Tesi: "Plant molecular genetics"

1

Lim, Saw Hoon. "Molecular analysis of porphobilinogen deaminase in higher plants". Thesis, University of Cambridge, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.259764.

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2

Phelan, Thomas Joseph. "GENETIC AND MOLECULAR ANALYSIS OF PLANT NUCLEAR MATRIX PROTEINS". NCSU, 2001. http://www.lib.ncsu.edu/theses/available/etd-20011104-233111.

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PHELAN, THOMAS JOSEPH, Genetic and Molecular Analysis of Plant Nuclear Matrix Proteins. (Under the direction of Steven L. Spiker.)The eukaryotic nucleus is composed of DNA, RNA and protein, encapsulated by a nuclear envelope. DNA is compacted up to ten thousand times in order to be packaged into the nucleus. The nucleus must maintain order in the presence of a very high density and variety of protein and RNA. The nuclear matrix is a proteinaceous network thought to provide structure and organization to the nucleus. We believe that relatively stable interactions of nuclear molecules with the nuclear matrix are key to organization of the nucleus. Numerous "Matrix Attachment Region" DNA elements (MARs), have been isolated from plants, animals, and fungi. Evidence suggests that these MARs attach to the nuclear matrix, delimiting loops of chromosomal DNA. In studies of transgenic plants and animals, MARs have been shown to give important advantages to organisms transformed with genes flanked by these elements. Unlike most DNA elements, no specific sequence elements have been identified in MAR DNAs. Partly due to the insolubility of the matrix, and to the heterogeneity of MAR DNA, very few of the protein components of the nuclear matrix have been identified. This work presents analysis the proteins of the plant nuclear matrix. We have characterized a set of related proteins from the model plant Arabidopsis that associate with MAR DNA in vitro. These proteins appear to be similar to the NOP56/NOP58 family of proteins previously identified in several eukaryotic organisms. The NOP56/NOP58 proteins are thought to be involved in modifications of ribosomal RNA. Binding studies presented in this work suggest that these plant proteins may participate in RNA/DNA/protein complexes in the nucleus.

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3

Cowan, Rebecca. "Molecular domestication and transposon contributions to plant genome evolution". Thesis, McGill University, 2005. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=82211.

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Despite the ubiquity of transposons in eukaryotic genomes, their evolutionary role remains controversial. The discovery of several domesticated genes has suggested that transposons can gain host functions, and thus contribute to the evolution of their host. Here, I present the results of a genome-wide screen for transposon-derived host genes, which was based on the idea that, once domesticated, the open reading frame of such elements would be maintained, while terminal structures necessary for transposition would be lost. Eight-hundred-and-sixty-three such transposon-dissociated elements were mined from the genome of Arabidopsis thaliana var. Columbia-0, of which less than 10% are associated with expression data. Phylogenetic analysis of Mutator superfamily genes in the genomes of Oryza sativa ssp. japonica (cv Nipponbare) and Arabidopsis, including 121 Mutator-derived transposon-dissociated elements, found that only two gene families are taxonomically widespread. MUSTANG1, a member of one of these families, appears to be under purifying selection. Thus, despite the dearth of taxonomically widespread and/or expressed transposon-dissociated elements, MUSTANG1, as well as three transposon-dissociated elements that may be associated with mutant phenotypes, might be newly discovered transposon-derived host genes.

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4

Ryan, Lucy Anne. "The molecular biology of plant growth control". Thesis, De Montfort University, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.328065.

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5

Bitalo, Daphne Nyachaki. "Implementation of molecular markers for triticale cultivar identification and marker-assisted selection". Thesis, Stellenbosch : Stellenbosch University, 2012. http://hdl.handle.net/10019.1/71670.

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Thesis (MSc)--Stellenbosch University, 2012.
Triticale is an amphidiploid that consists of wheat (A and B) and rye (R) genomes. This cereal is fast becoming important on a commercial basis and warrants further assessment for the better management and breeding of the hybrid. The assessment of the genetic diversity among the wheat and rye genomes within triticale can be obtained by using molecular markers developed in both donor genomes. Simple sequence repeats markers (SSRs) and amplified fragment length markers (AFLPs) have been previously used to assess the genetic diversity among triticale lines. SSRs are highly polymorphic markers that are abundant and which have been shown to be highly transferable between species in previous studies while AFLP markers are known to generate plenty of data as they cover so many loci. Thus, the aim of this study was to develop a marker system suitable to assess the genetic diversity and relationships of advanced breeding material (and cultivars) of the Stellenbosch University’s Plant Breeding Laboratory (SU-PBL). Therefore, both AFLP and SSR markers were initially analysed using eight triticale cultivars (with known pedigrees) to facilitate cultivar identification. Fourty-two AFLP primer combinations and 86 SSR markers were used to assess the genetic diversity among the Elite triticale cultivars. The AFLP primer combinations generated under average polymorphism information content (PIC) values. Furthermore, these markers generated neighbour-joining (NJ) and unweighted pair group method with arithmetic average (UPGMA) dendograms that displayed relationships that did not correspond with the available pedigree information. Therefore, this marker system was found not to be suitable. A set of 86 SSRs previously identified in both wheat and rye, was used to test the genetic diversity among the eight cultivars. The markers developed in wheat achieved 84% transferability while those developed in rye achieved 79.3% transferability. A subset of SSR markers was able to distinguish the cultivars, and correctly identify them by generating NJ and UPGMA dendograms that exhibited relationships that corroborated the available pedigree data. This panel of markers was therefore chosen as the most suitable for the assessment of the advanced breeding material. The panel of seven SSR markers was optimised for semi-automated analysis and was used to screen and detect the genetic diversity among 306 triticale entries in the F6, Senior and Elite phases of the SU-PBL triticale breeding programme. An average PIC value of 0.65 was detected and moderate genetic variation was observed. NJ and UPGMA dendograms generated showed no clear groupings. However, the panel of markers managed to accurately identify all cultivars within the breeding program. The marker panel developed in this study is being used to routinely distinguish among the advanced breeding material within the SU-PBL triticale breeding programme and as a tool in molecular-assisted backcross.

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6

Juretic, Nikoleta. "The role of transposons in shaping plant genomes /". Thesis, McGill University, 2008. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=115687.

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Transposons, also known as transposable elements (TEs), are genetic elements capable of changing their location in the genome and amplifying in number. Because of their ability to cause mutations in the host genome, often with detrimental consequences to the host, yet avoid being eliminated by natural selection, transposons have been labeled selfish elements or genomic parasites. However, the advent of genomics has allowed the identification of numerous instances where transposons have played a crucial role in host genome evolution. In this thesis, I evaluate the extent to which transposons have influenced the genomes of their hosts, with an emphasis on plant genomes. I review the present knowledge of different mechanisms by which this is achieved and provide examples to illustrate them. Next, I tackle the problem of annotating transposons in the completed genomic sequence of domestic rice by comparing RepeatMasker, the standard approach used in transposon annotation, with an alternative approach employing hidden Markov models. In addition, I perform a genome-wide analysis of gene fragment capture by rice Mutator-like transposons. I conclude that, while this is a widespread phenomenon in rice, it is unlikely to represent a major force in generating novel protein-coding genes. Nevertheless, the duplicated gene fragments that are transcribed may playa role in the regulation of host genes they arose from via an RNAi-like mechanism. Finally, I conduct an in silico analysis of a gene family derived from a domesticated Mutator-like transposase, called MUSTANG (MUG), in conjunction with an experimental characterization of the MUG family in Arabidopsis. The results of the study indicate that the MUG family arose in a common ancestor of flowering plants and that the Arabidopsis genes AtMUG1 and/or AtMUG2 may act as global regulators of mitochondrial function. I conclude that our appreciation of the role of transposons in host function and evolution will undoubtedly continue to grow as our understanding of these processes deepens.

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7

Horsley, David. "Molecular and structural studies of plant clathrin coated vesicles". Thesis, University of Oxford, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.291323.

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8

Moulton, Paul Jonathan. "The molecular genetics of Pseudomonas syringae pv. pisi". Thesis, University of the West of England, Bristol, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.278900.

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9

Russell, Joanne Ritchie. "Molecular variation in Theobroma species". Thesis, University of Reading, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.386981.

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10

Husselmann, Lizex H. H. "Molecular characterisation of the commercially important Agathosma species". Thesis, Stellenbosch : University of Stellenbosch, 2006. http://hdl.handle.net/10019.1/3068.

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Thesis (MSc (Plant Biotechnology))--University of Stellenbosch, 2006.
The development of a reliable and reproducible method for the genetic characterisation and identification of the commercially important Agathosma species was investigated. Previous research attempts aimed at developing a reliable and reproducible method of identifying these Agathosma species failed, mostly because these studies were based on phenotypic traits and these methods were therefore influenced by environmental factors. In this study amplified fragment length polymorphisms (AFLPs) were successfully used to quantify the genetic variation between the Agathosma species and as a result three distinct groups could be identified. The data obtained were elaborated with the Dice genetic similarity coefficient, and analysed using different clustering methods and Principle Coordinate Analysis (PCoA). Cluster analysis of the genotypes revealed an overall genetic similarity between the populations of between 0.85 and 0.99. The AFLP-based dendrogram divided the populations into three major groups: (1) the A. serratifolia and A. crenulata populations, (2) the putative hybrid, A. betulina X A crenulata populations, and (3) the A. betulina populations, confirming that this technique can be used to identify species. The question of hybridisation was also clarified by the results of the PCoA, confirming that the putative hybrid is not genetically intermediately spread between the A. crenulata and A. betulina populations, and that it is genetically very similar to A. betulina. The putative hybrid can therefore rather be viewed as a genetically distinct ecological variant of A. betulina. As the AFLP technique cannot be directly applied in large-scale, routine investigations due to its high cost and complicated technology, the development of polymerase chain reaction (PCR)-based molecular markers, able to accurately identify the species, was undertaken. Due to the superior quality of A. betulina oil, the development of such markers is especially critical for this species. Several species-specific AFLP markers were identified, converted to sequence characterised amplified regions (SCARs) and ultimately single nucleotide polymorphisms (SNPs) were characterised. The developed SCARs were unable to distinguish between the species. The conversion of AFLP fragments to SCARs is problematic due to multiple fragments being amplified with the AFLP fragment of interest. The diagnostic feature of the SNP-based markers was not sensitive enough, since this technique could not distinguish between the A. betulina and A. crenulata and/or the putative hybrid populations. The SNPs that were characterised were found not to be species-specific; they were only specific to the particular clone. Although a quick and robust marker specific for A. betulina has not yet been developed, this study sets the stage for future genetic studies on Agathosma species. Such a marker, or set of markers, would be an invaluable contribution to a blooming buchu oil industry.

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11

Docking, T. Roderick. "The evolution of retrotransposon sequences in four asexual plant species /". Thesis, McGill University, 2004. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=81327.

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Since their discovery, transposable elements (TEs) have been regarded either as useful building blocks of genomes, or as "selfish DNA": genetic parasites that exploit the sexual cycle to spread in copy number within populations to the detriment of their hosts. If the "selfish DNA" hypothesis is correct, TEs are expected to deteriorate and be lost from asexual populations. This thesis tests the predictions of the "selfish DNA" hypothesis in four asexual plant species, focusing on patterns of nucleotide diversity and nucleotide substitution. Sequences bearing strong resemblance to known TE families including Ty1/copia, Ty3/gypsy, and LINE-like elements were successfully isolated from all four plant species, and showed patterns of nucleotide substitution consistent with a long history of purifying selection. Stochastic simulations were also conducted, and suggested that this result is expected if the host species has been asexual for less than tens of thousands of generations.

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12

Poole, Deborah Marie. "Molecular analysis of plant cell wall hydrolases of bacterial origin". Thesis, University of Newcastle Upon Tyne, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.238939.

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13

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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14

Saleh, Norihan Mohamad. "Molecular studies of 'wild-abortive' and fertile cytoplasms in rice". Thesis, University of Nottingham, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.277933.

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15

Sarjeant, Adrian B. "The molecular genetic characterisation of the Arabidopsis thaliana LAX1 gene". Thesis, University of Warwick, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.343147.

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16

Lonergan, Paul Francis. "Genetic characterisation and QTL mapping of zinc nutrition in barley (Hordeum vulgare)". Title page, contents and abstract only, 2001. http://web4.library.adelaide.edu.au/theses/09PH/09phl847.pdf.

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17

Jenkin, Mandy Jane. "Genetics of boron tolerance in barley /". Adelaide : Thesis (Ph.D.) -- University of Adelaide, Department of Plant Science, 1993. http://web4.library.adelaide.edu.au/theses/09PH/09phj514.pdf.

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18

Filkowski, Jody, e University of Lethbridge Faculty of Arts and Science. "The effect of pathogens on plant genome stability". Thesis, Lethbridge, Alta. : University of Lethbridge, Dept. of Biological Sciences, 2004, 2004. http://hdl.handle.net/10133/254.

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Abstract (sommario):

Resistance (R) genes, a key factor in determining the resistance of plants, have been shown often to be highly allelic entities existing in duplicated regions of the genome. This characteristic suggests that R-gene acquisition may have arisen through frequent genetic rearrangements as a result of transient, reduced genome stability. Tabacco plants transgenic for a recombination construct exhibited reduced genome stability upon infection with a virulent pathogen (tobacco mosaic virus). The reduced genome stability manifested as an increase in recombination events in the transgene. Such increases were observed following a virulent pathogen attack. This increase in recombination was shown to be systemic and was observed prior to systemic viral movement suggesting the presence of a systemic recombination signal. Further molecular analyses revealed that specific R-gene loci experience a large frequency of rearrangements following a virulent pathogen encounter. The possible targeting of instability to R-gene regions may be controlled through epigenetic processes, in particular, DNA methylation.
xiii, 119 leaves ; 29 cm.

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19

Mahmoud, Sayed Hassan. "Biochemical marker genes for molecular genetics and plant breeding in Pisum sativum L". Thesis, Durham University, 1985. http://etheses.dur.ac.uk/7853/.

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Three isoenzyme systems (amylase, esterase and glutamate oxalo acetate transaminase) were examined in seeds of pea ( Pisum sativum L.) and showed clear variations in their band patterns on gel electro phoresis between different lines. The inheritance of these isoenzyme systems, and the location of their structural genes on the pea genome were investigated. Reciprocal crosses were made between lines, F2 seeds were analysed for segregation in the band patterns of the isoenzymes, and F2 plants were investigated to find linkage between the genes for these isoenzymes and genes for selected morphological markers. The results obtained showed that each of the investigated isoenzyme systems is genetically controlled by co-dominant alleles at a single locus. The gene for amylase ( Amy ) was found to be on chromosome 2, linked to the loci k and wb ( wb.. .9-k. . .25.. .Amy ). The gene for esterase ( Est ) was found to be linked to the gene Br (chromosome 4) but the exact location is uncertain because of a lack of morphological markers. The gene for glutamate oxaloacetate transaminase ( Got ) was found to be on chromosome 1 linked to the loci a and d ( a...24...Got...41.. d). Gel electrophoresis techniques have also been used to investigate genetically controlled variation in the major subunits (50,000 Mr) of vicilin, a storage protein of Pisum sativum L. The Fl protein band patterns were shown to be additive with respect to those of the parental lines and to be identical in reciprocal crosses. Genetic analysis of the F2 plants indicated that the 50,000 Mr vicilin subunits band pattern is controlled by a pair of co-dominant genes at a single locus. The F2 data were used to locate this major vicilin gene locus ( Vc-1 ) to chromoscane 7, closely linked to the r locus (for round and wrinkled seed surface). A third member of pea legumin gene family, denoted legB, has been sequenced using the "dideoxy chain termination" method with the M1 3 sequencing system. The complete nucleotide sequence showed that this gene has a general form typical of an eukaryotic gene. The homolgies between this gene and the previously published gene "legA" 'were estimated and showed strong homology between the two genes with eight amino acid substitutions and deletion of 14 bp in the third intron (IVS-3).The inheritance of ribosomal RNA (rRNA) genes in ( Pisum sativum L.) was investigated in a cross between two different lines, where length variation in rDNA fragments of Eco RI digests was observed. The results obtained showed that the rRNA genes are controlled by simple Mendelian system with "co-dominance" between alleles. In order to locate the rRNA gene sites to positions on the chromosomes, the segregation of ECO. RI restriction fragments of rDNA from F2 plants with respect to genes for selected morphological markers on chromosomes 4 and 7 (the chromosomes known to have nucleolus organizer regions) were tested. The F2 data showed no linkages between the selected markers and rRNA genes, therefore, in situ hybridization using rDNA radioactive probe ((^3)H- labelled rDNA clone, pHAI) and physical mapping procedures were used. The results obtained have located the rRNA gene sites to nucleolus organizer regions (satellite constrictions) at 138 and 60 map units from the centromeres of chromosomes 4 and 7, respectively.

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20

Chaulk, Christine Annie 1964. "Chromosome number, fertility, and mitochondrial genome of backcross populations derived from Medicago sativa x Medicago dzhawakhetica hybrids". Thesis, The University of Arizona, 1989. http://hdl.handle.net/10150/277157.

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Abstract (sommario):

Backcross populations (BC) from Medicago sativa L. x M. dzhawakhetica Bordz. hybrids were analyzed for chromosome number, fertility and morphological characteristics. Previously obtained F1 hybrids were recovered when diploid (2n = 2x = 16) M. sativa was crossed with tetraploid (2n = 4x = 32) M. dzhawakhetica. Resulting F1 hybrids were triploid (2n = 3x = 24), completely male sterile and had low levels of female fertility. Subsequent populations were obtained by successive backcrossing to unrelated (4x) M. sativa clones. The BC1 plants were pentaploid (2n = 5x = 40) and both male and female fertile. BC2 populations had chromosome numbers ranging from 2n = 32 to 48, and most plants (94% were male and female fertile. BC3 populations were tetraploid (2n = 32) or near tetraploid (2n = 33) and were morphologically similar to M. sativa. Preliminary analysis of mitochondrial nucleic acids by agarose gel electrophoresis, indicated biparental inheritance of this organelle in the F1 hybrids; however, further analysis provided inconclusive results.

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21

Wan, Yao. "From Powerhouse to Processing Plant: Conserved Roles of Mitochondrial Outer Membrane Proteins in tRNA Splicing". The Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu1531410494675571.

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22

Lee, Sungkeun. "Molecular genetic analysis of nucleotide excision repair genes in Dictyostelium discoideum /". free to MU campus, to others for purchase, 1997. http://wwwlib.umi.com/cr/mo/fullcit?p9841209.

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23

Venter, Mauritz. "Isolation of grapevine promoters with special emphasis on the vacuolar pyrophosphatase". Thesis, Stellenbosch : University of Stellenbosch, 2004. http://hdl.handle.net/10019.1/16078.

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Abstract (sommario):

Dissertation (PhD)--University of Stellenbosch, 2004.
ENGLISH ABSTRACT: Understanding the complex nature of grapevine molecular biology is of great importance for viticulturists. Progress in the elucidation of key events on a genetic level could provide further insight into the underlying cues responsible for the precise control of physiological and metabolic changes during a specific condition such as fruit development. The use and analysis of molecular ‘tools’, such as promoters controlling the site and level of gene activity, could assist in the understanding of grapevine biology and serve as a platform for the future design and development of recombinant DNA protocols and strategies for Vitis vinifera L. A high-throughput gene expression system, cDNA-AFLPs, was successfully used to analyse large-scale transcriptional activity during berry ripening. Candidate cDNA fragments were selected on the basis of desired expression patterns and/or known gene function for subsequent promoter isolation. From three candidate cDNAs selected, the promoter of a gene encoding vacuolar pyrophosphatase (V-PPase) was isolated for computational and comparative analyses. Promoter activity was evaluated on a transient level using the green fluorescent protein (GFP) reporter gene. Comparative integration has allowed for putative correlation of cis-elements, acting as receptors within promoter regions, to regulate V-PPase gene expression in response to development, environmental stress and tissue-specificity. In this study, integration of genetic data have advanced the understanding and transcriptional role of a key enzyme (V-PPase) during grape ripening. Although never a replacement for experimental verification, this integrative strategy of combining gene expression profiles with bioinformatics and regulatory data will greatly assist in further elucidation of various other key components and regulatory cues associated with grapevine molecular biology. This study has allowed us to use molecular tools that could assist in gaining further insight into genetic complexities and could serve as a platform for a more refined genetic manipulation strategy in Vitis vinifera L.
AFRIKAANSE OPSOMMING: Begrip van die komplekse aard van wingerd molekulêre biologie is van groot belang vir wingerdkundiges. Vooruitgang in die begrip van belangrike gebeurtenisse op ń genetiese vlak behoort verdere insig in die onderliggende instruksies vir die noukeurige beheer van fisiologiese en metaboliese veranderinge tydens ń spesifieke kondisie soos vrug rypwording te bevorder. Die gebruik en analise van molekulêre ‘instrumente’ soos promoters, wat die posisie en vlak van geen aktiwiteit beheer, kan bydra tot n beter begrip van wingerd biologie en sodoende dien as ń platform vir die toekomstige ontwerp en ontwikkeling van rekombinante DNS (deoksiribonukleiensuur) protokolle en strategieë vir Vitis vinifera L. ń Hoë-kapasiteit geen uitdrukkings sisteem, nl. kDNS-AFLPs (komplementêre deoksiribonukleiensuur- geamplifiseerde fragment lengte polimorfisme), is suksesvol gebruik vir die analise van grootskaalse transkripsionele aktiwiteit tydens druif rypwording. Kandidaat kDNS fragmente is geselekteer, gebaseer op verlangde uitdrukkings-patrone en/of bekende geen funksie vir daaropvolgende promoter isolering. Van drie geselekteerde kandidaat kDNS fragmente, is die promoter van ń geen wat vakuolêre pirofosfatase (V-PPase) kodeer geïsoleer vir rekenaar- en vergelykende analise. Promoter aktiwiteit is op ń nie-stabiele vlak deur die gebruik van ń groen-fluoresserende proteien (GFP) verklikker geen geëvalueer. Vergelykende integrering het dit moontlik gemaak om veronderstelde korrelasies van cis-elemente, wat as reseptore binne ń promoter area dien, en die regulering van V-PPase geen uitdrukking, in reaksie tot ontwikkeling, omgewings stres en weefsel-spesifisiteit, te maak. Tydens hierdie studie, het die integrering van genetiese data gehelp om die transkripsionele rol van ń belangrike ensiem (V-PPase) tydens druif rypwording beter te verstaan. Alhoewel dit nooit ń plaasvervanger vir eksperimentele bewyse sal wees nie, kan hierdie gëintegreerde strategie, wat die kombinasie van geen-uitdrukkingsprofiele met bioinformatika en regulatoriese data behels, grootliks bydra om verskeie ander belangrike komponente en regulatorieseaanwysings geassosieërd met wingerd molekulêre biologie te ontrafel. Hierdie studie het verdere insig in genetiese kompleksiteite verleen, en kan nou dien as ń platform vir ń meer presiese genetiese manipulering strategie in Vitis vinifera L.

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24

Zheng, Liansheng 1955. "Gene expression in two different genotypes of alfalfa under salt stressed and unstressed conditions". Thesis, The University of Arizona, 1988. http://hdl.handle.net/10150/276936.

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Gene expression in two different genotypes of alfalfa, salt-tolerant and salt-sensitive, was examined by studying differences in protein products coded for by poly(A+) RNA isolated from shoot and root tissue. Plants were grown in hydroponics under unstressed or salt-stressed conditions. Two salinity levels (low salt: 30 mM NaCl and 6 mM CaCl2 and high salt: 133 mM NaCl and 27 mM CaCl2) and one unstressed control were applied. The salt-tolerant genotype showed higher biomass accumulation than the salt-sensitive genotype under both control and salt-stressed conditions. The difference in biomass accumulation between the two genotypes was greatest at the highest salt level. The effect of salt stress on gene expression was studied via in vitro translation of poly (A+) RNA with (35S) -methionine. The labeling pattern was similar in all treatments when analyzed by one dimensional SDS-PAGE. However, a two dimensional analysis (isoelectric focusing followed by SDS-PAGE) showed that salt-stress induced a number of new proteins and repressed several others.

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25

Posthuma, Karin Ingeborg. "Molecular detection of strawberry crinkle virus and cloning of plant genes associated with infection". Thesis, Imperial College London, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.342275.

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26

Al-Mamari, Al-Ghaliya Humaid. "Application of genomics and molecular genetics in date palm (Phoenix dactylifera L.)". Thesis, University of Nottingham, 2013. http://eprints.nottingham.ac.uk/27894/.

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Date palm (Phoenix dactylifera L.) is a diploid with 18 pairs of chromosomes and an estimated genome size of 658 Mb. It is a dioecious perennial monocot, with a long generation time (a period of 4-5 years until first flowering). Date palm is one of the major fruit crops grown in the Gulf countries and particularly in the Sultanate of Oman. Approximately 250 varieties of date palm are recorded throughout the country with evaluation and characterization based on morphological and reproductive traits (e.g. fruit color, fruit shape and fruit weight). Limited molecular characterization work has been undertaken for date palm germplasm in general and Omani date palm germplasm, in particular. The principal focus of this study was to: investigate the genetic diversity of Omani date palm germplasm and compare it with 'exotic' germplasm, to differentiate between female and male plants at the molecular level and to construct an initial genetic map for date palm. Samples were taken from eight parents of the available Omani date palm controlled crosses (Khalas 4, Khalas 13 male, Um-Alsela, Khori male, Bami, Naghal, Bahlani male, and Khasab) with 90 date palms from the BC1 and F1 populations, from 194 Omani date palm accessions (151 female cultivars and 43 male trees), together with samples from Italy (Sanremo and Bordighera), USDA-ARS, France, Iraq, Libya, Sudan and Iran. The F-statistics analysis showed that the genetic variation between female and male accessions based on random markers was only 2.1 %, while within the broader group of Omani female and male accessions the molecular variation was 97%, suggesting that the Omani female and male accessions have little consistent divergence, compared to the large-scale divergence within Omani germplasm, so male palm have been derived from most genetic origins in Oman. Additionally, the Principal Coordinates Analysis (PCA) and bootstrap consensus phenetic tree showed that the Omani accessions were closely related to each other and there was no clear genetic differentiation between female and male cultivars. A high degree of genetic variation was observed between germplasm from Oman, Italy, USDA-ARS, France, Iraq, Libya, Sudan and Iran as measured by Fst (19.7 %). The PCA showed that the Europe-Africa (Italy, France, Libya and Sudan) accessions are distinguished from West-Asia (Oman, Iraq and Iran) accessions and have their own autochthonous origin, a finding which was strongly validated by bootstrap consensus tree test. A medium density genetic map in date palm was constructed using 53 individuals from BC1 and 30 individuals from F1 populations. The BC1 map consisted of 270 markers (28 SSR and 242 SNP) distributed into 29 linkage groups with total genetic length of 1.486.7 cM, while the F1 map consisted of 591 markers (21 SSR and 570 SNP) distributed into 30 linkage groups with total genetic length of 2,385.6 cM. A total of 25 combined linkage groups were possible by combining both BC1 and F1 maps through common markers. A sex-link marker locus was developed and found to predict a high level of discrimination between male and female date palms among multiple varieties distributed across the wide range of cultivation, with an accuracy of 100% in the Omani crosses, 96% in the broad Omani material and 86% in the broadest date palm germplasm. This marker was also mapped in both BC1 and F1 at 42.8 cM and 4.9 cM in linkage groups 18 and 29, respectively and on combined group 19 at 42.8cM.

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27

Lai, Kwok-wai, e 賴國偉. "Molecular studies of {221}-cyanoalanine synthase from rice (Oryza sativa)". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2007. http://hub.hku.hk/bib/B39349238.

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28

Wright, Stephen 1975. "Transposon dynamics in self- and cross-fertilizing plant populations". Thesis, McGill University, 2000. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=33453.

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The population dynamics of transposons in self- and cross-fertilizing plant populations are investigated both theoretically and empirically. Models were developed to evaluate the influence of host breeding system on transposon populations. Modeling results suggest that the selfing rate is likely to have important effects on the abundance and polymorphism patterns of transposable elements in plant genomes. A primary characterization of diversity and abundance of transposons in the self-pollinating species Arabidopsis thaliana was conducted using genomic sequencing data, providing strong evidence for recent element mobility. Utilizing this information, a PCR-based approach was implemented to examine transposon dynamics in populations of Arabidopsis thaliana and its outcrossing relative, Arabidopsis lyrata. The results provide evidence for the importance of purifying selection in controlling transposon abundance in outcrossing populations, but not in selfers. Differences observed between the species are consistent with the hypothesis that host breeding systems influence the selective pressure acting on transposons.

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29

Zhang, Yun-Heng. "Biochemistry and molecular biology of binding proteins for plant growth regulators". Thesis, De Montfort University, 2000. http://hdl.handle.net/2086/13254.

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Plant growth regulators have a vital role in plant growth and development. The cellular response to these regulators depends on the presence and the action of specific receptors. The plant growth regulators and their receptors act together in complexes which determine the final effects of the plant growth regulators. In the research reported here, emphasis has been given to the regulation of the activity of the receptors themselves. The regulation of the N-l-naphthylphthalamic acid (N~A) receptor through phosphorylation and dephosphorylation and the regulation of the auxin binding protein (ABP) through gene manipulation have been investigated. NPA, an auxin transport inhibitor, was found to bind specifically to a crude membrane preparation from sugar beet seedling leaf cell suspension cultures. The in vitro binding was optimal at pH 4.5 and 4?C. Binding parameters for NP A binding were determined by Scatchard analysis. The dissociation constant (Kd) and binding protein concentration were found to be 1.71 x 10-7 mol dm-3 and 220 pmoles g-I membrane protein respectively. It was found that the amount of specific 3H-NPA binding was significantly increased by adding Mg2+ A TP to the binding assay solution; treatment of membrane preparations with acid phosphatase, prior to the NP A binding assay, resulted in lower specific binding. A TP activation and phosphatase inactivation were culture stage dependent. Although a considerable effect could be detected when using cells from day 8 (representing the linear phase), the same treatment did not alter the binding if cells from day I (representing lag phase) or day 14 (representing the stationary phase) were used. These observations have strongly highlighted the possible involvement of a phosphorylation and dephosphorylation mechanism in vivo in the regulation of the activity of the NP A receptor. High phosphatase activity was found in the supernatant, but not in the membrane pellet, after 50,000 g centrifugation. The presence of a membrane-bound auxin receptor, ABP, was demonstrated by Scatchard analysis in sugar beet seedlings. The Kd value and the receptor concentration were found to be 2.15 x 10-6 mol dm-3 and 68 pmoles g-I membrane protein. The protein could be solubilised either with the detergent Triton X-I 00 or by acetone-washing, with a recovery of about 40%. An acetone-solubilised ABP preparation could be partially purified by DEAE-Sephacel ion exchange chromatography, NAA-linked AH-Sepharose 4B affmity chromatography or Sephadex G-200 gel filtration. The recovery after any of these chromatographic treatments was very low so that successive chromatography for further purification was unsuccessful. The low level of detectable binding after purification resulted mainly from the low abundance of ABP in the plant material. Non-radioactive labelling and detection techniques were used to show that an ABP-probe hybridized to sugar beet genomic DNA during dot blotting. The present study has indicated that receptor activity could be regulated by a phosphorylation and dephosphorylation mechanism in plants. The investigation has also suggested that the effect of plant growth regulators on plant development could be regulated through the manipulation of the expression of their receptor genes.

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30

Rodpothong, Patsarin, e n/a. "Host-specific Nod factor requirements for nodulation of Lotus species by Mesorhizobium loti". University of Otago. Department of Microbiology & Immunology, 2008. http://adt.otago.ac.nz./public/adt-NZDU20080910.113419.

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Mesorhizobium loti possesses a symbiosis island (ICEMlSym[R7A]) that confers upon the bacterium the ability to form a symbiotic association with legumes of the genus Lotus. Nodulation (nod, nol and noe) genes located on the ICEMlSym[R7A] encode enzymes that are responsible for the production of a species-specific signaling molecule, named Nod factor. Perception of Nod factors by plant receptors triggers several plant responses and facilitates bacterial invasion, leading to the formation of root nodules. The studies in this thesis aimed to examine the impact of various structural components of the M. loti Nod factor on host specificity and recognition within Lotus species. The minimal gene requirement for eliciting nodule development on Lotus plants was also determined. The M. loti strain R7A Nod factor has a backbone of five N-acetyl-D-glucosamine (GlcNAc) residues. The non-reducing terminal GlcNAc residue carries an acyl chain of either a vaccenic acid (C[18:1]) or palmitic acid (C[16:0]), a carbamoyl group and a methyl group, while an acetylfucose is present at the reducing terminus. Analysis of loss-of-function [Delta]nodZ and [Delta]nolL mutants showed that the acetylfucose at the reducing terminus was required for efficient nodulation of Lotus species, especially during the initiation of infection threads and for induction of symbiotic gene, NIN. Upon inoculation with R7A[Delta]nodZ, nodulation of Lotus corniculatus and L. filicaulis was significantly delayed and reduced, while only a delay in the onset of nodulation was observed with L. japonicus. Interestingly, nodulation of L. burttii induced by R7A[Delta]nodZ was as efficient as that induced by R7A. Hence, the absolute requirement for the acetylfucose during nodulation was host-dependent. In planta complementation and domain swap experiments using transgenic L. japonicus nfr1 and nfr5 mutants were employed to investigate the role of the reducing terminal acetylfucose in the perception of Nod factor. Nodulation of complemented L. japonicus nfr1 and nfr5 mutants inoculated with R7A[Delta]nodZ was poor, whereas similar plants inoculated with R7A nodulated well. This suggests that the in planta complementation was inefficient and as a result accentuated the effect of the acetylfucose on the Nod factor recognition. The responses of recombinant inbred lines (RILs) derived from a cross between L. filicaulis and L. japonicus to inoculation with strain R7A[Delta]nodZ suggested that at least two genetic loci on chromosome 4, in addition to the Nfr1 and Nfr5 genes, contribute to Nod factor perception and in particular the host-specific recognition of the acetylfucose, This suggests the involvement of multiple receptors or a receptor with multiple components in the perception of Nod factors. A gain-of-function study demonstrated that the presence of nodulation genes alone in nonsymbiotic mesorhizobia was sufficient to induce nodulation and bacteroid formation on Lotus plants, indicating that no other ICEMlSym[R7A] genes were required for infection thread formation or bacterial release. Nodulation assays of four Lotus species indicated host-specific requirements for nodulation genes. The presence of the nodA, nodC, nodD1, nodD2, nodZ, noeL and nolK genes was sufficient to permit nodulation of L. burttii, but was insufficient to induce nodulation of L. japonicus, L. corniculatus and L. filicaulis. The importance of the carbamoyl and methyl groups, and the influence of Nod factor concentration during nodulation were also implicated in this study. A model for the Nod factor perception in Lotus was proposed.

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31

Harding, Michael W. "Genetic and molecular analyses of avirulence in the phytopathogenic fungus Magnaporthe grisea". Diss., The University of Arizona, 2004. http://hdl.handle.net/10150/280608.

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Magnaporthe grisea is a filamentous ascomycete fungus that causes blast disease on rice and other grasses. Blast is a serious deterrent to rice production and negatively affects production of other cereals, forage crops and economically important grasses. The primary means of blast disease management involves the development and implementation of genetically resistant plants. Understanding the molecular basis of plant resistance is the foundation for the development of unique and durable plant protection. The results presented here focus on genes in the rice blast fungus called avirulence genes that encode molecules acting as effectors of host resistance. Until recently, two avirulence loci had been shown to induce resistance in rice cultivar Maratelli. This study gives an update on the current status of one, the AVR1-MARA locus, and describes a new Maratelli avirulence locus that is not allelic to AVR1-MARA or AVR2-MARA. Additionally, evidence is given that indicates a genome rearrangement is responsible for generation of the newly described avirulence locus. Genetic data, hybridization results and DNA sequence analysis demonstrate the translocation of a large AT-rich fragment from one chromosomal location to another. Molecular detection of the translocation is demonstrated by hybridization of certain AVR1-MARA markers that only follow the avirulent phenotype in strains after the rearrangement. The rearrangement is detectable genetically, as the avirulent phenotype controlled at this locus segregates independently from progenitor strains that also contain a single Maratelli-specific avirulence gene. CHEF electrophoretic separation of chromosome-sized DNA shows that the AT rich sequences are located on one of the larger M. grisea chromosomes both before and after cross 4134. Hybridization of CHEF blots indicates that two chromosomes may have been involved in a translocation, however a reorganization of chromosome 2 cannot be ruled out. A homing enzyme strategy for determining the size of the translocated fragment is described. These results demonstrate an example of genomic plasticity leading to a translocation and creation of a new avirulence locus in the rice blast fungus M. grisea.

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32

To, Kevin S. "Loss of Promoter Methylation is Correlated with mRNA Induction of Senescence Upregulated Gene UGT78D1". Thesis, California State University, Long Beach, 2017. http://pqdtopen.proquest.com/#viewpdf?dispub=10600929.

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Leaf senescence is the final stage of leaf development where older leaves undergo an active degenerative process. This highly coordinated event is characterized by a cascade of differential gene expression resulting in senescence upregulated and senescence downregulated genes. Cytosine methylation, a mechanism of epigenetic control, has been shown to play a role in regulating gene expression. Gene body cytosine methylation is correlated with transcriptional activation while promoter cytosine methylation is correlated with transcriptional repression. Evidence from previous work suggests CG methylation (^mCG) in promoter regions plays a role in repressing gene expression and that a correlation between demethylation and mRNA induction is most likely within 500 bp up- and downstream of TSSs. The purpose of this study is to investigate the correlation between promoter cytosine methylation and transcriptional repression by identifying potential cytosine methylation-regulated senescence upregulated genes (CMR-SURGs). Four candidate CMR-SURGs were identified from previously generated RNA-seq data and an online cytosine methylome. We hypothesized that the four CMR-SURGs would display a correlation between mRNA induction and loss of promoter ^mCG. mRNA expression was measured by real-time qPCR, and cytosine methylation was quantified by bisulfite treatment of genomic DNA followed by PCR, cloning, and sequencing of PCR products. These data however, showed that only UGT78D1 displayed a negative correlation between promoter cytosine methylation and age-related mRNA induction.

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33

Bradley, Bernadette. "The granule-bound starch synthase genes of wheat". Thesis, Bradley, Bernadette (2003) The granule-bound starch synthase genes of wheat. PhD thesis, Murdoch University, 2003. https://researchrepository.murdoch.edu.au/id/eprint/442/.

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Wheat (Triticum aestivum) is the world's most widely grown and economically important crop. It is both a staple food for humans and a raw material for many industrial processes. World trade in wheat is important for economic stability and an ability to grow wheat is a valuable national resource. Wheat is Australia's major crop with an annual production of about 23 million tonnes. One-quarter of this is used domestically and meets all of Australia's requirements; the remaining three-quarters is exported. Therefore, Australia's wheat industry provides both the national staple food source and the basis of an export industry worth almost 2 billion dollars. There is great potential for further genetic improvement of wheat, not only by increasing grain yields by improved resistance to pathogens and tolerance to adverse environmental conditions, but also by improving functional quality. For example, one can change the physical properties of the storage components, starch and protein, to increase their usefulness in conventional applications and for novel uses. Some examples of the physical properties of starch affecting its uses are, the large starch granules from wheat that are suitable to make carbonless copy paper (Bligh, 1999), the small starch granules from rice that are used as a fat substitute because the a comparable mouthfeel, the high-amylose starches that have film-forming properties desirable for fried food coating batters and some forms of plastics, and the low-amylose starch that swells more in water and can be used for soft foods such as Asian noodles. Continued improvement of wheat is vital to meet the quantity and quality demands of the local and international wheat markets. One specialty market for Western Australian wheat, is export to Japan and South Korea for the production of Japanese white salted Udon noodles, an export market worth more than $200M pa (Garlinge, 1996). Udon noodles have specific eating qualities including a light, creamy, uniform colour, a 'bright' appearance to the noodle, a soft but elastic texture to the noodle, and a smooth 'mouthfeel', all of which result from the quality of the wheat flour starch they are made from(Crosbie, 1991; Batey et al., 1997; Zeng et al., 1997). The Australian Standard White Noodle (ASWN) wheat that Australia exports to produce Udon noodles is soft-grained, white coloured, contains between 9.5% and 11.5% protein, and produces flour of fine particle size with little starch damage (V. Reck, DAWA, pers. comm.). The flour also has good starch-swelling characteristics, moderate dough strength and good dough extensibility. The good starch-swelling characteristics of the flour result, for the most-part, from containing relatively less of the starch amylose than other varieties (22-23% compared to 25%), a property controlled by the GBSS genes (Nelson and Rines, 1962; Garlinge, 1996). When less amylose is present in the starch granule as it is heated in water, the amylopectin matrix inside the granule can swell, causing the finished Udon noodle to be soft. When more amylose is present in the starch granule, the amylopectin matrix cannot swell as much, and the finished noodle is too hard to have the desired 'mouthfeel' of an Udon noodle. The amylose fraction of starch is produced by the granule-bound starch synthase (GBSS) enzymes, encoded by the GBSS genes. The overall aim of the research described in this thesis was to investigate the genomic organization of the GBSS genes of wheat. Since the GBSS genes influence wheat starch quality, an understanding of the action of these genes is needed for future improvement of starch quality in noodle-wheats. There are three loci for GBSS genes in wheat, and these are located on chromosomes 4A, 7A and 7D. Both wild-type alleles and non-functional 'null' alleles exist at each locus. At the start of the project, these alleles had not been sequenced and the molecular differences between the alleles were not known. Other GBSS alleles were also thought to exist in Australian varieties that had yet to be identified and characterised. GBSS genes from a selection of wheat varieties, and from all three GBSS loci, were sequenced searching for DNA polymorphisms that were different between the different alleles. If any DNA polymorphisms were found to result in GBSS protein sequence differences, or differences in GBSS enzyme expression, they could influence the functional characteristics of the starch. Identifying GBSS allelic variants would enable molecular markers to be developed to detect the alleles and investigate their potential effects upon starch quality. Different PCR-based methods and one non-PCR-based method were used to investigate the genomic organization of the GBSS genes in a selection of genetically diverse wheat varieties. The 31 wheat varieties studied included noodle-wheat varieties from the ASWN classification, varieties with similar genetic background to ASWN wheat varieties but of unsuitable quality for noodle production, unrelated varieties of Australian Standard White wheat, and were compared with those 'Chinese Spring' varieties described in the literature. Most of the varieties are grown in the Western Australian wheatbelt and southern regions, either for export and the production of Asian noodles, or for the production of domestic baked-goods. A 500bp section from the middle of the GBSS genes was amplified, from a selection of wheat varieties, and sequenced to search for polymorphisms. Twenty-one single nucleotide differences were found between genes at the three loci and two PCR-based tests were designed to validate these differences as Single Nucleotide Polymorphisms (SNPs). A novel microsatellite was also discovered in intron 4 of the GBSS 7A genes. This (TGCCG)n microsatellite was variable between wheat varieties and so defines a novel allele in the Australian germplasm present at a frequency of 40%. A PCR-based test was developed to identify this variable locus. However, the new GBSS allele was not linked to Flour Swelling Volume (FSV) quality properties. The variable microsatellite locus Xsun1 (Shariflou and Sharp, 1999) in the 3' untranslated region of the GBSS genes and linked to GBSS allelic variation was used to genotype a wheat breeding population for its GBSS status. The population (n=69) contained combinations of wild-type and null alleles at the 7A and 7D loci. Once genotyped using this marker, the GBSS alleles were assessed for possible likage to starch variation. Although the trend suggested that the presence ofnull alleles increased the FSV, the size of the population tested was too small for the differences in FSV between wild-type and partially-waxy wheats to be statistically significant. The linkage between the Xsun1 microsatellite variation and the (TGCCG)n microsatellite variation from intron 4 of the GBSS 7A genes was studied. By combining these two microsatellite loci, which are closely linked to the GBSS coding regions, GBSS genes at the 7A locus could be separated into 12 allelic groups. Although none of these groups could be linked to specific changes in starch qualities, they can be analysed further for functional differences. In order to access a larger section of the GBSS genes using PCR, new PCR primers were designed and optimized to amplify segments of the GBSS genes. Primers for GBSS genes tend to generate many PCR products, but many of these were shown to be non-specific. These artifacts could be reduced by increasing the annealing temperatures, and non-specific priming was repressed by the presence of the second primer in the PCR reaction. Using one primer set, a nearly 2000bp segment of the GBSS 7A genes from wheat varieties 'Kulin' and 'Eradu' was amplified and sequenced. These sequences indicated the presence of single nucleotide differences that resulted in changed amino acids in the protein when compared to published GBSS sequences. The sequencing should be repeated to validate this result, which indicates that these are novel alleles, but it does suggest that allelic variation for GBSS exists in Australian wheat varieties and that these alleles are different from those described internationally. The EcoR1, HindIII and BamH1 restriction enzyme sites surrounding the GBSS genes were identified using Southern hybridisation. This provided the potential to access the entire GBSS gene, including the promoter and untranscribed regions, by restriction enzyme mediated cloning of genomic DNA. However, attempts to clone the genomic GBSS genes into both plasmid and viral vectors were not successful.The potential existence of pseudogene copies of the GBSS genes in the wheat genome was investigated using both PCR and Southern hybridisation techniques. No evidence of GBSS pseudogenes was found, and this suggests that the wheat genome does not contain them. This result was unexpected since organisms with large genomes, such as wheat, normally contain repeated sequences and pseudogenes. However, the absence of repeated sequences and pseudogenes should be beneficial in molecular wheat breeding because it suggests that there will not be interference from non-coding GBSS sequences in identifying molecular markers to GBSS genes. The GBSS genes present in Australian wheat varieties were similar enough to those described internationally that Australian breeders can make full use of research and molecular tests for GBSS genes developed elsewhere. However, enough variation exists between overseas and domestic varieties to warrant further investigation of novel GBSS alleles in domestic wheat, which may relate to differences in functionality.

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34

Bradley, Bernadette. "The granule-bound starch synthase genes of wheat". Murdoch University, 2003. http://wwwlib.murdoch.edu.au/adt/browse/view/adt-MU20040706.142601.

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Abstract (sommario):

Wheat (Triticum aestivum) is the worlds most widely grown and economically important crop. It is both a staple food for humans and a raw material for many industrial processes. World trade in wheat is important for economic stability and an ability to grow wheat is a valuable national resource. Wheat is Australias major crop with an annual production of about 23 million tonnes. One-quarter of this is used domestically and meets all of Australias requirements; the remaining three-quarters is exported. Therefore, Australias wheat industry provides both the national staple food source and the basis of an export industry worth almost 2 billion dollars. There is great potential for further genetic improvement of wheat, not only by increasing grain yields by improved resistance to pathogens and tolerance to adverse environmental conditions, but also by improving functional quality. For example, one can change the physical properties of the storage components, starch and protein, to increase their usefulness in conventional applications and for novel uses. Some examples of the physical properties of starch affecting its uses are, the large starch granules from wheat that are suitable to make carbonless copy paper (Bligh, 1999), the small starch granules from rice that are used as a fat substitute because the a comparable mouthfeel, the high-amylose starches that have film-forming properties desirable for fried food coating batters and some forms of plastics, and the low-amylose starch that swells more in water and can be used for soft foods such as Asian noodles. Continued improvement of wheat is vital to meet the quantity and quality demands of the local and international wheat markets. One specialty market for Western Australian wheat, is export to Japan and South Korea for the production of Japanese white salted Udon noodles, an export market worth more than $200M pa (Garlinge, 1996). Udon noodles have specific eating qualities including a light, creamy, uniform colour, a bright appearance to the noodle, a soft but elastic texture to the noodle, and a smooth mouthfeel, all of which result from the quality of the wheat flour starch they are made from(Crosbie, 1991; Batey et al., 1997; Zeng et al., 1997). The Australian Standard White Noodle (ASWN) wheat that Australia exports to produce Udon noodles is soft-grained, white coloured, contains between 9.5% and 11.5% protein, and produces flour of fine particle size with little starch damage (V. Reck, DAWA, pers. comm.). The flour also has good starch-swelling characteristics, moderate dough strength and good dough extensibility. The good starch-swelling characteristics of the flour result, for the most-part, from containing relatively less of the starch amylose than other varieties (22-23% compared to 25%), a property controlled by the GBSS genes (Nelson and Rines, 1962; Garlinge, 1996). When less amylose is present in the starch granule as it is heated in water, the amylopectin matrix inside the granule can swell, causing the finished Udon noodle to be soft. When more amylose is present in the starch granule, the amylopectin matrix cannot swell as much, and the finished noodle is too hard to have the desired mouthfeel of an Udon noodle. The amylose fraction of starch is produced by the granule-bound starch synthase (GBSS) enzymes, encoded by the GBSS genes. The overall aim of the research described in this thesis was to investigate the genomic organization of the GBSS genes of wheat. Since the GBSS genes influence wheat starch quality, an understanding of the action of these genes is needed for future improvement of starch quality in noodle-wheats. There are three loci for GBSS genes in wheat, and these are located on chromosomes 4A, 7A and 7D. Both wild-type alleles and non-functional null alleles exist at each locus. At the start of the project, these alleles had not been sequenced and the molecular differences between the alleles were not known. Other GBSS alleles were also thought to exist in Australian varieties that had yet to be identified and characterised. GBSS genes from a selection of wheat varieties, and from all three GBSS loci, were sequenced searching for DNA polymorphisms that were different between the different alleles. If any DNA polymorphisms were found to result in GBSS protein sequence differences, or differences in GBSS enzyme expression, they could influence the functional characteristics of the starch. Identifying GBSS allelic variants would enable molecular markers to be developed to detect the alleles and investigate their potential effects upon starch quality. Different PCR-based methods and one non-PCR-based method were used to investigate the genomic organization of the GBSS genes in a selection of genetically diverse wheat varieties. The 31 wheat varieties studied included noodle-wheat varieties from the ASWN classification, varieties with similar genetic background to ASWN wheat varieties but of unsuitable quality for noodle production, unrelated varieties of Australian Standard White wheat, and were compared with those Chinese Spring varieties described in the literature. Most of the varieties are grown in the Western Australian wheatbelt and southern regions, either for export and the production of Asian noodles, or for the production of domestic baked-goods. A 500bp section from the middle of the GBSS genes was amplified, from a selection of wheat varieties, and sequenced to search for polymorphisms. Twenty-one single nucleotide differences were found between genes at the three loci and two PCR-based tests were designed to validate these differences as Single Nucleotide Polymorphisms (SNPs). A novel microsatellite was also discovered in intron 4 of the GBSS 7A genes. This (TGCCG)n microsatellite was variable between wheat varieties and so defines a novel allele in the Australian germplasm present at a frequency of 40%. A PCR-based test was developed to identify this variable locus. However, the new GBSS allele was not linked to Flour Swelling Volume (FSV) quality properties. The variable microsatellite locus Xsun1 (Shariflou and Sharp, 1999) in the 3 untranslated region of the GBSS genes and linked to GBSS allelic variation was used to genotype a wheat breeding population for its GBSS status. The population (n=69) contained combinations of wild-type and null alleles at the 7A and 7D loci. Once genotyped using this marker, the GBSS alleles were assessed for possible likage to starch variation. Although the trend suggested that the presence ofnull alleles increased the FSV, the size of the population tested was too small for the differences in FSV between wild-type and partially-waxy wheats to be statistically significant. The linkage between the Xsun1 microsatellite variation and the (TGCCG)n microsatellite variation from intron 4 of the GBSS 7A genes was studied. By combining these two microsatellite loci, which are closely linked to the GBSS coding regions, GBSS genes at the 7A locus could be separated into 12 allelic groups. Although none of these groups could be linked to specific changes in starch qualities, they can be analysed further for functional differences. In order to access a larger section of the GBSS genes using PCR, new PCR primers were designed and optimized to amplify segments of the GBSS genes. Primers for GBSS genes tend to generate many PCR products, but many of these were shown to be non-specific. These artifacts could be reduced by increasing the annealing temperatures, and non-specific priming was repressed by the presence of the second primer in the PCR reaction. Using one primer set, a nearly 2000bp segment of the GBSS 7A genes from wheat varieties Kulin and Eradu was amplified and sequenced. These sequences indicated the presence of single nucleotide differences that resulted in changed amino acids in the protein when compared to published GBSS sequences. The sequencing should be repeated to validate this result, which indicates that these are novel alleles, but it does suggest that allelic variation for GBSS exists in Australian wheat varieties and that these alleles are different from those described internationally. The EcoR1, HindIII and BamH1 restriction enzyme sites surrounding the GBSS genes were identified using Southern hybridisation. This provided the potential to access the entire GBSS gene, including the promoter and untranscribed regions, by restriction enzyme mediated cloning of genomic DNA. However, attempts to clone the genomic GBSS genes into both plasmid and viral vectors were not successful.The potential existence of pseudogene copies of the GBSS genes in the wheat genome was investigated using both PCR and Southern hybridisation techniques. No evidence of GBSS pseudogenes was found, and this suggests that the wheat genome does not contain them. This result was unexpected since organisms with large genomes, such as wheat, normally contain repeated sequences and pseudogenes. However, the absence of repeated sequences and pseudogenes should be beneficial in molecular wheat breeding because it suggests that there will not be interference from non-coding GBSS sequences in identifying molecular markers to GBSS genes. The GBSS genes present in Australian wheat varieties were similar enough to those described internationally that Australian breeders can make full use of research and molecular tests for GBSS genes developed elsewhere. However, enough variation exists between overseas and domestic varieties to warrant further investigation of novel GBSS alleles in domestic wheat, which may relate to differences in functionality.

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35

Storey, Benjamin 1973. "AQX : a novel gene in plant ubiquinone biosynthesis". Thesis, McGill University, 2002. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=80882.

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C. elegans worms with mutations in the gene CLK-1 develop slowly and have an extended lifespan. CLK-1 encodes a mitochondrial protein that is responsible for the hydroxylation of 5-demethoxyubiquinone (DMQ), the penultimate step of ubiquinone (Coenzyme-Q or UQ) biosynthesis. Structural homologues of CLK-1 are found in mammals, fruit flies, yeast and some types of bacteria. Interestingly, however, there is no structural homologue of CLK-1 in the Arabidopsis genome and no plant homologue can be found in other sequence databases. Yeast with the CLK-1 homologue COQ7 deleted fail to grow on non-fermentable carbon sources. To identify a plant functional homologue of COQ7/CLK-1, an Arabidopsis cDNA expression library was screened for complementation of a yeast coq7 deletion mutant. A clone was identified that rescued the coq7 respiratory deficiency. Although the sequence of the encoded protein has no structural similarity to proteins in the COQ7/CLK-1 family, it contains a monooxygenase/hydroxylase domain that has sequence similarity with the E. coli DMQ hydroxylase encoded by the UBIF gene. Like the structural homologues of COQ7/CLK-1 found in other eukaryotes, the gene (AQX for 'Alternate Quinone monooXygenase') contains a likely mitochondrial targeting presequence at its N-terminus. HPLC analysis of quinone extracts from rescued cog7 strains does not detect ubiquinone, but instead shows another peak that may be DMQ. It is likely that AQX does not hydroxylate yeast DMQ effectively enough to generate detectable levels of UQ. A unique pathway for UQ biosynthesis in plants is proposed that is defined by AQX and Arabidopsis genes identified on the basis of homology to known E. coli and yeast UQ biosynthesis genes.

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36

Drager, Robert Gray. "Molecular cloning of spinach chloroplast DNA isolated by alkaline lysis". PDXScholar, 1987. https://pdxscholar.library.pdx.edu/open_access_etds/3747.

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Chloroplast genomes of land plants show conservation of structure and gene arrangement. The spinach chloroplast genome is comprised of a covalently closed. circular DNA molecule of 150 kilobases and is typical of these plants. Approximately 20% of the proteins found in the spinach chloroplast are encoded by the chloroplast genome and translated on chloroplast ribosomes. The remainder are encoded on chromosomes in the nucleus, translated on cytoplasmic ribosomes and transported into the chloroplast. Spinach chloroplast DNA was isolated from crude 2 chloroplast preparations by a new method. Chloroplasts were lysed with alkaline sodium dodecyl sulfate, contaminating macromolecules precipitated with acidified potassium acetate and plastid DNA was purified by phenol:chloroform extraction and ethanol:ammonium acetate precipitation. The yield was approximately 50 ug chloroplast DNA per 100 grams leaf material. The DNA consisted of 10% circular molecules and 90% linear molecules. The chloroplast DNA was digested with restriction enzyme PstI and the fragments were cloned into the plasmid vector pUC9. Several recombinant plasmids were isolated and the chloroplast DNA inserts identified. The recombinant plasmid pRD105 containing the PstI #5 fragment was subjected to further investigation. The ClaI restriction sites of the PstI #5 fragment were mapped and the insert was subcloned into the plasmid vector pGEM4, which bears bacteriophage SP6 and T7 RNA polymerase promoter sequences.

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37

Wang, Tina Y. "Determining the Fate of Hybridized Genomes in the Allopolyploid Brassica napus". DigitalCommons@CalPoly, 2010. https://digitalcommons.calpoly.edu/theses/358.

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Polyploidy is widely acknowledged as a widespread mechanism in the evolution and speciation of the majority of flowering plants. Allopolyploid forms through interspecific hybridization and whole genome duplication. While allopolyploids may display increased vigor relative to their progenitors, they can also face challenges to fertility following hybridization. Genetic changes in allopolyploids result from recombination between the hybridized subgenomes, which can influence phenotype and ultimately determine fitness of future generations. To study dynamic changes that follow allopolyploid formation, Brassica napus lineages were derived by hybridizing Brassica oleracea and Brassica rapa. Two lineages of B. napus were analyzed for genetic and phenotypic changes in the S2, S7, and S12 generations. Although these lineages were genetically identical at the time of hybridization, divergence was apparent by the S2 generation. There was a significant increase in sequence loss across generations within both lineages. Four of six generations from both lineages displayed no significant differences to each other in sequence loss relative to the parental generation. In both lineages, there was a bias towards losing sequences from the B. olereacea subgenome. Some individual plants showed novel phenotypes; however, there was no correlation between the examined genetic changes and selected phenotypes.

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38

Campeol, Nadia. "Detection of markers in a low-density region of the barley (Hordeum vulgare L.) genome and their effects on the mapping of quantitative traits". Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape10/PQDD_0002/MQ44137.pdf.

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39

Sheldon, Candice Claire. "Hammerhead mediated self-cleavage of plant pathogenic RNAs /". Title page, contents and summary only, 1992. http://web4.library.adelaide.edu.au/theses/09PH/09phs544.pdf.

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40

Kassa, Mulualem Tamiru. "Molecular analysis of genetic diversity in dometicated pigeonpea (Cajanus cajan (L.) Millsp.) and wild relatives". Thesis, Rhodes University, 2011. http://hdl.handle.net/10962/d1003773.

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Cajanus cajan (L.) Millsp. (Pigeonpea) belongs to the Leguminosae genus Cajanus which is composed of 34 species. Pigeonpea is the only cultivated member of the genus, while the remaining species are wild relatives belonging mainly to the secondary gene pool. DNA sequence data from the nuclear ITS region and the chloroplast trnL-F spacer were utilized to investigate the phylogenetic relationships between Cajanus and five other allied genera in the subtribe Cajaninae. This study revealed the non-monophyly of Cajanus and Rhynchosia and supported the monophyly of Eriosema and Flemingia, but more sampling ,especially from the large genera of Rhynchosia and Eriosema, is recommend to adequately test the hypothesis of generic monophyly. The phylogenetic relationships within the genus Cajanus resolved Cajanus scarabaeoides (L.) Thouars as the most basal species in the Cajanus clade. The study also utilized Single Nucleotide Polymorphism (SNP) markers derived from low copy orthologous genes and genotyped using the high throughput SNP-OPA Illumina golden gate assay. The aim was to understand phylogenetic and domestication history, genetic structure, patterns of genetic diversity, gene flow and historical hybridization between Cajanus cajan (pigeonpea) and wild relatives. The neighbor-joining tree resolved well-supported clusters, which reflect the distinctiveness of species and congruence with their geographical origin. It supported the ITS based phylogeny and resolved C. scarabaeoides as basal to the Cajanus clade. The phylogenetic signal and genetic signatures revealed insights into the domestication history of pigeonpea. Our results supported Cajanus cajanifolius as the presumed progenitor of pigeonpea and we speculate that for pigeonpea there was a single major domestication event in India. Genetic admixture and historical hybridization were evident between pigeonpea and wild relatives. Abundant allelic variation and genetic diversity was found in the wild relatives, with the exception of wild species from Australia, as compared to the domesticated pigeonpea. There was a reduction of about 75% in genetic polymorphism in domesticated pigeonpea as compared to the wild relatives, indicating a severe “domestication bottleneck” during pigeonpea domestication. We discovered SNP markers associated with disease resistance (NBS-LRR) loci. The SNPs were mined in a comparison of BAC-end sequences (BES) of C. cajan and amplicons of the wild species, C. scarabaeoides. A total of ~3000 SNPs were identified from 304 BES. These SNPs could potentially be used in constructing a genetic map and for marker assisted breeding.

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41

Das, Sanjeev. "Subcellular Localization of Tobacco SABP2 under Normal and Stress Conditions". Digital Commons @ East Tennessee State University, 2020. https://dc.etsu.edu/honors/569.

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Subcellular Localization of Tobacco SABP2 under Normal and Stress Conditions Salicylic acid (SA), a phytohormone, plays an important role in plant physiology. SA mediated innate immune pathway is an important pathway for plant immunity against pathogens. Plants resisting pathogen infection synthesize higher levels of Methyl Salicylate (MeSA), which is then converted to SA by the esterase activity of Salicylic Acid Binding Protein 2 (SABP2). The high level of the converted SA leads to enhanced pathogen resistance. The study of subcellular localization of a protein is critical in explaining its potential biochemical functions. SABP2 tagged with eGFP was expressed transiently in Nicotiana benthamiana leaves. The SABP2-eGFP expressing leaves were challenged with bacterial and viral pathogens and observed under confocal microscopy. Fluorescent signals were seen throughout the cell and more concentrated towards the cell periphery. To verify the localization, mCherry fluorescent organelle markers with specific targeting sequences were used. The results indicate that the SABP2 is likely a cytoplasmic protein, and there is no change in its localization upon infection by plant pathogens.

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42

Devisetty, Upendra Kumar. "Molecular investigation of RAD51 and DMC1 homoeologous genes of hexaploid wheat (Triticum aetivum L.)". Thesis, University of Nottingham, 2010. http://eprints.nottingham.ac.uk/13340/.

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Meiotic recombination in eukaryotes requires two orthologues of the E. coli RecA proteins, Rad51 and Dmc1. Both genes play an important role in the binding of single strand DNA, homology search, strand invasion and strand exchange resulting in Holliday junctions which are resolved into crossovers or non-crossovers events. Even though both genes are well characterized in a variety of organisms including plants, very little information is available from hexaploid wheat. In most diploid plant species, deletion of either the RAD51 or DMC1 orthologues leads to sterility but wheat being a polyploid, offers a unique opportunity to examine the effects of the deletion of specific homoeologue, while maintaining a degree of fertility. The transcript expression profiling of RAD51 and DMC1 genes in Arabidopsis, rice and wheat using available microarray databases indicated higher levels of expression in mitotically and meiotically active tissues compared to other tissues. However, the possible function of the DMC1 gene in mitotic-active tissues needs to be investigated further. Previously cDNA sequences of TaRAD51 and TaDMCl of hexaploid wheat were cloned and reported. In this study, it has been demonstrated that the reported TaRAD51A1 and TaRAD51A2 cDNA sequences are (D) and (A) homoeologues of TaRAD51 respectively and TaDMCl cDNA sequence is (D) homoeologue of the TaDMC1. This study also found that the amino acid sequences and evolutionary relationships of RAD51 and DMC1 cDNA homoeologues are highly conserved across eukaryotes. Functional characterization of TaRAD51 and TaDMCl gene homoeologues was undertaken in planta using Forward Genetics, Reverse Genetics and Complementation methods. Forward and Reverse Genetic screening of a subset of a Highbury mutant population could not identify any mutants that have deletions in TaRAD51 and TaDMC1 genes. However, Reverse Genetics screening of Paragon mutant population identified mutant lines that tested as having deletions for all the three homoeologues of TaRAD51 and TaDMCl. However, most likely due to high mutational load and a deleterious phenotype, only a few mutant lines survived. Phenotypic and cytogenetic analysis indicated the probable functional redundancy of TaRAD51 (B) homoeologue in meiosis, although the unknown size of the deletion and limited phenotype makes it impossible to completely certain of this. The single mutants for TaDMC1 (B) and (D) indicated a reduction in pollen viability and ear fertility compared to wild-type. The cytological examination of these mutants indicated low levels of abnormal diakinesis, resulting in the formation of dyads. However, the single mutants were still able to produce normal tetrads. This suggests that there is a possible dosage effect of these homoeologues in hexaploid wheat. Unless deletion lines for the (A) and (D) homoeologues of TaRAD51 and (B) homoeologue of TaDMC1 can be recovered and characterized the above assumptions will remain inconclusive. The results of complementation assays using over-expressing CaMV35S::TaRAD51(D)±GFP constructs demonstrated a very low (-14% and -2%, respectively, with +GFP and -OFP constructs) functional complementation in terms of seed set compared to 0% in homozygous Atrad51 mutants. One explanation of these results is that the wheat genes are not complete functional orthologues for the inactivated Arabidopsis genes. The functional complementation experiments could not be performed for TaDMC1 gene because of time limitation, although the transformants were produced in AtDMC1/atdmc1 background. Finally, overexpression of the TaRAD51 gene suggests 2-fold increase in genetic distances in Arabidopsis using CaMV35S::TaRAD51(D) construct. This was done by crossing the appropriate transformant with fluorescent tetrad lines. However the results need to be confirmed by a large scale analysis.

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43

Bonnardeaux, Yumiko Graciela. "Seed dormancy in barley (Hordeum vulgare L.) : comparative genomics, quantitative trait loci analysis and molecular genetics". University of Western Australia. Faculty of Natural and Agricultural Sciences, 2008. http://theses.library.uwa.edu.au/adt-WU2009.0019.

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[Truncated abstract] Under prolonged wet and damp conditions, barley grain with low dormancy can germinate precociously, a condition known as preharvest sprouting that causes a number of detrimental effects in grain quality. In particular, preharvest sprouting renders the grain unsuitable for malting. The aim of this study was to take a genomics approach to identify and characterise candidate genes that could be linked to the control of seed dormancy in barley. This thesis developed a bioinformatic strategy that exploited the availability of gene sequences with functional evidence in the model species of Arabidopsis and rice. The bioinformatic strategy integrated phenotypic data (QTL data) and comparative genomics for a targeted approach in identifying candidate genes with a high probability of having a conserved function in cereals. This bioinformatic study identified two candidate genes ERA1 and ABI2 with strong evidence for a role in seed dormancy based on their function in Arabidopsis in abscisic acid (ABA) signal transduction and their co-location to seed dormancy QTLs in Arabidopsis, rice and wheat. In order to establish whether the candidate genes mapped to seed dormancy QTLs in barley, QTL analyses were performed on a double haploid population, not previously studied, developed from a cross between Stirling, a major Australian malting cultivar, and Harrington, a major Canadian malting cultivar. This cross was specifically chosen for this study, as elucidation of chromosomal regions associated with seed dormancy in the background of a malting cultivar would make a significant contribution for the malting industry. '...' Identification of a seed dormancy QTL on the long arm of 3H, in a region syntenic to the wheat chromosome locations of ESTS aligning to the ERA1 and ABI2 genes, laid the foundation for physical and genetic mapping of the candidate genes to investigate whether the genes co-located to the QTL on 3H. Physical mapping of the genes in wheat barley addition lines confirmed their positions on the long arm of 3H. Genetic mapping of the ERA1 gene was performed using a CAPS marker developed in this thesis. The genetic mapping of the ERA1 gene did not place the gene within either of the minor QTLs on 3HL, although segregation distortion may have influenced the map position of this gene. Further investigation is required to resolve the positioning of the ERA1 and ABI2 genes in relation to the 3H seed dormancy QTL. The main outcomes of this study have been 1) identification of candidate genes for further study; 2) identification of QTLs on the long arm of 3H that were previously unknown; 3) demonstration of the potential differences in dormancy that can be achieved through the use of specific gene combinations, highlighting the importance of minor genes and the epistatic interactions that occur between them and; 4) the development of a CAPS marker for the ERA1 gene, which can be used to track the gene in barley breeding programs to observe its association with important agronomic traits. This thesis also pioneered the implementation of several new technologies including multiplex-ready PCR (Hayden et al. 2008) for fluorescencebased SSR genotyping and QTLNetwork (Yang et al. 2008) for statistical analysis of QTLs. Seed dormancy is a complex trait and is likely to involve the interplay of a number of genes that have a role in other developmental and regulatory processes.

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44

Harris, Darby M. "MOLECULAR AND CHEMICAL DISSECTION OF CELLULOSE BIOSYNTHESIS IN PLANTS". UKnowledge, 2011. http://uknowledge.uky.edu/pss_etds/3.

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Plant cell walls are complex structures that must not only constrain cellular turgor pressure but also allow for structural modification during the dynamic processes of cell division and anisotropic expansion. Cell walls are composed of highly glycosylated proteins and polysaccharides, including pectin, hemicellulose and cellulose. The primary cell wall polysaccharide is cellulose, a polymer composed of high molecular weight !- 1,4-glucan chains. Although cellulose is the most abundant biopolymer on Earth, there is still a lot to learn about its biosynthesis and regulation. This research began by applying a variety of analytical techniques in an attempt to understand differences in cell wall composition and cellulose structure within the plant body, between different plant species and as a result of acclimation by the plant to different environmental conditions. Next, a number of different Arabidopsis thaliana lines possessing mutations affecting cell wall biosynthesis were analyzed for changes in cellulose structure (crystallinity) and biomass saccharification efficiency. One of these mutants, isoxaben resistance1-2 (ixr1- 2), which contains a point mutation in the C-terminal transmembrane region (TMR) of cellulose synthase 3 (CESA3), exhibited a 34% lower biomass crystallinity index and a 151% improvement in saccharification efficiency relative to that of wild-type. The culmination of this research began with a chemical screen that identified the molecule quinoxyphen as a primary cell wall cellulose biosynthesis inhibitor. By forward genetics, a semi-dominant mutant showing strong resistance to quinoxyphen named aegeus was identified in A. thaliana and the resistance locus mapped to a point mutation in the TMR of CESA1. cesa1aegeus occurs in a similar location to that of cesa3ixr1-2, illustrating both subunit specificity and commonality of resistance locus. These drug resistant CESA TMR mutants are dwarfed and have aberrant cellulose deposition. High-resolution synchrotron X-ray diffraction and 13C solid-state nuclear magnetic resonance spectroscopy analysis of cellulose produced from cesa1aegeus, cesa3ixr1-2 and the double mutant shows a reduction in cellulose microfibril width and an increase in mobility of the interior glucan chains of the cellulose microfibril relative to wild-type. These data demonstrate the importance of the TMR region of CESA1 and CESA3 for the arrangement of glucan chains into a crystalline cellulose microfibril in primary cell walls.

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45

Rendell, Sarah. "Population genetic structure of Faidherbia albida (Del.) A. Chev. (Leguminosae, Mimosoideae)". Thesis, University of Oxford, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.299160.

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46

Nuthikattu, Saivageethi. "Diverse mechanisms of Athila retrotransposon epigenetic silencing in Arabidopsis thaliana". The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1417685369.

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47

Gouws, Liezel Michelle, e Jens Kossmann. "The molecular analysis of the effects of lumichrome as a plant growth promoting substance". Thesis, Stellenbosch : University Stellenbosch, 2009. http://hdl.handle.net/10019.1/4825.

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PhD
Dissertation presented for the degree of Doctor of Philosophy at Stellenbosch University
Embargo(30)lift date 2009-12-31 plt 2010
ENGLISH ABSTRACT: Through powerful signal molecules, rhizobacteria affect fundamental processes in plants. In recent years, a number of novel rhizobial molecules have been identified that positively affect plant growth and development. Previous studies have shown that Sinorhizobium meliloti, which form symbiotic relationships with leguminous plants, increases CO2 availability by enhancing root respiration in alfalfa. The active compound was identified as lumichrome, a previously unrecognized rhizosphere signal molecule that has been shown to promote plant growth in various studies. Lumichrome is a common breakdown product of riboflavin and produced by both chemical and biological factors. Various studies on lumichrome have proven its growth promoting effect in the interaction with plants. The mechanism through which lumichrome increases plant growth remains to be clarified. This study provides new insight into the molecular effects of the plant growth promoter lumichrome on the root metabolism of plants. The main aim of the work presented in this thesis was to investigate the molecular mechanism of the plant growth promoting substance lumichrome in the roots of the model plants Lotus japonicus and Solanum lycopersicon (tomato). To asses the impact of lumichrome on the root metabolism of Lotus japonicus and tomato and identify key genes involved in the growth stimulation, a comprehensive profile of differentially expressed genes, proteins and metabolites was compiled. As the effects of lumichrome as a plant growth promoter have not previously been tested on Lotus japonicus and tomato, basic growth studies were completed to determine if lumichrome indeed elicits plant growth at nanomolar concentrations, as was proven in numerous previous studies. Both Lotus japonicus and tomato showed significant increases in root biomass when treated with 5 nM of lumichrome. The treatment with lumichrome caused complex changes in gene expression. Generally, transcript profiling showed that the categories that were predominantly affected by lumichrome in both Lotus and tomato, were genes associated with RNA regulation of transcription and signaling, protein synthesis/degradation/modification and stress and defence. Proteomic studies revealed that the majority of the differentially expressed proteins were down-regulated. Lumichrome seems to largely influence proteins involved in protein folding and down-regulate proteins involved in glycolysis. Proteomics studies revealed that GS1 (Lotus) and GAPDH (Lotus and tomato) were present in lower abundance in lumichrome treated roots, therefore targeted analysis utilizing northern blots, western blots and the measurement of enzyme activities were completed to determine and verify their specific role in the lumichrome mediated growth promotion. The results indicated that GAPDH and GS1 seem to be under post-translational modification. The influence of lumichrome on the metabolome of Lotus roots was immense, however minute in tomato roots. The knowledge gained in the parallel analyses of both Lotus japonicus and tomato aided us in finding key genes involved in the growth stimulation. Overall, one of the most significant observations was that for the first time to our knowledge, six genes related to defence and pathogen responses were identified that are concurrently expressed in both Lotus and tomato. Through identifying a small number of genes involved in mediating the growth stimulation, these can be used for their functional analysis in the future, using reverse genetics to provide more insight into the molecular mechanisms that are triggered by lumichrome as a plant growth promoter.
AFRIKAANSE OPSOMMING: Deur kragtige sein-molekules, beïnvloed rhizobakterieë basiese prosesse in plante. In die laaste jare is ŉ aantal nuwe molekules, afkomstig van rhizobakterieë, geidentifiseer wat plantgroei en ontwikkeling positief beïnvloed. Voorafgaande studies het bewys dat Sinorhizobium meliloti, wat simbiotiese verhoudings met peulplante aangaan, die beskikbaarheid van CO2 vermeerder deur wortel respirasie in alfalfa te verhoog. Die aktiewe komponent is as lumikroom geidentifiseer, 'n vroeë onerkenbare risosfeer sein-molekule, wat deur vorige studies bewys is dat dit plantgroei stimuleer. Lumikroom is ŉ algemene afbreekproduk van riboflavin en word geproduseer deur chemiese en biologiese faktore. Verskeie studies op lumikroom het bewys dat dit 'n groei stimuleerende effek het op die groei van plante as dit daarmee in wisselwerking tree. Die meganisme waarmee lumikroom plante groei verhoog, is nog nie opgeklaar nie. Hierdie studie verleen nuwe insigte in die molekulêre effekte van die plantgroei stimuleerende molekuul lumikroom op die wortel metabolisme van plante. Die hoofdoel van die werk wat voorgestel word in hierdie tesis, was om die molekulêre meganisme van die plantgroei stimuleerende stof, genaamd lumikroom, in die wortels van die model plante Lotus japonicus en Solanum lycopersicon (tamatie), te ondersoek. Om die uitwerking van lumikroom op die wortel metabolisme van Lotus japonicus en tamatie te bepaal, asook sleutelgene wat betrokke is by die groei stimulasie te identifiseer, is 'n breedvoerige profiel van differensiële uitgedrukte gene, proteïne en metaboliete saamgestel. Die effekte van lumikroom as 'n plantgroei stimuleerende stof is nog nooit op Lotus japonicus en tamatie getoets nie. Om díe rede is eers basiese plantgroei studies gedoen, om vas te stel of lumikroom inderdaad plantgroei teen nanomolare konsentrasies stimuleer, soos in vele voorafgaande studies bevestig is. Beide Lotus japonicus en tamatie het aansienlike verhogings in wortel biomassa getoon as dit met 5 nM lumikroom behandel is. Die behandeling van plante met lumikroom het komplekse veranderinge in geen-uitdrukking veroorsaak. Oor die algemeen het die transkrip-profiele gewys dat die kategorieë wat die meeste geraak is deur lumikroom behandeling, in beide Lotus en tamatie, gene was wat geassosieer word met RNS regulasie van transkripsie en sein-netwerke, proteïen sintese/degradasie/wysiging en stres en verdedigings prosesse in plante. Proteïen studies het gewys dat daar 'n daling in die meerderheid van die proteïen vlakke was wat differensieël uitgedruk was. Dit blyk dat lumikroom in 'n groot mate proteïene beïnvloed wat betrokke is by proteïen-vouing en veroorsaak dat proteïen vlakke van glikolitiese ensieme daal. Proteïen studies het gewys dat GS1 en GAPDH in laer vlakke teenwoordig was in lumikroom behandelde plante en daarom is 'n meer doelgerigte analiese gedoen deur gebruik te maak van "northern blot", "western blot" en deur die ensiem aktiwiteite te meet om hulle spesifieke rol in die lumikroom bemiddelde groei vas te stel. Die resultate wys daarop dat GAPDH en GS1 mag onder die invloed van na-translasionele verandering wees. Die invloed van lumikroom op die metabolietvlakke was groot in Lotus wortels, maar dit het minder van 'n effek gehad op tamatie wortels. Die kennis wat opgedoen is deur die paralelle analiese van beide Lotus japonicus en tamatie plante help ons om sleutel gene wat betrokke is by groeistimulasie te identifiseer. Een van die betekenisvolste waarnemings van hierdie studie was dat vir die eerste keer, sover ons kennis strek, ses gene wat almal betrekking het tot verdediging en patogene-reaksies, geidentifiseer is wat gelyktydig in beide Lotus en tamatie uitgedruk word. Deur 'n klein aantal gene te identifiseer, wat betrokke is by groeistimulasie, kan die gene in die toekoms vir funksionele analieses gebruik word deur van keerkoppeling-genetika gebruik te maak. Daardeur sal meer insig verkry word in die molekulêre meganisme wat deur lumikroom as 'n plantgroei stof veroorsaak word.

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48

Lindsay, Robert C. "QUANTITATIVE AND MOLECULAR ANALYSIS OF HABITUATION AT THE MAIZE r1 LOCUS". VCU Scholars Compass, 2018. https://scholarscompass.vcu.edu/etd/5655.

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Epigenetics is the study of heritable changes in phenotypes that are not the result of changes in DNA sequence. Examples of epigenetic affecters include methylation changes, chromatin modifications, transcription factors, and RNA-based changes. The molecular mechanisms behind epigenetic changes are not fully understood. Canalization is the buffering of gene expression against environmental changes over time, while habituation is semi-stable expression change over time due to selection. This work characterized the molecular changes associated with the kernel color changes of the R-sc:86-17pale allele at the maize red color1 (r1) locus to determine if the changes are epigenetic in nature. The research; 1) quantified the color differences between the progenitor and habituated sublines; 2) Determined that there are not sequence differences between the progenitor and habituated sublines at the 3` end of the Sc||nc1 gene that could account for changes in seed color; 3) and examined the cytosine methylation patterns at the 3` end of the Sc||nc1 gene of the habituated sublines and the progenitor to determine whether there are methylation differences that correspond with the kernel color changes. Quantification of the kernel colors of the R-sc:86-17pale selection sublines showed that there was a statistically significant difference in kernel color. The identical sequence of the R-sc:86 line and the R-sc:86-17pale Lightest and R-sc:86-17pale Darkest sublines at the 3` end of the Sc||nc1 gene is evidence that the kernel color change is not driven by differences in sequence within the r1 gene. The methylation data suggests that some methylation differences in the R-sc:86-17pale Lightest and R-sc:86-17pale Darkest sublines are present, and suggests that the molecular basis of the kernel color is epigenetic in nature.

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49

Krothapalli, Kartikeya. "Association of plastid lipid metabolism with the activation of systemic acquired resistance in Arabidopsis thaliana". Diss., Manhattan, Kan. : Kansas State University, 2008. http://hdl.handle.net/2097/1058.

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50

Pena, Michelle Mendonça [UNESP]. "DNA Barcoding em Utricularia (Lentibulariaceae)". Universidade Estadual Paulista (UNESP), 2015. http://hdl.handle.net/11449/136705.

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A família Lentibulariaceae Rich. é considerada o maior grupo de plantas carnívoras dentre as angiospermas. Utricularia é o gênero de maior riqueza, com aproximadamente 250 espécies. Diversos estudos de identificação baseados em morfologia foram realizados para a família Lentibulariaceae, porém eles se mostram limitados para determinados grupos de espécies. Com base nisso a aplicação do DNA Barcoding pode ser uma importante alternativa. No presente estudo foram utilizadas sequências de DNA dos espaçadores intergênicos cloroplastidiais trnS-trnG e trnL-trnF e também do gene mitocondrial coxI com o objetivo de testá-las com a abordagem DNA Barcoding na diferenciação intraespecífica, interespecífica e entre as seções do gênero Utricularia. Com base nas matrizes de distâncias, a distância intraespecífica média foi de 0,004 para ambos os marcadores cloroplastidiais e de 0,006 para o gene coxI, a distância interespecífica média foi de 0,260 para trnS-trnG, 0,190 para trnL-trnF, 0,043 para coxI e a distância média entre as seções foi de 0,036, 0,029 e 0,025 para trnS-trnG, trnL-trnF e coxI, respectivamente. A análise baseada na árvore de Neighbor-Joining indicou que a maioria das espécies se agruparam em seções de acordo com o proposto para a filogenia do gênero, formando grupos monofiléticos. A eficácia de discriminação interespecífica foi 82% para trnS-trnG e 61% trnL-trnF, a discriminação intraespecífica foi de 36% para trnS-trnG e 23% para trnL-trnF. O gene mitocondrial coxI apresentou 24% de discriminação inter e intraespecífica, com resolução baixa de espécies na árvores de Neighbor-Joining. Esses resultados demonstram que as regiões cloroplastidiais apresentam informações satisfatórias para separação das espécies em clados que corroboram com a filogenia do grupo e que portanto trnS-trnG e trnL-trnF podem ser considerados bons barcodes para o...
The family Lentibulariaceae Rich. is considered the largest group of carnivorous plants among the angiosperms. Utricularia is the richest genus with approximately 250 species. Several studies based on morphological identification have been published for the family Lentibulariaceae, but they are limited regarding some groups of species. Hence, DNA Barcoding may be an important alternative. The present study used DNA sequences of chloroplast intergenic spacers trnS-trnG and trnL-trnF and also the mitochondrial gene coxI in order to test them with the DNA Barcoding approach to intraspecific, interspecific and between sections differentiation in the Utricularia genus. Based on the distance analyses, the average intraspecific distance was 0.004 for both chloroplast markers and 0.006 for the coxI gene, the average interspecific distance was 0.260 to trnS-trnG, 0.190 to trnL-trnF, 0.043 to coxI and the average distance between sections was 0.036, 0.029 and 0.025 to trnS-trnG, trnL-trnF and coxI, respectively. The analysis based on Neighbor-Joining tree indicated that most species were grouped into sections according to the proposed for the phylogeny of the genus, forming monophyletic groups. The efficacy of interspecies discrimination was 82% to trnS-trnG and 61% to trnL-trnF, intraspecific discrimination was 36% to trnS-trnG and 23% to trnL-trnF. The mitochondrial gene coxI showed 24% of inter and intraspecific discrimination, with low resolution of species on trees Neighbor-Joining. These results demonstrate that the chloroplast regions have satisfactory information to separate species in clades that corroborate the phylogeny of the group and therefore trnS-trnG and trnL-trnF can be considered good barcodes for the Utricularia genus

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