxyribonucleic acid as a molecule is a subject to chemical reactions with agents that can come from environment as well as from internal metabolism processes. These reactions can induce damage to DNA and thus compromise the genetic information, and result in disease and death of an organism. To mitigate the damage to DNA, cells have evolved to have multiple DNA repair pathways. Presented here is a computational study of DNA repair genes. The structure of the Homo sapiens direct DNA repair gene ALKBH1 is predicted utilizing homology modeling methods and using AlkB and DBL proteins as templates. Analysis of the obtained structure and molecular dynamics simulations give insights into potentially functionally important residues of the protein. In particular, zinc finger domains are predicted, and lysines that could perform catalytic activities are investigated. Subsequent mutagenesis experiments revealed the effect of the residues predicted to form zinc fingers on activity of ALKBH1. Structure and dynamics of AlkD, a Bascillus cereus base excision DNA repair protein is also studied. This protein has been shown to bind DNA with large alkyl adducts and perform excision catalysis without base flipping which is characteristic to other enzymes in the same family. MD simulations of AlkD revealed that B helix, which interacts with DNA, has higher fluctuations when AlkD is not bound to DNA, and thus could have a role in binding and recognition of DNA. For the purpose of finding biomarkers and to further our understanding of a mode of action of DNA repair genes, statistical methods were applied to identify mutations that are linked to cancer phenotypes. Analysis was based on case-control studies of patients with cancers of prostate, breast, pancreas, lung as well as chronic lymphocytic leukemia from NCBI dbGAP database. Those mutations that result in missense mutations were further investigated. In particular, extensive MD simulations and experimental investigations were performed on the mutation in the ALKBH7 gene that was found to be linked to prostate cancer.
37
Miyagi, Mikiko. « Exploitation of bacterial artificial chromosome (BAC) libraries to enhance the efficiency of genome mapping ». Thesis, Queensland University of Technology, 2002. https://eprints.qut.edu.au/37140/6/37140_Digitised%20Thesis.pdf.
Texte intégral
38
Liu, Siyang. « Application of molecular markers in selected breeding material and plant genetic resources of Lolium perenne L ». Doctoral thesis, 2015. http://hdl.handle.net/11858/00-1735-0000-0028-8681-7.
Texte intégral
39
BOVE, ANDREA. « Analisi della diversità genetica in 2 specie arboree mediterranee : palma da dattero (Phoenix dactylifera) e pino nero (Pinus nigra) ». Doctoral thesis, 2013. http://hdl.handle.net/2158/797489.
Texte intégralRésumé :
Questo progetto di ricerca del dottorato si articola su due casi di studio simili nelle metodiche per generare i dati, basate su tecniche di genotipizzazione molecolare, ma con approcci differenti nell’analisi e soprattutto nell’interpretazione dei dati. In entrambi i casi di studio la diversità genetica è stata stimata mediante marcatori molecolari (microsatelliti-SSR-short sequence repeat- e SNP-single nucleotide polimorphism), ma mentre nel caso della palma da dattero è utilizzata per caratterizzare il germoplasma, nel caso del pino nero costituisce il prerequisito per la comprensione del ruolo relativo dei fenomeni selettivi e demografici nel definire la struttura genetica delle popolazioni, per studi di associazione molecolare, di filogeografia e più in generale di genetica della conservazione.
The Ph.D. thesis refers to two case studies where similar methods to generate the molecular data but different approaches of data analyses and interpretation were adopted. In both cases the genetic diversity has been estimated by molecular markers (microsatellites-SSR-short sequence repeat- and SNP-single nucleotide polymorphism). In the date palm case the genetic variability is used for the characterization of germplasm, while in the Pinus nigra case a more detailed analysis for understanding the relative role of selection and demography on the genetic structure of populations, for molecular association and phylogeographic studies were performed.
40
Shaw, Eric. « Genetic Basis of Tocopherol Accumulation in Soybean (Glycine Max [L.] Merr.) Seeds ». Thesis, 2012. http://hdl.handle.net/10214/4621.
Texte intégralRésumé :
This thesis is an investigation of the genetic basis of tocopherol accumulation in soybean (Glycine max [L.] Merrill) seeds. Soybean is the world’s most widely grown protein and oilseed crop and the principle source of vitamin E (tocopherols) as a supplement. Tocopherols (α-, β-, γ- and δ-isomers) are powerful antioxidants that contain human health benefits, including a decrease in the risk of lung cancer, heart disease and osteoporosis. The purpose of this research was to identify genetic and biochemical components affecting tocopherol accumulation in soybean seeds. The objectives were to: 1) investigate location and year effects on soybean seed tocopherol levels in the field; 2) determine environmental factors affecting soybean seed tocopherol levels under controlled conditions; 3) identify simple sequence repeat (SSR) markers that tag quantitative trail loci (QTL) for individual and total tocopherols; and 4) evaluate the potential role of VTE1, VTE3 and VTE4 genes in tocopherol accumulation using the candidate gene approach. Seventy nine recombinant inbred lines (RILs) derived from the cross between OAC Bayfield and OAC Shire were grown in the field at Elora, Woodstock and St. Pauls, ON, in 2009 and 2010. The tocopherol components were quantified using high performance liquid chromatography (HPLC). The results showed a significant (p < 0.001) genotype, environment and genotype x environment effect for each tocopherol component. It was discovered that a 2 x phosphate fertilizer (K2SO4 at 1.0M/150mL) and 30 ˚C temperature treatment increased each tocopherol component, whereas drought had no effects. Single marker analysis identified 42 QTL and interval mapping identified 26 QTL across 17 chromosomes. Significant two-locus epistatic interactions were found with a total of 122 and 152 in the 2009 and 2010 field seasons, respectively. The multiple locus models explained 18.4% to 72.2% with an average of 45.7% of the total phenotypic variation. The candidate gene approach using nucleotide sequences from the coding regions identified two single nucleotide polymorphisms (SNPs) in VTE1, five SNPs in VTE4 and none in VTE3. The SNPs were predicted to cause functional protein changes and the genes co-localized with some of the identified QTL. The results of this study provide a better understanding of the environmental factors and genetic mechanisms that influence the accumulation of tocopherols in soybean seeds.Grain Farmers of Ontario, Vitamin Research Award
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Chiu, Yu-Ting, et 邱宇廷. « Study on SSR and SNP Markers of Growth Trait in Potato Grouper (Epinephelus tukula) ». Thesis, 2019. http://ndltd.ncl.edu.tw/handle/f3w6x4.
Texte intégralRésumé :
碩士國立臺灣海洋大學
水產養殖學系
107
Potato grouper (Epinephelus tukula) is a new aquaculture species and fast growth which is a high economic potential species, however, it still has different degrees of variation during rearing. The aquaculture sector in Taiwan is significantly behind foreign countries in applying selective breeding program, thus, aquaculture sector whom in southern Taiwan hoped to raise their provenance’s quality and management through molecular markers-assisted selection and breeding platform in potato grouper species. The purpose of this study was to develop a scheme which manage of broodstock and identify paternity. We injected RFID in the broodstock of potato grouper in two years for tracking and analyzed the genetic diversity. We constructed and sequenced cDNA libraries from potato grouper with seven tissues of brain, gill, head kidney, heart, spleen, liver and muscle in the transcriptome. Of these, approximately 51.3411G nt raw sequencing reads were generated and assembled 111,490 unigene, total length 172,770,477 bp and average length 1,549 bp. Through five protein databases and Venny analysis have annotated 22,031 unigenes. Furthermore, a total of 44,565 putative SSRs and 122,220 putative SNPs were identified. We also screened the molecular markers involved in growth-related genes from the transcriptomic database of potato grouper established by the next-generation sequencing. The experience not only screened the transcriptome database in growth-related genes which established out of 65 functional SSR and 46 SNP candidate markers but also contained two SSR markers studied before in our Lab. These molecular markers were genotyped in potato grouper’s offspring which subjected to growing test less than ninety days. We utilized mtDNA COI to identify the offspring of maternal potato grouper. The PCR- RFLP technology could help us to distinguish between three maternal potato grouper with restriction enzyme Hha I and Hinc II in mtDNA D-loop region. The offspring that we got from the aquaculture sector had been confirmed to breed from the M6 maternal grouper. The results of 10 functional SSRs showed polymorphism in the offspring by using capillary electrophoresis technology, especially; the offspring had more than three genotypes in five functional SSR markers. MassARRAY platform showed 46 SNPs average call rate were 76.73%. After statistical analyze the association between growth-related with molecular markers which had 2 SNP makers (Unigene 7626、CL8791.Contig3) showed significant association with the wieght (p<0.05). The purpose in our experiment not only provide a genetic management of broodstock but also assist the seedling industry in growth breeding, accelerated aquaculture traceability systems and improvement of quality-based potato grouper in the future.
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Li, Jia-Xian, et 李嘉銜. « Development of Cold Tolerance Gene Associated SSR and SNP Markers Based on Transcriptome Sequencing in Taiwan Tilapia ». Thesis, 2018. http://ndltd.ncl.edu.tw/handle/uvnpj7.
Texte intégralRésumé :
碩士國立臺灣海洋大學
水產養殖學系
106
Taiwan tilapia is one of the major aquaculture species in Taiwan. The tropical fishes are sensitive to cold, and thus leading to mass mortality of fish when cold current arrived. The genetics and brood stock management strategies of molecular marker-assisted selection and breeding are the most important key tools to promote improved varieties of seed in the Taiwan tilapia species. Microsatellite (SSR) and single nucleotide polymorphism (SNP) are common DNA variation among individuals, which may cause phenotypic variation and influence adaptively economic traits. The purpose of this study was to develop molecular markers of cold tolerance related genes by using next-generation transcriptome sequencing in Nile tilapia (Oreochromis niloticus). We constructed and sequenced cDNA libraries from four tissues (brain, gill, liver and muscle) in cold-tolerance (CT) and cold-sensitivity (CS) groups by using the digital gene expression analysis of next-generation transcriptome sequencing. Of these, approximately 35,214,833,100 nt raw sequencing reads were generated and assembled 128,147 unigene, total length 185,382,926 bp and average length 1,446 bp. Through five protein databases and Venny analysis have annotated 25,844 unigenes. Furthermore, a digital gene expression analysis revealed differentially expressed genes which were up-regulated and down-regulated in four related tissues, of these, 2,081 were up-regulated and 2,110 were down-regulated in brain, 2,261 were up-regulated and 1,974 were down-regulated in gill, 1,824 were up-regulated and 1,340 were down-regulated in liver, 1,200 were up-regulated and 1,239 were down-regulated in muscle. A total of 38,377 putative SSRs and 65,527 putative SNPs were identified from differentially expressed genes. Among these, cold tolerance-related gene sequences were established out of 13 functionality SSR and 37 SNP candidate loci. These markers were genotyping in different Taiwan tilapia populations which subjected to low-temperature stress. Eleven SSRs showed polymorphism by using capillary electrophoresis technology. Thirty-seven SNPs average call rate and conservative calls were 99.3% and 87.9% respectively. Of these, 27 SNPs showed polymorphism which detected by Sequenom MassARRAY platform. The association between molecular markers and individual cold-tolerance performance were then examined. Results showed that 5 SSR and 1 SNP gene makers have significant associations with the estimated cold-tolerance breeding values in the experimental animals (p-value < .05). The findings of the research can provide industry with the improvement of cold-tolerance strains breeding programs and apply in marker-assisted selection to develop more industrial competitiveness fine strains.
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Batista, Cláudia Maria Alves. « Traceability of Portuguese white musts through molecular markers ». Master's thesis, 2009. http://hdl.handle.net/10348/2089.
Texte intégralRésumé :
Dissertação de Mestrado em Biotecnologia e Qualidade AlimentarO continente Europeu reúne várias regiões vitivinícolas importantes possuindo uma longa história e tradição na área vitivinícola. Mundialmente, existem cerca de 16 000 variedades de Vitis vinifera L. Em Portugal a viticultura é extremamente rica em termos de recursos genéticos, com cerca de 300 variedades utilizadas na produção de vinho. A qualidade final de determinado vinho está intimamente correlacionada com as características intrínsecas encontradas nas variedades utilizadas na sua produção. Os vinhos monovarietais definem-se como sendo produzidos utilizando uma única variedade, no entanto, a adição de outras variedades são permitidas em percentagens definidas por lei. Este facto associado à inexistência de metodologias para detecção e quantificação varietal em mostos e vinhos podem conduzir a práticas fraudulentas. Para garantir a qualidade e autenticidade dos mostos/vinhos, é importante desenvolver metodologias adequadas para a detecção e identificação das variedades de videiras usadas na sua produção. Os objectivos deste trabalho foram desenvolver um método de extracção de ADN a partir de mostos e avaliar o uso de marcadores moleculares como os SSRs e os ISSRs na identificação varietal. Para este estudo foram escolhidas seis variedades brancas portuguesas (‘Alvarinho’, ‘Fernão Pires’, ‘Loureiro’, ‘Malvasia Fina’, ‘Moscatel Galego’ e ‘Viosinho’), considerando-se amostras de folhas e mostos monovarietais. O protocolo de extracção do ADN foi optimizado para os mostos. Os resultados mostraram que o ADN genómico obtido a partir de folhas e mostos monovarietais era amplificável utilizando marcadores moleculares do tipo SSRs e ISSRs. Foram seleccionados seis primers nucleares de SSRs, considerados como marcadores universais num projecto europeu, para a genotipagem da videira. A análise do dendrograma mostrou que todas as amostras (considerando o binómio folha/mosto) apresentavam o mesmo perfil para todos os SSRs estudados revelando uma similaridade genética de 1,00. Na totalidade, foram detectados 32 alelos, com uma média de 5,3 alelos por primer. Para as seis variedades analisadas, o marcador VVMD27 foi o mais discriminatório. Seleccionaram-se 14 primers ISSRs para caracterizar as seis variedades de videira escolhidas considerando folhas e mostos monovarietais. Os produtos amplificados foram utilizados para avaliar a reprodutibilidade e o nível de polimorfismo. Todos os primers ISSRs apresentaram bandas polimórficas. O dendrograma, obtido utilizando o coeficiente SM, apresentou dois grupos principais embora não tenha sido possível encontrar uma correspondência entre as folhas e os mostos. Ambas as metodologias utilizadas foram capazes de caracterizar as variedades estudadas, embora os resultados obtidos com os marcadores moleculares SSRs tivessem sido inequívocos quando comparados com os encontrados para os ISSRs. O presente estudo demonstrou que é possível utilizando métodos baseados no ADN (marcadores SSRs) fazer uma correcta identificação varietal e que esta metodologia poderá ser utilizada no controle de qualidade, certificação e rastreabilidade do mosto protegendo os consumidores contra falsificações e assim promover um comércio justo entre pares.
Europe assembles several vitiviniculture important regions, with an old history and tradition in this area. Worldwide, there are about 16 000 Vitis vinifera L. varieties. Portugal’s viticulture is exceptionally rich in what concerns genetic resources, having approximately 300 varieties used in wine production. Wine quality is highly correlated with intrinsic characteristics specific of the varieties used in its production. Monovarietal wines are defined as made from a unique variety, nevertheless, the addition of other varieties is allowed under legally defined percentages. This fact associated with the nonexistence of methodologies for varietal detection and quantification in musts and wines may lead to fraudulent practices. To assure must/wine quality and authenticity it is important to develop suitable methodologies for grapevine varieties detection and identification in these matrices. The aims of this study were to develop a technique for DNA extraction from musts and to evaluate the potential use of SSRs and ISSRs markers in must varietal identification. Six Portuguese white varieties (‘Alvarinho’, ‘Fernão Pires’, ‘Loureiro’, ‘Malvasia Fina’, ‘Moscatel Galego’ and ‘Viosinho’), considering leaf and monovarietal must, were chosen for this study. A DNA extraction protocol was optimized for must. Results showed that genomic DNA obtained from leaves and monovarietal must samples was suitable for SSR and ISSR amplification. Six nuclear primers, considered as universal markers for grapevine genotyping were chosen. Dendrogram resulting from UPGMA analyses revealed that all leaf and must samples have exactly the same profile for all SSR studied revealing a genetic similarity of 1.00. A total of 32 alleles were detected, with an average of 5.3 alleles per primer. For the six varieties analyzed, the most discriminatory marker was VVMD27. Fourteen ISSR primers were selected to characterize six white grape varieties considering both leaf and monovarietal must samples. Amplified products were used to evaluate the reproducibility and the level of polymorphism. All ISSR primers showed a high number of polymorphic bands. The dendrogram obtained using SM coefficient presented two main clusters although there was not a correspondence between leaf and monovarietal must samples. Both DNA typing based methodologies were able to distinguish between the varieties studied although the results obtained with SSR molecular markers were unambiguous when compared with the ones found for ISSR markers. The current study showed that it may be possible to use DNA fingerprinting (SSR) for must varietal identification and this type of markers may be used for quality control, certification and traceability purposes protecting consumers against misleading information and promoting a fair trade.
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Sharma, Vivek. « IDENTIFICATION OF DROUGHT-RELATED QUANTITATIVE TRAIT LOCI (QTLs) IN SUGARCANE (Saccharum spp.) USING GENIC MARKERS ». Thesis, 2009. http://hdl.handle.net/1969.1/ETD-TAMU-2009-05-595.
Texte intégralRésumé :
Population based association studies in crops that were established by domestication and
early breeding can be a valuable basis for the identification of QTLs. A case control
design in a population is an ideal way to identify maximum candidate sites contributing
to a complex polygenic trait such as drought. In the current study, marker loci associated
with drought related QTLs were identified in sugarcane (Saccharum spp), one of the
most complex crop genomes, with its polyploid nature (>8), chromosome number
(>100) and interspecific origin. The objectives of this investigation were: 1)
development of genic markers, which can be used for marker-assisted selection of
drought tolerant genotypes of sugarcane. 2) genotypic characterization of sugarcane
population at drought related loci using EST-SSR markers. Using 55 microsatellite
markers, 56 polymorphisms were scored among 80 modern sugarcane genotypes.
Homogeneity of the population was confirmed by determining the distribution of allele
frequencies obtained by random genomic microsatellite markers. This analysis was
conducted in the STRUCTURE program and the population was divided in 3 subgroups
based on the allelic distribution. Phenotypic data to evaluate drought tolerance among
the genotypes was collected by measuring chlorophyll content, chlorophyll fluorescence,
leaf temperature and leaf relative water content. A generalized linear model in SPSS was
used to find association between marker loci and phenotypic data. Markers with
significant association (P 0.001 level) with the trait were subjected to linear regression
to screen the spurious associations. Based on the results, 21 EST-SSR markers and 11 TRAP markers related to drought-defining physiological parameters were considered as
genuine associations in this study. Fifty-six polymorphisms produced by 13 EST-SSR
primers were used to produce genetic similarity matrix for 80 genotypes. Dendrogram
prepared from this genetic similarity matrix will be useful in selecting parents carrying
diversity at drought specific loci.
45
Erasmus, Tertia Elizabeth. « Genetic diversity of proprietary inbred lines of sunflower, determined by mapped SSR markers and total protein analysis ». Thesis, 2008. http://hdl.handle.net/10413/879.
Texte intégral
46
Watts, Roger. « Development of linkage map of Brassica juncea using molecular markers and detection of quantitative trait loci for oil content, seed protein and fatty acids ». 2013. http://hdl.handle.net/1993/15726.
Texte intégralRésumé :
A genetic linkage map of mustard (Brassica juncea) was developed using two double haploid populations produced from crosses between a low erucic cultivar “ZEM1” and two moderate erucic acid lines “Vniimk351” and “Vniimk405” with the use of SSR and SRAP markers. The linkage map of the ZEM1xVniimk351 population included 13 linkage groups with an overall length of 791 cM with an average marker interval of 5.7 cM. The linkage map of the ZEM1xVniimk405 population also contained 13 linkage groups with a distance of 623 cM and an average marker interval of 4.6 cM. Using the linkage maps for the two populations, QTLs were detected for seed oil, protein and fatty acids. QTL analysis for fatty acids indentified QTLs on LG1, 7 and 12 for the ZEM1xVniimk351 population and LG1, 3 and 4 for the ZEM1xVniimk405 population. Analysis for the seed oil and protein content in the ZEM1xVniimk351 population identified 2 QTLs on LG1 and LG4 and 1 QTL on LG1 respectively. The QTL analysis ZEM1xVniimk405 of oil and protein content identified 1 QTL for oil and protein on LG1. The variation of fatty acids was shown to be the result of monogenic inheritance of the FAE1 gene in both populations.
47
Rahman, Md Mukhlesur. « Development of molecular markers for marker assisted selection for seed quality traits in oilseed rape ». 2007. http://hdl.handle.net/1993/2846.
Texte intégralRésumé :
Molecular markers for seed quality traits including erucic acid content genes, seed coat color genes in Brassica napus and seed coat color genes in B. rapa were developed. A single base change in the Bn-FAE1.1 gene in the A genome and a two-base deletion in the Bn-FAE1.2 gene in the C genome produce the nearly zero content of erucic acid observed in canola. The single base change was detected as single nucleotide polymorphic (SNP) marker with an ABI SNaPshot kit. A multiplexing primer set was designed by adding a polyT to the 5´ primer end to increase SNP detection throughput through sample pooling. The two-base deletion in the C genome gene was detected as a sequence characterized amplified region (SCAR) marker in an ABI 3100 Genetic analyzer. To increase the throughput, one genome specific primer was labeled with four fluorescence dyes and combined with 20 different primers to produce PCR products with different fragment sizes. These multiplexed high throughput molecular markers have been successfully implemented in our canola/rapeseed breeding programs. Trigenic inheritance was observed for seed coat color in B. napus. Three Sequenced Related Amplified Polymorphism (SRAP) markers very closely linked to the three different seed coat color genes were developed. Chromosome-walking technology was used to convert the SRAP marker into a SCAR marker and a SNP marker. Subsequently, the first seed coat color gene (Bn1) marker was converted into a SCAR marker, and the second seed coat color gene (Bn2) marker was converted into a SNP marker. Digenic inheritance was observed for seed coat color genes in B. rapa. A SRAP marker was identified as being tightly linked to the major seed coat color gene (Br1). The SRAP marker was sequenced and extended sequences were obtained using chromosome-walking technology. The flanking sequences of the SRAP marker contained 24 SNPs and a 12-bp deletion position that allowed the marker to be converted into a co-dominant SNP marker and a co-dominant SCAR marker, respectively. The SCAR marker was detected in the ABI 3100 genetic analyzer with four fluorescently labeled M13 primers integrated with different SCAR primers, which permitted pooling of PCR samples for high throughput detection.October 2007
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Carvalho, Márcia Raquel Gomes de. « Genetic diversity and molecular responses to drought stress in Vigna unguiculata L. Walp ». Doctoral thesis, 2018. http://hdl.handle.net/10348/9226.
Texte intégralRésumé :
Doctoral Degree in Agricultural Production Chains - From Fork to FarmClimate change is considered as one of the major threats to agriculture sustainability and biodiversity. Drought is a severe environmental stress with major impacts on plant development and productivity. The use and improvement of crops with the ability to mitigate the effects of drought will be a key step for future crop sustainability. Cowpea (Vigna unguiculata L. Walp) is a warm-season grain legume, considered as an interesting crop, due to its high adaptability to heat and drought, as well as to its association with nitrogen fixing rhizobia. As other legumes, cowpea plays a major role in the global food security by providing an affordable dietary source of nutrients mainly proteins. The thesis main objective is to contribute for a higher cowpea production in Europe, anticipating the upcoming climate changes. To achieve this goal, multidisciplinary approaches were undertaken involving field trials and molecular genetics, physiology and biochemistry approaches. Regarding genetic diversity, the morphological and agronomical characterization of 24 Iberian Peninsula cowpea genotypes was performed, thus emphasizing the high genetic diversity among genotypes. From this characterization, ten cowpea genotypes were selected and further used for determining the stability of morphological and agronomical traits in three different environments (two in Portugal and one in Spain), during two consecutive years. A high interaction between genotype and environment was found and Elvas (Portugal) revealed to have the most appropriated environment for the production of this set of cowpea genotypes. The recently developed Cowpea iSelect Consortium Array (Illumina, Inc.) provided an excellent opportunity for further determination of cowpea genetic diversity. This array contains 51,128 SNPs and was used in a set of 96 cowpea genotypes, 43 of which from Iberian Peninsula and 23 from 22 other worldwide countries. Cowpea genotypes were clustered in four subpopulations, mainly differentiated by their geographical origin, allowing the suggestion of a new hypothesis about cultivated cowpea dispersion routes. Most of Iberian Peninsula genotypes and those from other Southern European and Northern African countries were grouped in the same subpopulation, indicating a high genetic similarity among them. However, three Iberian Peninsula cowpea genotypes did not belong to this subpopulation, being two of them classified as ‘admixed’ and another from a different subpopulation. These genotypes could be considered as interesting sources of diversity for future cowpea breeding programs. To get new insights on cowpea drought stress responses, the selection of the best approachesfor screening cowpea genotypes with enhanced drought tolerance is fundamental. Four cowpea genotypes (two Portuguese and two international tolerant references) were submitted to three different watering regimens, during 15 days. Several physiological, biochemical and molecular approaches were tested, revealing that stomatal function parameters, free proline and anthocyanins contents were the most effective in discriminating cowpea tolerance levels. Furthermore, two drought-related genes (VuCPRD14 and VuHsp17.7) were identified as the most effective for drought tolerance selection. For screening cowpea genotypes with enhanced drought tolerance, a worldwide collection of cowpea genotypes (58 genotypes) was tested for seed germination, seedling emergence and proline content under different osmotic potentials. A total of seven drought tolerant genotypes were suggested, which could represent starting material for future cowpea breeding programs. This thesis gave a good contribution for increasing cowpea production in Europe, being the selection of more productive and drought tolerant genotypes the first step. These genotypes could be integrated into breeding programs for enhancing cowpea resilience to climate change. Furthermore, the methodologies tested and proposed in this study allow an effective and fast screening of cowpea genotypes drought tolerance.
As alterações climáticas são consideradas uma das principais ameaças à sustentabilidade da agricultura e à biodiversidade global, sendo o stresse abiótico um dos seus maiores constrangimentos. A seca é um dos stresses ambientais mais severo e com um grande impacto no desenvolvimento e produtividade das plantas. A utilização e melhoramento de culturas com capacidade de mitigar os efeitos da seca assumem cada vez mais um papel relevante para o aumento da sustentabilidade das culturas. O feijão-frade (Vigna unguiculata L. Walp) é uma cultura de Primavera/Verão considerada muito versátil devido à sua capacidade de tolerar elevadas temperaturas e défice hídrico, tendo ainda a capacidade de fixar azoto atmosférico através da simbiose com bactérias Rhizobium. Como todas as leguminosas de grão, o feijãofrade possui um elevado valor nutritivo, em particular um alto teor em proteína, tornando-a assim importante na segurança alimentar global. O principal objetivo da tese é desenvolver estudos que venham a contribuir para uma maior produção de feijão-frade na Europa tendo em consideração as futuras alterações climáticas. Para atingir este objetivo desenvolveram-se estudos integrados que envolveram ensaios de campo e abordagens de genética molecular, de fisiologia e de bioquímica. Em relação à diversidade genética, foi realizada uma caracterização morfológica e agronómica de um conjunto de 24 genótipos de feijão-frade, da Península Ibérica, onde ficou evidenciada a elevada diversidade entre genótipos. Desta caracterização foram selecionados, com base em características morfológicas e agronómicas, os 10 genótipos mais promissores para ensaios comparativos que foram instalados, em três ambientes diferentes (dois em Portugal e um em Espanha), durante dois anos consecutivos. Este estudo revelou uma elevada interação entre genótipo e ambiente, verificando-se que Elvas (Portugal) é o ambiente mais adequado para a produção desta leguminosa. O recém-desenvolvido Cowpea iSelect Consortium Array (Illumina, Inc.) veio permitir uma avaliação mais precisa e pormenorizada da diversidade genética existente no feijão-frade. Esta metodologia, que contém 51.128 SNPs, foi utilizada em 96 genótipos de feijão-frade sendo 43 provenientes da Península Ibérica e os restantes de 22 países de todo mundo. Este conjunto de genótipos foram agrupado em quatro subpopulações diferenciadas principalmente pela sua origem geográfica. A maioria dos genótipos de feijãofrade da Península Ibérica foram agrupados numa única subpopulação juntamente com os de outros países do sul da Europa e do norte de África, indicando uma semelhança genética entre eles. Contudo, dois genótipos da Península Ibérica foram classificados como "admixed" e um terceiro pertencente a outra subpopulação. Estes genótipos podem ser considerados interessantes fontes de diversidade para futuros programas de melhoramento de plantas. Os dados agora obtidos com os SNPs conduziram ainda a novas indicações sobre as possíveis rotas de dispersão do feijão-frade cultivado. Para obter novos dados sobre as respostas do feijão-frade ao stresse hídrico foram analisadas diferentes metodologias para a seleção de genótipos de feijão-frade com maior tolerância à seca. Quatro genótipos de feijão-frade (dois portugueses e duas referências internacionais) foram submetidos a três regimes de rega durante 15 dias e o comportamento das plantas estudado a nível fisiológico, bioquímico e molecular. A condutância estomática, o conteúdo de prolina livre e de antocianinas foram as determinações mais eficazes na discriminação dos níveis de tolerância das plantas à seca. Para além disso, foi possível identificar os genes VuCPRD14 e VuHsp17.7 como sendo os que revelam maior expressão em condições de stresse hídrico. De forma a selecionar os genótipos de feijão-frade mais tolerantes à seca, uma coleção mundial de feijão-frade (58 genótipos) foi avaliada ao nível da germinação das sementes, emergência de plântulas e conteúdo de prolina livre sob diferentes potenciais osmóticos. Sete genótipos foram considerados tolerantes à seca podendo assim vir a ser incluídos em programas de melhoramento. Esta tese pretendeu oferecer uma contribuição para o aumento da produção de feijãofrade na Europa, para o qual a seleção de genótipos mais produtivos e tolerantes à seca foi o primeiro passo. Os genótipos selecionados podem vir a ser integrados em programas de melhoramento de forma a aumentar a resiliência do feijão-frade às alterações climáticas. Para além disso, disponibilizaram-se metodologias que permitem de uma forma expedita identificar os genótipos com maior tolerância à seca.