Academic literature on the topic 'Molecular markers (SNP e SSR)'
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Journal articles on the topic "Molecular markers (SNP e SSR)"
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Khatoon, Arifa, Sumeet Verma, Gayatri Wadiye, and Anuprita Zore. "Molecular markers and their potentials." International Journal of Bioassays 5, no. 01 (January 1, 2016): 4706. http://dx.doi.org/10.21746/ijbio.2016.01.003.
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The use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in plant molecular biotechnology and their genetic studies. There are three different types of markers viz. morphological, biochemical and DNA based molecular markers. These DNA based markers are differentiating in two types 1. Non PCR based (RFLP) and 2. PCR based markers (RAPD, AFLP, SSR, SNP etc.). Amongst others, the microsatellite DNA marker is one of the most widely used marker due to its easy use by simple PCR, followed by a denaturing gel electrophoresis. SNP (Single Nucleotide Polymorphism) is nowadays is the one which is used mainly. In this review, we are going to discuss about the biochemical and molecular markers which are recently developed, the important characteristics of molecular markers their advantages, disadvantages and the applications of these markers in comparison with other markers types.
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Sa, Kyu Jin, Hyeon Park, So Jung Jang, and Ju Kyong Lee. "Association Mapping of Amylose Content in Maize RIL Population Using SSR and SNP Markers." Plants 12, no. 2 (January 4, 2023): 239. http://dx.doi.org/10.3390/plants12020239.
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The ratio of amylose to amylopectin in maize kernel starch is important for the appearance, structure, and quality of food products and processing. This study aimed to identify quantitative trait loci (QTLs) controlling amylose content in maize through association mapping with simple sequence repeat (SSR) and single-nucleotide polymorphism (SNP) markers. The average value of amylose content for an 80-recombinant-inbred-line (RIL) population was 8.8 ± 0.7%, ranging from 2.1 to 15.9%. We used two different analyses—Q + K and PCA + K mixed linear models (MLMs)—and found 38 (35 SNP and 3 SSR) and 32 (29 SNP and 3 SSR) marker–trait associations (MTAs) associated with amylose content. A total of 34 (31 SNP and 3 SSR) and 28 (25 SNP and 3 SSR) MTAs were confirmed in the Q + K and PCA + K MLMs, respectively. This study detected some candidate genes for amylose content, such as GRMZM2G118690-encoding BBR/BPC transcription factor, which is used for the control of seed development and is associated with the amylose content of rice. GRMZM5G830776-encoding SNARE-interacting protein (KEULE) and the uncharacterized marker PUT-163a-18172151-1376 were significant with higher R2 value in two difference methods. GRMZM2G092296 were also significantly associated with amylose content in this study. This study focused on amylose content using a RIL population derived from dent and waxy inbred lines using molecular markers. Future studies would be of benefit for investigating the physical linkage between starch synthesis genes using SNP and SSR markers, which would help to build a more detailed genetic map and provide new insights into gene regulation of agriculturally important traits.
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Lyu, Pin, Jianhua Hou, Haifeng Yu, and Huimin Shi. "High-density Genetic Linkage Map Construction in Sunflower (Helianthus annuus L.) Using SNP and SSR Markers." Current Bioinformatics 15, no. 8 (January 1, 2021): 889–97. http://dx.doi.org/10.2174/1574893615666200324134725.
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Background: Sunflower (Helianthus annuus L.) is an important oil crop only after soybean, canola and peanuts. A high-quality genetic map is the foundation of marker-assisted selection (MAS). However, for this species, the high-density maps have been reported limitedly. Objective: In this study, we proposed the construction of a high-density genetic linkage map by the F7 population of sunflowers using SNP and SSR Markers. Methods: The SLAF-seq strategy was employed to further develop SNP markers with SSR markers to construct the high-density genetic map by the HighMap software. Results: A total of 1,138 million paired-end reads (226Gb) were obtained and 518,900 SLAFs were detected. Of the polymorphic SLAFs, 2,472,245 SNPs were developed and finally, 5,700 SNPs were found to be ideal to construct a genetic map after filtering. The final high-density genetic map included 4,912 SNP and 93 SSR markers distributed in 17 linkage groups (LGs) and covered 2,425.05 cM with an average marker interval of 0.49 cM. Conclusion: The final result demonstrated that the SLAF-seq strategy is suitable for SNP markers detection. The genetic map reported in this study can be considered as one of the most highdensity genetic linkage maps of sunflower and could lay a foundation for quantitative trait loci (QTLs) fine mapping or map-based gene cloning.
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Hsu, Te-Hua, Yu-Ting Chiu, Hung-Tai Lee, Hong-Yi Gong, and Chang-Wen Huang. "Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper (Epinephelus tukula)." Biology 10, no. 1 (January 7, 2021): 36. http://dx.doi.org/10.3390/biology10010036.
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The accuracy and efficiency of marker-assisted selection (MAS) has been proven for economically critical aquaculture species. The potato grouper (Epinephelus tukula), a novel cultured grouper species in Taiwan, shows large potential in aquaculture because of its fast growth rate among other groupers. Because of the lack of genetic information for the potato grouper, the first transcriptome and expressed sequence tag (EST)-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were developed. Initially, the transcriptome was obtained from seven cDNA libraries by using the Illumina platform. De novo transcriptome of the potato grouper yielded 51.34 Gb and 111,490 unigenes. The EST-derived SSR and SNP markers were applied in genetic management, in parentage analysis, and to discover the functional markers of economic traits. The F1 juveniles were identified as siblings from one pair of parents (80 broodstocks). Fast- and slow-growth individuals were analyzed using functional molecular markers and through their association with growth performance. The results revealed that two SNPs were correlated with growth traits. The transcriptome database obtained in this study and its derived SSR and SNP markers may be applied not only for MAS but also to maintain functional gene diversity in the novel cultured grouper.
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Hsu, Te-Hua, Yu-Ting Chiu, Hung-Tai Lee, Hong-Yi Gong, and Chang-Wen Huang. "Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper (Epinephelus tukula)." Biology 10, no. 1 (January 7, 2021): 36. http://dx.doi.org/10.3390/biology10010036.
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The accuracy and efficiency of marker-assisted selection (MAS) has been proven for economically critical aquaculture species. The potato grouper (Epinephelus tukula), a novel cultured grouper species in Taiwan, shows large potential in aquaculture because of its fast growth rate among other groupers. Because of the lack of genetic information for the potato grouper, the first transcriptome and expressed sequence tag (EST)-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were developed. Initially, the transcriptome was obtained from seven cDNA libraries by using the Illumina platform. De novo transcriptome of the potato grouper yielded 51.34 Gb and 111,490 unigenes. The EST-derived SSR and SNP markers were applied in genetic management, in parentage analysis, and to discover the functional markers of economic traits. The F1 juveniles were identified as siblings from one pair of parents (80 broodstocks). Fast- and slow-growth individuals were analyzed using functional molecular markers and through their association with growth performance. The results revealed that two SNPs were correlated with growth traits. The transcriptome database obtained in this study and its derived SSR and SNP markers may be applied not only for MAS but also to maintain functional gene diversity in the novel cultured grouper.
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Gonzaga, Zennia Jean, Kashif Aslam, Endang M. Septiningsih, and Bertrand C. Y. Collard. "Evaluation of SSR and SNP Markers for Molecular Breeding in Rice." Plant Breeding and Biotechnology 3, no. 2 (June 30, 2015): 139–52. http://dx.doi.org/10.9787/pbb.2015.3.2.139.
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Kang, Sung-Taeg, and M. A. Rouf Mian. "Genetic map of the powdery mildew resistance gene in soybean PI 243540." Genome 53, no. 5 (May 2010): 400–405. http://dx.doi.org/10.1139/g10-015.
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Powdery mildew (caused by Microsphaera diffusa Cooke & Peck) is a common disease of soybean in many soybean-growing regions of the world and under greenhouse conditions. The previously reported Rmd locus of soybean for resistance to powdery mildew was mapped on soybean molecular linkage group J (chromosome 16). We have discovered a single dominant gene in PI 243540 that provides season-long resistance to powdery mildew. The objective of this study was to map the powdery mildew resistance gene in PI 243540 with PCR-based molecular markers. One hundred eighty-four F2 plants and their F2:3 families from a cross between the powdery mildew susceptible cultivar ‘Wyandot’ and PI 243540 were screened with M. diffusa in greenhouses. Bulked segregant analysis (BSA) with SSR markers was used to identify the tentative genomic location of the gene. The BSA localized the gene to a genomic region in soybean chromosome 16. A linkage map with seven SSR and six SNP markers flanking the gene was constructed. We positioned the gene between SSR marker Sat_224 and SNP marker BARC-021875-04228 at distances of 9.6 and 1.3 cM from the markers, respectively. The map position of the gene was slightly different from previously reported map positions of the only known Rmd locus. We have mapped a single dominant gene, tentatively called Rmd_PI243540, near the previously known Rmd locus on chromosome 16. The molecular markers flanking the gene will be useful for marker-assisted selection of this gene.
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Susanto, Untung, Nofi Anisatun Rohmah, and Made Jana Mejaya. "Distinguishing Rice Genotypes using Morphological, Agronomical,." Jurnal Penelitian Pertanian Tanaman Pangan 34, no. 2 (November 12, 2015): 79. http://dx.doi.org/10.21082/jpptp.v34n2.2015.p79-87.
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<p align="LEFT">Complete data on characteristics of a rice variety is very important to race the authenticity of the variety at the field. Sometimes a name of a variety had changed, due to the informal seed distribution among farmers. This could become problem in the property right of the variety. Distinguishing among rice varieties using only morphological and agronomical traits are sometimes not sufficient. Currently, molecular markers such as SSR (Simple Sequence Repeats) and SNP (Single Nucleotide Polymorphism) markers have become available and are powerfull to distinguish rice genotypes. This research was aimed to distinguish nine rice varieties grown by farmers, using morphological characters (47 traits), agronomical characters (9 traits), SSR markers (12 primer pairs, related with important traits of rice plant), and 384 SNP markers, and to compare the effectiveness of each technique in distinguishing among genotypes. A field experiment was conducted in Ranca Jaya village, Patok Beusi, Subang, West Java during Wet Season (WS) of 2011/2012, using a Randomized Complete Block Design in three replications. A modified CTAB method was used to extract DNA for detection using 12 SSR markers and 384 SNP markers. The results revealed that the use of SSR markers that were linked to certain genes was more accurate than that of the SNP markers, agronomic, and morphological characters, in distinguishing differences among the 9 rice genotypes. The complete data of morphologic, agronomic, and molecular are useful to distinguish the authenticity of a variety in order to protect the intelectual property right attached on the variety.</p>
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Fazio, Gennaro, Jack E. Staub, and Sang Min Chung. "Development and Characterization of PCR Markers in Cucumber." Journal of the American Society for Horticultural Science 127, no. 4 (July 2002): 545–57. http://dx.doi.org/10.21273/jashs.127.4.545.
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Highly polymorphic microsatellites or simple sequence repeat (SSR), along with sequence characterized amplified region (SCAR) and single nucleotide polymorphisms (SNP), markers are reliable, cost-effective, and amenable for large scale analyses. Molecular polymorhisms are relatively rare in cucumber (Cucumis sativus L.) (3% to 8%). Therefore, experiments were designed to develop SSR, SCAR and SNP markers, and optimize reaction conditions for PCR. A set of 110 SSR markers was constructed using a unique, strategically applied methodology that included the GeneTrapper (Life Technologies, Gaithersburg, Md.) kit to select plasmids harboring microsatellites. Of these markers, 58 (52%) contained dinucleotide repeats (CT, CA, TA), 21 (19%) possessed trinucleotide repeats (CTT, ATT, ACC, GCA), 3 (2.7%) contained tetranucleotide repeats (TGCG, TTAA, TAAA), 4 (3.6%) enclosed pentanucleotide repeat (ATTTT, GTTTT, GGGTC, AGCCC), 3 (2.7%) contained hexanucleotide repeats (CCCAAA, TAAAAA, GCTGGC) and 21 possessed composite repeats. Four SCARs (L18-3 SCAR, AT1-2 SCAR, N6-A SCAR, and N6-B SCAR) and two PCR markers based on SNPs (L18-2H19 A and B) that are tightly linked to multiple lateral branching (i.e., a yield component) were also developed. The SNP markers were developed from otherwise monomorphic SCAR markers, producing genetically variable amplicons. The markers L18-3 SCAR and AT1-2 SCAR were codominant. A three-primer strategy was devised to develop a codominant SCAR from a sequence containing a transposable element, and a new codominant SCAR product was detected by annealing temperature gradient (ATG) PCR. The use of a marker among laboratories can be enhanced by methodological optimization of the PCR. The utility of the primers developed was optimized by ATG-PCR to increase reliability and facilitate technology transfer. This array of markers substantially increases the pool of genetic markers available for genetic investigation in Cucumis.
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Wu, Jianhui, Qilin Wang, Liangsheng Xu, Xianming Chen, Bei Li, Jingmei Mu, Qingdong Zeng, Lili Huang, Dejun Han, and Zhensheng Kang. "Combining Single Nucleotide Polymorphism Genotyping Array with Bulked Segregant Analysis to Map a Gene Controlling Adult Plant Resistance to Stripe Rust in Wheat Line 03031-1-5 H62." Phytopathology® 108, no. 1 (January 2018): 103–13. http://dx.doi.org/10.1094/phyto-04-17-0153-r.
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Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most devastating diseases of wheat worldwide. Growing resistant cultivars is considered the best approach to manage this disease. In order to identify the resistance gene(s) in wheat line 03031-1-5 H62, which displayed high resistance to stripe rust at adult plant stage, a cross was made between 03031-1-5 H62 and susceptible cultivar Avocet S. The mapping population was tested with Chinese P. striiformis f. sp. tritici race CYR32 through artificial inoculation in a field in Yangling, Shaanxi Province and under natural infection in Tianshui, Gansu Province. The segregation ratios indicated that the resistance was conferred by a single dominant gene, temporarily designated as YrH62. A combination of bulked segregant analysis (BSA) with wheat 90K single nucleotide polymorphism (SNP) array was used to identify molecular markers linked to YrH62. A total of 376 polymorphic SNP loci identified from the BSA analysis were located on chromosome 1B, from which 35 kompetitive allele-specific PCR (KASP) markers selected together with 84 simple sequence repeat (SSR) markers on 1B were used to screen polymorphism and a chromosome region associated with rust resistance was identified. To saturate the chromosomal region covering the YrH62 locus, a 660K SNP array was used to identify more SNP markers. To develop tightly linked markers for marker-assisted selection of YrH62 in wheat breeding, 18 SNPs were converted into KASP markers. A final linkage map consisting of 15 KASP and 3 SSR markers was constructed with KASP markers AX-109352427 and AX-109862469 flanking the YrH62 locus in a 1.0 cM interval. YrH62 explained 63.8 and 69.3% of the phenotypic variation for disease severity and infection type, respectively. YrH62 was located near the centromeric region of chromosome 1BS based on the positions of the SSR markers in 1B deletion bins. Based on the origin, responses to P. striiformis f. sp. tritici races, and marker distances, YrH62 is likely different from the other reported stripe rust resistance genes/quantitative trait loci on 1B. The gene and tightly linked KASP markers will be useful for breeding wheat cultivars with resistance to stripe rust.
Dissertations / Theses on the topic "Molecular markers (SNP e SSR)"
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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.
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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.
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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/.
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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/.
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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.
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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.
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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.
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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.
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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.
Books on the topic "Molecular markers (SNP e SSR)"
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Klimenko, Irina, Nikolay Kozlov, Sergey Kostenko, Anastasia Shamustakimova, and Yulian Mavlyutov. Identification and certification of forage grasses (meadow clover, alfalfa, sowing and hop) based on DNA markers. ru: Federal Williams Research Center of Forage Production and Agroecology, 2020. http://dx.doi.org/10.33814/978-5-6043194-9-9.
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A technology has been developed for DNA identification and certification of varieties of meadow clover (Trifolium pratense L.), alfalfa (Medicago varia Mart.), Sowing (M. sativa L.) and hop (M. lupuli-na L.) based on molecular analysis with using SSR and SRAP markers. The recommendations contain a description of the sequence of experiments and protocols for DNA typing procedures. The presented methods were developed by the authors on the basis of their own experimental research and using the data available in the literature. A characteristic of informative primers for each marking system is given, a set of DNA identification markers is proposed, and unique molecular genetic formulas of varieties are drawn up as the basis for a reference genetic passport. Methodological recommendations were prepared with the aim of mastering the technology of DNA certification of forage grasses in practice. Designed for managers and specialists of research and control laboratories, can serve as a textbook for students and postgraduates in specialized specialties.
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Hajeer, Ali. Snp And Microsatellite Genotyping: Markers For Genetic Analysis (MOLECULAR LABORATORY METHODS (BIOTECHNIQUES BOOKS)). EATON PUBLISHING, 2000.
Find full textBook chapters on the topic "Molecular markers (SNP e SSR)"
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Ruff, Travis M., Karol Marlowe, Marcus A. Hooker, Yan Liu, and Deven R. See. "Genotyping by Multiplexed Sequencing (GMS) Using SNP Markers." In Methods in Molecular Biology, 9–21. New York, NY: Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-3024-2_2.
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Tandon, Gitanjali, Sarika Jaiswal, Mir Asif Iquebal, Anil Rai, and Dinesh Kumar. "Whole Genome Wide SSR Markers Identification Based on ddRADseq Data." In Methods in Molecular Biology, 59–66. New York, NY: Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-3024-2_5.
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Herrera, Maria del Rosario, and Marc Ghislain. "Robust and Inexpensive SSR Markers Analyses Using LI-COR DNA Analyzer." In Methods in Molecular Biology, 197–205. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-389-3_14.
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Zhao, Yongli, Manjunath Keremane, Channapatna S. Prakash, and Guohao He. "Characterization and Amplification of Gene-Based Simple Sequence Repeat (SSR) Markers in Date Palm." In Methods in Molecular Biology, 259–71. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7159-6_21.
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Bennetzen, Jeffrey L., Vaidyanathan Subramanian, Jichen Xu, Shanmukhaswami S. Salimath, Sujatha Subramanian, Dinakar Bhattramakki, and Gary E. Hart. "A framework genetic map of sorghum containing RFLP, SSR and morphological markers." In Advances in Cellular and Molecular Biology of Plants, 347–55. Dordrecht: Springer Netherlands, 2001. http://dx.doi.org/10.1007/978-94-015-9815-6_20.
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Tanaka, Tsuneki, Hiroyuki Tamaki, Kazunori Ashikaga, Hiroki Fujii, Ken-ichi Tamura, and Toshihiko Yamada. "Use of SSR Markers to Increase Forage Yield in Timoty (Phleum pratense L.)." In Molecular Breeding of Forage and Turf, 131–42. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-08714-6_12.
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Sretenovic Rajicic, Tatjana, Thomas Lübberstedt, Louise Bach Jensen, Uwe Scholz, W. Eberhard Weber, Andreas Graner, and Klaus J. Dehmer. "Single Nucleotide Polymorphism (SNP) Markers for Allele Quantification in Lolium (Poaceae): Development and First Applications." In Molecular Breeding of Forage and Turf, 143–63. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-08714-6_13.
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Mnasri Rahmani, Sameh, Olfa Saddoud Debbabi, and Ali Ferchichi. "Efficiency of SSR Markers to Analyze the Molecular Fingerprinting of Some Tunisian Olive Cultivars." In Recent Advances in Environmental Science from the Euro-Mediterranean and Surrounding Regions, 1307–9. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-70548-4_384.
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Pratsinakis, Emmanouil D., Lefkothea Karapetsi, Symela Ntoanidou, Angelos Markos, Panagiotis Madesis, Ilias Eleftherohorinos, and George Menexes. "Comparison of Hierarchical Clustering Methods for Binary Data From SSR and ISSR Molecular Markers." In Data Analysis and Rationality in a Complex World, 233–41. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-60104-1_26.
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Onyśk, Agnieszka, and Maja Boczkowska. "M13-Tailed Simple Sequence Repeat (SSR) Markers in Studies of Genetic Diversity and Population Structure of Common Oat Germplasm." In Methods in Molecular Biology, 159–68. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-6682-0_12.
Full textConference papers on the topic "Molecular markers (SNP e SSR)"
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Supari, Nurhaziqah, Yilmaz Kaya, Maral Biroudian, and Muhammad Arshad Javed. "Molecular characterization of Malaysian rice cultivars using SSR markers." In PROCEEDINGS OF THE 2ND INTERNATIONAL CONFERENCE ON BIOSCIENCES AND MEDICAL ENGINEERING (ICBME2019): Towards innovative research and cross-disciplinary collaborations. AIP Publishing, 2019. http://dx.doi.org/10.1063/1.5125520.
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"Application of SSR molecular markers in breeding and crop genetics." In 2020 Conference on Social Science and Modern Science. Scholar Publishing Group, 2020. http://dx.doi.org/10.38007/proceedings.0000799.
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"Molecular analysis of BC1F1 and BC2F1 cotton hybrids using SSR markers." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Novosibirsk ICG SB RAS 2021, 2021. http://dx.doi.org/10.18699/plantgen2021-022.
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KARA, Karima. "MOLECULAR CHARACTERIZATION OF BREAD WHEAT GENOTYPES TRITICUM AESTIVUM L. THROUGH MICROSATELLITES SSR MARKERS." In 18th International Multidisciplinary Scientific GeoConference SGEM2018. Stef92 Technology, 2018. http://dx.doi.org/10.5593/sgem2018/6.2/s25.050.
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Duca, Maria, Ana Mutu, Ina Bivol, and Steliana Clapco. "Eficiența unor marcheri moleculari în discriminarea populațiilor de lupoaie originare din China." In VIIth International Scientific Conference “Genetics, Physiology and Plant Breeding”. Institute of Genetics, Physiology and Plant Protection, Republic of Moldova, 2021. http://dx.doi.org/10.53040/gppb7.2021.35.
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In this study, the effectiveness of different types of molecular markers in assessing genetic diversity of populations of O. cumana from China was determined. ISSR and SSR markers detected different levels of genetic variability among and within broomrape populations. SSR markers analysis showed high level of genetic variation within the populations as revealed by high average values of Nei's gene diversity (H=0,75) and Shannon's information index (I=1,44), while genotyping with ISSR markers showed greater ability to discriminate genotypes according to Resolving power (Rp=7,24). Thus, the combined use of ISSR and SSR markers allowed the detection of higher polymorphism than either set of marker alone.
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Badyanov, E. V., and S. A. Ramazanova. "THE TESTING OF SSR MARKERS OF GENES CONTROLLING RESISTANCE TO P. HALSTEDII AND THE SELECTION OF OPTIMAL CONDITIONS FOR PCR." In 11-я Всероссийская конференция молодых учёных и специалистов «Актуальные вопросы биологии, селекции, технологии возделывания и переработки сельскохозяйственных культур». V.S. Pustovoit All-Russian Research Institute of Oil Crops, 2021. http://dx.doi.org/10.25230/conf11-2021-19-24.
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Downy mildew is one of the most harmful diseases of sunflower. The most effective measure of this disease control is the development of resistant varieties and hybrids. The use of molecular markers, in particular DNA markers, allows to control the presence of dominant resistance genes at each stage of breeding. We carried out the selection of the optimal method for the isolation of sunflower DNA and the selection of the optimal temperature regimes of amplification for 10 pairs of primers developed to mark the Pl6, Pl8, Pl13, and PlArg genes. Preliminary, we identified 13 allelic variants that are suitable for DNA genotyping of Helianthus annuus by these loci.
Reports on the topic "Molecular markers (SNP e SSR)"
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Zhang, Hongbin, Shahal Abbo, Weidong Chen, Amir Sherman, Dani Shtienberg, and Frederick Muehlbauer. Integrative Physical and Genetic Mapping of the Chickpea Genome for Fine Mapping and Analysis of Agronomic Traits. United States Department of Agriculture, March 2010. http://dx.doi.org/10.32747/2010.7592122.bard.
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Chickpea is the third most important pulse crop in the world and ranks first in the Middle East; however, it has been subjected to only limited research in modern genomics. In the first period of this project (US-3034-98R) we constructed two large-insert BAC and BIBAC libraries, developed 325 SSR markers and mapped QTLs controlling ascochyta blight resistance (ABR) and days to first flower (DTF). Nevertheless, the utilities of these tools and results in gene discovery and marker-assisted breeding are limited due to the absence of an essential platform. The goals of this period of the project were to use the resources and tools developed in the first period of the project to develop a BAC/BIBAC physical map for chickpea and using it to identify BAC/BIBACcontigs containing agronomic genes of interest, with an emphasis on ABR and DTF, and develop DNA markers suitable for marker-assisted breeding. Toward these goals, we proposed: 1) Fingerprint ~50,000 (10x) BACs from the BAC and BIBAC libraries, assemble the clones into a genome-wide BAC/BIBAC physical map, and integrate the BAC/BIBAC map with the existing chickpea genetic maps (Zhang, USA); 2) fine-map ABR and DTFQTLs and enhance molecular tools for chickpea genetics and breeding (Shahal, Sherman and DaniShtienberg, Israel; Chen and Muehlbauer; USA); and 3) integrate the BAC/BIBAC map with the existing chickpea genetic maps (Sherman, Israel; Zhang and Chen, USA). For these objectives, a total of $460,000 was requested originally, but a total of $300,000 was awarded to the project. We first developed two new BAC and BIBAC libraries, Chickpea-CME and Chickpea- CHV. The chickpea-CMEBAC library contains 22,272 clones, with an average insert size of 130 kb and equivalent to 4.0 fold of the chickpea genome. The chickpea-CHVBIBAC library contains 38,400 clones, with an average insert size of 140 kb and equivalent to 7.5 fold of the chickpea genome. The two new libraries (11.5 x), along with the two BAC (Chickpea-CHI) and BIBAC (Chickpea-CBV) libraries (7.1 x) constructed in the first period of the project, provide libraries essential for chickpea genome physical mapping and many other genomics researches. Using these four libraries we then developed the proposed BAC/BIBAC physical map of chickpea. A total of 67,584 clones were fingerprinted, and 64,211 (~11.6 x) of the fingerprints validated and used in the physical map assembly. The physical map consists of 1,945 BAC/BIBACcontigs, with each containing an average of 39.2 clones and having an average physical length of 559 kb. The contigs collectively span ~1,088 Mb, being 1.49 fold of the 740- Mb chickpea genome. Third, we integrated the physical map with the two existing chickpea genetic maps using a total of 172 (124 + 48) SSR markers. Fourth, we identified tightly linked markers for ABR-QTL1, increased marker density at ABR-QTL2 and studied the genetic basis of resistance to pod abortion, a major problem in the east Mediterranean, caused by heat stress. Finally, we, using the integrated map, isolated the BAC/BIBACcontigs containing or closely linked to QTL4.1, QTL4.2 and QTL8 for ABR and QTL8 for DTF. The integrated BAC/BIBAC map resulted from the project will provide a powerful platform and tools essential for many aspects of advanced genomics and genetics research of this crop and related species. These includes, but are not limited to, targeted development of SNP, InDel and SSR markers, high-resolution mapping of the chickpea genome and its agronomic genes and QTLs, sequencing and decoding of all genes of the genome using the next-generation sequencing technology, and comparative genome analysis of chickpea versus other legumes. The DNA markers and BAC/BIBACcontigs containing or closely linked to ABR and DTF provide essential tools to develop SSR and SNP markers well-suited for marker-assisted breeding of the traits and clone their corresponding genes. The development of the tools and knowledge will thus promote enhanced and substantial genetic improvement of the crop and related legumes.
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Sela, Hanan, Eduard Akhunov, and Brian J. Steffenson. Population genomics, linkage disequilibrium and association mapping of stripe rust resistance genes in wild emmer wheat, Triticum turgidum ssp. dicoccoides. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7598170.bard.
Full textAbstract:
The primary goals of this project were: (1) development of a genetically characterized association panel of wild emmer for high resolution analysis of the genetic basis of complex traits; (2) characterization and mapping of genes and QTL for seedling and adult plant resistance to stripe rust in wild emmer populations; (3) characterization of LD patterns along wild emmer chromosomes; (4) elucidation of the multi-locus genetic structure of wild emmer populations and its correlation with geo-climatic variables at the collection sites. Introduction In recent years, Stripe (yellow) rust (Yr) caused by Pucciniastriiformis f. sp. tritici(PST) has become a major threat to wheat crops in many parts of the world. New races have overcome most of the known resistances. It is essential, therefore, that the search for new genes will continue, followed by their mapping by molecular markers and introgression into the elite varieties by marker-assisted selection (MAS). The reservoir of genes for disease and pest resistance in wild emmer wheat (Triticumdicoccoides) is an important resource that must be made available to wheat breeders. The majority of resistance genes that were introgressed so far in cultivated wheat are resistance (R) genes. These genes, though confering near-immunity from the seedling stage, are often overcome by the pathogen in a short period after being deployed over vast production areas. On the other hand, adult-plant resistance (APR) is usually more durable since it is, in many cases, polygenic and confers partial resistance that may put less selective pressure on the pathogen. In this project, we have screened a collection of 480 wild emmer accessions originating from Israel for APR and seedling resistance to PST. Seedling resistance was tested against one Israeli and 3 North American PST isolates. APR was tested on accessions that did not have seedling resistance. The APR screen was conducted in two fields in Israel and in one field in the USA over 3 years for a total of 11 replicates. We have found about 20 accessions that have moderate stripe rust APR with infection type (IT<5), and about 20 additional accessions that have novel seedling resistance (IT<3). We have genotyped the collection using genotyping by sequencing (GBS) and the 90K SNP chip array. GBS yielded a total 341K SNP that were filtered to 150K informative SNP. The 90K assay resulted in 11K informative SNP. We have conducted a genome-wide association scan (GWAS) and found one significant locus on 6BL ( -log p >5). Two novel loci were found for seedling resistance. Further investigation of the 6BL locus and the effect of Yr36 showed that the 6BL locus and the Yr36 have additive effect and that the presence of favorable alleles of both loci results in reduction of 2 grades in the IT score. To identify alleles conferring adaption to extreme climatic conditions, we have associated the patterns of genomic variation in wild emmer with historic climate data from the accessions’ collection sites. The analysis of population stratification revealed four genetically distinct groups of wild emmer accessions coinciding with their geographic distribution. Partitioning of genomic variance showed that geographic location and climate together explain 43% of SNPs among emmer accessions with 19% of SNPs affected by climatic factors. The top three bioclimatic factors driving SNP distribution were temperature seasonality, precipitation seasonality, and isothermality. Association mapping approaches revealed 57 SNPs associated with these bio-climatic variables. Out of 21 unique genomic regions controlling heading date variation, 10 (~50%) overlapped with SNPs showing significant association with at least one of the three bioclimatic variables. This result suggests that a substantial part of the genomic variation associated with local adaptation in wild emmer is driven by selection acting on loci regulating flowering. Conclusions: Wild emmer can serve as a good source for novel APR and seedling R genes for stripe rust resistance. APR for stripe rust is a complex trait conferred by several loci that may have an additive effect. GWAS is feasible in the wild emmer population, however, its detection power is limited. A panel of wild emmer tagged with more than 150K SNP is available for further GWAS of important traits. The insights gained by the bioclimatic-gentic associations should be taken into consideration when planning conservation strategies.
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Paran, Ilan, and Molly Jahn. Analysis of Quantitative Traits in Pepper Using Molecular Markers. United States Department of Agriculture, January 2000. http://dx.doi.org/10.32747/2000.7570562.bard.
Full textAbstract:
Original objectives: The overall goal of the proposal was to determine the genetic and molecular control of pathways leading to the production of secondary metabolites determining major fruit quality traits in pepper. The specific objectives were to: (1) Generate a molecular map of pepper based on simple sequence repeat (SSR) markers. (2) Map QTL for capsaicinoids content (3) Determine possible association between capsaicinoids and carotenoid content and structural genes for capsaicinoid and carotenoid biosynthesis. (4) Map QTL for quantitative traits controlling additional fruit traits. (5) Map fruit-specific ESTs and determine possible association with fruit QTL (6) Map the C locus that determines the presence and absence of capsaicinoids in pepper fruit and identify candidate genes for C. Background: Pungency, color, fruit shape and fruit size are among the most important fruit quality characteristics of pepper. Despite the importance of the pepper crop both in the USA and Israel, the genetic basis of these traits was only little known prior to the studies conducted in the present proposal. In addition, molecular tools for use in pepper improvement were lacking. Major conclusions and achievements: Our studies enabled the development of a saturated genetic map of pepper that includes numerous simple sequence repeat (SSR) markers and the integration of several independent maps into a single resource map that consists of over 2000 markers. Unlike previous maps that consisted mostly of tomato-originated RFLP markers, the SSR-based map consists of largely pepper markers. Therefore, the SSR and integrated maps provide ample of tools for use in marker-assisted selection for diverse targets throughout the Capsicum genome. We determined the genetic and molecular bases of qualitative and quantitative variation of pungency, the most unique characteristics of pepper fruit. We mapped and subsequently cloned the Pun1 gene that serves as a master key for capsaicinoids accumulation and showed that it is an acyltransferase. By sequencing the Pun1 gene in pungent and non-pungent cultivars we identified a deletion that abolishes the expression of the gene in the latter cultivars. We also identified QTLs that control capsaicinoids content and therefore pungency level. These genes will allow pepper breeders to manipulate the level of pungency for specific agricultural and industrial purposes. In addition to pungency we identified genes and QTLs that control other key developmental processes of fruit development such as color, texture and fruit shape. The A gene controlling anthocyanin accumulation in the immature fruit was found as the ortholog of the petunia transcription factor Anthocyanin2. The S gene required for the soft flesh and deciduous fruit nature typical of wild peppers was identified as the ortholog of tomato polygalacturonase. We identified two major QTLs controlling fruit shape, fs3.1 and fs10.1, that differentiate between elongated and blocky and round fruit shapes, respectively. Scientific and agricultural implications: Our studies allowed significant advancement of our understanding at the genetic and molecular levels of important processes of pepper fruit development. Concomitantly to gaining biological knowledge, we were able to develop molecular tools that can be implemented for pepper improvement.
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Ozrenk, Koray, Gursel Ozkan, Meleksen Akin, Emine Orhan, Sadiye Peral Eyduran, and Sezai Ercisli. Molecular Characterization and Genetic Relationships of Wild Apricots (Prunus Armeniaca L.) from Turkey Using SSR Markers. "Prof. Marin Drinov" Publishing House of Bulgarian Academy of Sciences, May 2020. http://dx.doi.org/10.7546/crabs.2020.05.06.
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Veilleux, Richard E., Jossi Hillel, A. Raymond Miller, and David Levy. Molecular Analysis by SSR of Genes Associated with Alkaloid Synthesis in a Segregating Monoploid Potato Family. United States Department of Agriculture, May 1994. http://dx.doi.org/10.32747/1994.7570550.bard.
Full textAbstract:
More than 15,000 anthers of an interspecific hybrid (CP2) between two diploid (2n=2x=24) potato species, Solanum chacoense (weedy) and S. phureja (cultivated), were cultured to generate a family of monoploid (haploid, 2n-1x=12) plants. Of 260 regenerated plants, 34 were monoploid, 210 diploid and 16 tetraploid. SSR analysis revealed that six monoploids were genetically identical and 14 diploids were homozygous, thus limiting the population to 42 (28 monoploids and 14 homozygous diploids). New microsatellite loci were developed for potato from database sequences (15), a conventional genomic library (6), an enriched library (18) and tomato (11). Of these, 13 were polymorphic in the CP2 family and 11 were used to study genetic segregatin. Four of 11 exhibited skewed segregation in the monoploid family. Seven of 18 microsatellite markers were polymorphic and informative on a set of 12 tetraploid potato cultivars. Acetylleptinidine (ALD) is the aglycone of leptines, a natural defense against insects, especially the highly destructuve Colorado potato beetle. ALD is absend in S. phureja but highly expressed in the S. chacoense parent of CP2. A backcross population between CP2 and tis S. phureja parent was used to examine segregation for ALD. Bulks of 10 backcross individuals that expressed ALD and 10 that did not were used to identify putative RAPD markers associatd with the trait. Of 80 primers tested, one putative marker amplified by OPQ02 was present in eight of ten individuals comprising the high bulk and absent in all 10 individuals comprising the low bulk. This is a putative marker for ALD expression in potato.
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Rocheford, Torbert, Yaakov Tadmor, Robert Lambert, and Nurit Katzir. Molecular Marker Mapping of Genes Enhancing Tocol and Carotenoid Composition of Maize Grain. United States Department of Agriculture, December 1995. http://dx.doi.org/10.32747/1995.7571352.bard.
Full textAbstract:
The overall objective of this research was to identify chromosomal regions and candidate genes associated with control of concentration and forms of carotenoids (includes pro-Vitamin A) and tocopherols (Vitamin E), which are both antioxidants and are associated with health advantages. Vitamin A and E are included in animal feeding supplements and the eventual goal is to increase levels of these compounds in maize grain so that the cost of these supplements can be reduced or eliminated. Moreover, both compounds are antioxidants that protect unsaturated fatty acids from oxidation and thus maintaining maize oil quality for longer periods. We identified three SSR markers that are associated with 38% of the variation for total carotenoids and three SSR markers associated with 44% of the variation for total tocopherols in the cross W64a x A632. We identified two candidate genes associated with levels of carotenoids: phytoene synthase and zeta carotene desaturase. Evaluation of (Illinois High Oil x B73) B73 BC 1S1 population for tocopherols detected additional chromosomal regions influencing the level of total tocopherols, and detected a common region on chromosome 5 associated with ratio of the more desirable alpha from to the gamma form of tocopherol. The results suggest molecular marker assisted selection for higher levels of these antioxidants in corn grain should be feasible.
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Joel, Daniel M., Steven J. Knapp, and Yaakov Tadmor. Genomic Approaches for Understanding Virulence and Resistance in the Sunflower-Orobanche Host-Parasite Interaction. United States Department of Agriculture, August 2011. http://dx.doi.org/10.32747/2011.7592655.bard.
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Oroginal Objectives: (i) identify DNA markers linked to the avirulence (Avr) locus and locate the Avr locus through genetic mapping with an inter-race Orobanche cumana population; (ii) develop high-throughput fingerprint DNA markers for genotypingO. cumana races; (iii) identify nucleotide binding domain leucine rich repeat (NB-LRR) genes encoding R proteins conferring resistance to O. cumana in sunflower; (iv) increase the resolution of the chromosomal segment harboring Or₅ and related R genes through genetic and physical mapping in previously and newly developed mapping populations of sunflower; and (v) develop high-throughput DNA markers for rapidly and efficiently identifying and transferring sunflower R genes through marker-assisted selection. Revisions made during the course of project: Following changes in O. cumana race distribution in Israel, the newly arrived virulent race H was chosen for further analysis. HA412-HO, which was primarily chosen as a susceptible sunflower cultivar, was more resistant to the new parasite populations than var. Shemesh, thus we shifted sunflower research into analyzing the resistance of HA412-HO. We exceeded the deliverables for Objectives #3-5 by securing funding for complete physical and high-density genetic mapping of the sunflower genome, in addition to producing a complete draft sequence of the sunflower genome. We discovered limited diversity between the parents of the O. cumana population developed for the mapping study. Hence, the developed DNA marker resources were insufficient to support genetic map construction. This objective was beyond the scale and scope of the funding. This objective is challenging enough to be the entire focus of follow up studies. Background to the topic: O. cumana, an obligate parasitic weed, is one of the most economically important and damaging diseases of sunflower, causes significant yield losses in susceptible genotypes, and threatens production in Israel and many other countries. Breeding for resistance has been crucial for protecting sunflower from O. cumana, and problematic because new races of the pathogen continually emerge, necessitating discovery and deployment of new R genes. The process is challenging because of the uncertainty in identifying races in a genetically diverse parasite. Major conclusions, solutions, achievements: We developed a small collection of SSR markers for genetic mapping in O. cumana and completed a diversity study to lay the ground for objective #1. Because DNA sequencing and SNPgenotyping technology dramatically advanced during the course of the study, we recommend shifting future work to SNP discovery and mapping using array-based approaches, instead of SSR markers. We completed a pilot study using a 96-SNP array, but it was not large enough to support genetic mapping in O.cumana. The development of further SNPs was beyond the scope of the grant. However, the collection of SSR markers was ideal for genetic diversity analysis, which indicated that O. cumanapopulations in Israel considerably differ frompopulations in other Mediterranean countries. We supplied physical and genetic mapping resources for identifying R-genes in sunflower responsible for resistance to O. cumana. Several thousand mapped SNP markers and a complete draft of the sunflower genome sequence are powerful tools for identifying additional candidate genes and understanding the genomic architecture of O. cumana-resistanceanddisease-resistance genes. Implications: The OrobancheSSR markers have utility in sunflower breeding and genetics programs, as well as a tool for understanding the heterogeneity of races in the field and for geographically mapping of pathotypes.The segregating populations of both Orobanche and sunflower hybrids are now available for QTL analyses.
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Zhang, Hongbin B., David J. Bonfil, and Shahal Abbo. Genomics Tools for Legume Agronomic Gene Mapping and Cloning, and Genome Analysis: Chickpea as a Model. United States Department of Agriculture, March 2003. http://dx.doi.org/10.32747/2003.7586464.bard.
Full textAbstract:
The goals of this project were to develop essential genomic tools for modern chickpea genetics and genomics research, map the genes and quantitative traits of importance to chickpea production and generate DNA markers that are well-suited for enhanced chickpea germplasm analysis and breeding. To achieve these research goals, we proposed the following research objectives in this period of the project: 1) Develop an ordered BAC library with an average insert size of 150 - 200 kb (USA); 2) Develop 300 simple sequence repeat (SSR) markers with an aid of the BAC library (USA); 3) Develop SSR marker tags for Ascochyta response, flowering date and grain weight (USA); 4) Develop a molecular genetic map consisting of at least 200 SSR markers (Israel and USA); 5) Map genes and QTLs most important to chickpea production in the U.S. and Israel: Ascochyta response, flowering and seed set date, grain weight, and grain yield under extreme dryland conditions (Israel); and 6) Determine the genetic correlation between the above four traits (Israel). Chickpea is the third most important pulse crop in the world and ranks the first in the Middle East. Chickpea seeds are a good source of plant protein (12.4-31.5%) and carbohydrates (52.4-70.9%). Although it has been demonstrated in other major crops that the modern genetics and genomics research is essential to enhance our capacity for crop genetic improvement and breeding, little work was pursued in these research areas for chickpea. It was absent in resources, tools and infrastructure that are essential for chickpea genomics and modern genetics research. For instance, there were no large-insert BAC and BIBAC libraries, no sufficient and user- friendly DNA markers, and no intraspecific genetic map. Grain sizes, flowering time and Ascochyta response are three main constraints to chickpea production in drylands. Combination of large seeds, early flowering time and Ascochyta blight resistance is desirable and of significance for further genetic improvement of chickpea. However, it was unknown how many genes and/or loci contribute to each of the traits and what correlations occur among them, making breeders difficult to combine these desirable traits. In this period of the project, we developed the resources, tools and infrastructure that are essential for chickpea genomics and modern genetics research. In particular, we constructed the proposed large-insert BAC library and an additional plant-transformation-competent BIBAC library from an Israeli advanced chickpea cultivar, Hadas. The BAC library contains 30,720 clones and has an average insert size of 151 kb, equivalent to 6.3 x chickpea haploid genomes. The BIBAC library contains 18,432 clones and has an average insert size of 135 kb, equivalent to 3.4 x chickpea haploid genomes. The combined libraries contain 49,152 clones, equivalent to 10.7 x chickpea haploid genomes. We identified all SSR loci-containing clones from the chickpea BAC library, generated sequences for 536 SSR loci from a part of the SSR-containing BACs and developed 310 new SSR markers. From the new SSR markers and selected existing SSR markers, we developed a SSR marker-based molecular genetic map of the chickpea genome. The BAC and BIBAC libraries, SSR markers and the molecular genetic map have provided essential resources and tools for modern genetic and genomic analyses of the chickpea genome. Using the SSR markers and genetic map, we mapped the genes and loci for flowering time and Ascochyta responses; one major QTL and a few minor QTLs have been identified for Ascochyta response and one major QTL has been identified for flowering time. The genetic correlations between flowering time, grain weight and Ascochyta response have been established. These results have provided essential tools and knowledge for effective manipulation and enhanced breeding of the traits in chickpea.
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Katzir, Nurit, Rafael Perl-Treves, and Jack E. Staub. Map Merging and Homology Studies in Cucumis Species. United States Department of Agriculture, September 2000. http://dx.doi.org/10.32747/2000.7575276.bard.
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List of original objectives (1) Construct a saturated map of melon, using RFLP, SSR, RAPD and Inter-SSR genetic markers. (2) Study the homology between the genomes of cucumber and melon. (3) Add to the Cucumis map, biologically important genes that had been cloned in other plant systems. Background Cucumber and melon are important vegetable crops in Israel and the US. Genome analysis of these crops has lagged behind the major plant crops, but in the last few years genetic maps with molecular markers have been developed. The groups that participated in this program were all involved in initial mapping of cucurbit crops. This grant was meant to contribute to this trend and promote some of the more advanced applications of genome analysis, i.e., map saturation and comparative mapping between cucurbit species. Major achievements The main achievements of the research were (a) the construction of melon maps that include important horticultural traits and Resistance Gene Homologues, (b) the development of approximately 200 SSR markers of melon and cucumber, (c) the preliminary map merging of melon maps and of comparative mapping between melon and cucumber. Implications As a result of this program, we have a good estimate of the applicability of different types or markers developed in one cucurbit species to genetic mapping in other species. Since the linkage groups of melon and cucumber can now be related to each other, future identification of important genes in the two crops will be facilitated. Moreover, the further saturation of the maps with additional markers will now allow us to target several disease resistance loci, horticultural traits for marker-assisted selection, fine mapping and positional cloning.
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Paran, Ilan, and Molly Jahn. Genetics and comparative molecular mapping of biochemical and morphological fruit characters in Capsicum. United States Department of Agriculture, March 2005. http://dx.doi.org/10.32747/2005.7586545.bard.
Full textAbstract:
Original objectives: The overall goal of our work was to gain information regarding the genetic and molecular control of pathways leading to the production of secondary metabolites determining major fruit quality traits in pepper and to develop tools based on this information to assist in crop improvement. The specific objectives were to: (1) Generate a molecular map of pepper based on simple sequence repeat (SSR) markers. (2) Map QTL for capsaicinoid (pungency) content (3) Determine possible association between capsaicinoid and carotenoid content and structural genes for capsaicinoid and carotenoid biosynthesis. (4) Map QTL for quantitative traits controlling additional fruit traits. (5) Map fruit-specific ESTs and determine possible association with fruit QTL (6) Map the C locus that determines the presence and absence of capsaicinoid in pepper fruit and identify candidate genes for C.locus. Background: Pungency, color, fruit shape and fruit size are among the most important fruit quality characteristics of pepper. Despite the importance of the pepper crop both in the USA and Israel, the genetic basis of these traits was poorly understood prior to the studies conducted in the present proposal. In addition, molecular tools for use in pepper improvement were lacking. Major conclusions and achievements: Our studies enabled the development of a saturated genetic map of pepper that includes numerous SSR markers. This map has been integrated with a number of other independent maps resulting in the publication of a single resource map consisting of more than 2000 markers. Unlike previous maps based primarily on tomato-originated RFLP markers, the new maps are based on PCR markers that originate in Capsicum providing a comprehensive and versatile resource for marker-assisted selection in pepper. We determined the genetic and molecular bases of qualitative and quantitative variation of pungency, a character unique to pepper fruit. We mapped and subsequently cloned the Pun1 gene that serves as a master regulatoar for capsaicinoid accumulation and showed that it is an acyltransferase. By sequencing the Pun1 gene in pungent and non-pungent cultivars we identified a deletion that abolishes the expression of the gene in the latter cultivars. We also identified QTL that control capsaicinoid content and therefore pungency level. These genes will allow pepper breeders to manipulate the level of pungency for specific agricultural and industrial purposes. In addition to pungency we identified genes and QTL that control other key developmental processes of fruit development such as color, texture and fruit shape. The A gene controlling anthocyanin accumulation in the immature fruit was found as the ortholog of the petunia transcription factor Anthocyanin2. The S gene required for the soft flesh and deciduous fruit nature typical of wild peppers was identified as the ortholog of tomato polygalacturonase. We identified two major QTL controlling fruit shape, fs3.1 and fs10.1, that differentiate elongated and blocky and round fruit shapes, respectively. Scientific and agricultural implications: Our studies allowed significant advances in our understanding of important processes of pepper fruit development including the isolation and characterization of several well known genes. These results also provided the basis for the development of molecular tools that can be implemented for pepper improvement. A total of eleven refereed publications have resulted from this work, and several more are in preparation.