Academic literature on the topic 'DArT-seq'

Fusarium oxysporum f. sp. cubense (Foc) is a soil-borne fungus that causes Fusarium wilt, a destructive plant disease that has resulted in devastating economic losses to banana production worldwide. The fungus has a complex evolutionary history and taxonomic repute and consists of three pathogenic races and at least 24 vegetative compatibility groups (VCGs). Surveys conducted in Asia, Africa, the Sultanate of Oman and Mauritius encountered isolates of F. oxysporum pathogenic to banana that were not compatible to any of the known Foc VCGs. Genetic relatedness between the undescribed and known Foc VCGs were determined using a multi-gene phylogeny and diversity array technology (DArT) sequencing. The presence of putative effector genes, the secreted in xylem (SIX) genes, were also determined. Fourteen novel Foc VCGs and 17 single-member VCGs were identified. The multi-gene tree was congruent with the DArT-seq phylogeny and divided the novel VCGs into three clades. Clustering analysis of the DArT-seq data supported the separation of Foc isolates into eight distinct clusters, with the suite of SIX genes mostly conserved within these clusters. Results from this study indicates that Foc is more diverse than hitherto assumed.

We identified Rph24 as a locus in barley (Hordeum vulgare L.) controlling adult plant resistance (APR) to leaf rust, caused by Puccinia hordei. The locus was previously reported as a quantitative trait locus in barley line ND24260-1 and named qRphND. We crossed ND24260-1 to the leaf-rust-susceptible standard Gus and determined inheritance patterns in the progeny. For the comparative marker frequency analysis (MFA), resistant and susceptible tails of the F2 were genotyped with Diversity Arrays Technology genotyping-by-sequencing (DArT-Seq) markers. The Rph24 locus was positioned at 55.5 centimorgans on chromosome 6H on the DArT-Seq consensus map. Evaluation of F2:3 families confirmed that a single locus from ND24260-1 conferred partial resistance. The haploblock strongly associated with the Rph24 locus was used to estimate the allele frequency in a collection of 282 international barley cultivars. Rph24 was frequently paired with APR locus Rph20 in cultivars displaying high levels of APR to leaf rust. The markers identified in this study for Rph24 should be useful for marker-assisted selection.

Leaf rust (LR) and stripe rust (YR) are important diseases of wheat worldwide. We used 148 recombinant inbred lines (RIL) from the cross of Avocet × Kundan for determining and mapping the genetic basis of adult plant resistance (APR) loci. The population was phenotyped LR and YR for three seasons in field trials conducted in Mexico and genotyped with the diversity arrays technology sequencing (DArT-Seq) and simple sequence repeat markers. The final genetic map was constructed using 2,937 polymorphic markers with an average distance of 1.29 centimorgans between markers. Inclusive composite interval mapping identified two co-located APR quantitative trait loci (QTL) for LR and YR, two LR QTL, and three YR QTL. The co-located resistance QTL on chromosome 1BL corresponded to the pleiotropic APR gene Lr46/Yr29. QLr.cim-2BL, QYr.cim-2AL, and QYr.cim-5AS could be identified as new resistance loci in this population. Lr46/Yr29 contributed 49.5 to 65.1 and 49.2 to 66.1% of LR and YR variations, respectively. The additive interaction between detected QTL showed that LR severities for RIL combining four QTL ranged between 5.3 and 25.8%, whereas the lowest YR severities were for RIL carrying QTL on chromosomes 1BL + 2AL + 6AL. The high-density DArT-Seq markers across chromosomes can be used in fine mapping of the targeted loci and development SNP markers.

Common valerian (Valeriana officinalis L.) is one of the most important medicinal plants, with a mild sedative, nervine, antispasmodic and relaxant effect. Despite a substantial number of studies on this species, the genetic diversity and population structure have not yet been analyzed. Here, we use a next-generation sequencing-based Diversity Array Technology sequencing (DArT-seq) technique to analyze Polish gene bank accessions that originated from wild populations and cultivars. The major and, also, the most astounding result of our work is the low level of observed heterozygosity of individual plants from natural populations, despite the fact that the species is widespread in the studied area. Inbreeding in naturally outcrossing species such as valerian decreases reproductive success. The analysis of the population structure showed the potential presence of a metapopulation in the central part of Poland and the formation of a distinct gene pool in the Bieszczady Mountains. The results also indicate the presence of the cultivated gene pool within wild populations in the region where the species is cultivated for the needs of the pharmaceutical industry, and this could lead to structural and genetic imbalances in wild populations.

Genomic selection has been widely used in terrestrial animals but has had limited application in aquaculture due to relatively high genotyping costs. Genomic information has an important role in improving the prediction accuracy of breeding values, especially for traits that are difficult or expensive to measure. The purposes of this study were to (i) further evaluate the use of genomic information to improve prediction accuracies of breeding values from, (ii) compare different prediction methods (BayesA, BayesCπ and GBLUP) on prediction accuracies in our field data, and (iii) investigate the effects of different SNP marker densities on prediction accuracies of traits in the Portuguese oyster (Crassostrea angulata). The traits studied are all of economic importance and included morphometric traits (shell length, shell width, shell depth, shell weight), edibility traits (tenderness, taste, moisture content), and disease traits (Polydora sp. and Marteilioides chungmuensis). A total of 18,849 single nucleotide polymorphisms were obtained from genotyping by sequencing and used to estimate genetic parameters (heritability and genetic correlation) and the prediction accuracy of genomic selection for these traits. Multi-locus mixed model analysis indicated high estimates of heritability for edibility traits; 0.44 for moisture content, 0.59 for taste, and 0.72 for tenderness. The morphometric traits, shell length, shell width, shell depth and shell weight had estimated genomic heritabilities ranging from 0.28 to 0.55. The genomic heritabilities were relatively low for the disease related traits: Polydora sp. prevalence (0.11) and M. chungmuensis (0.10). Genomic correlations between whole weight and other morphometric traits were from moderate to high and positive (0.58–0.90). However, unfavourably positive genomic correlations were observed between whole weight and the disease traits (0.35–0.37). The genomic best linear unbiased prediction method (GBLUP) showed slightly higher accuracy for the traits studied (0.240–0.794) compared with both BayesA and BayesCπ methods but these differences were not significant. In addition, there is a large potential for using low-density SNP markers for genomic selection in this population at a number of 3000 SNPs. Therefore, there is the prospect to improve morphometric, edibility and disease related traits using genomic information in this species.

The striped catfish Pangasianodon hypophthalmus is an important freshwater fish cultured in many countries where the collection of wild brooders is still widely practiced. Global farming development of this species makes use of significant natural resources that pose challenges for the genetic diversity of striped catfish. Hence, this study aims to conduct a systematic genetic diversity assessment of wild and farmed catfish stocks collected from four major pangasius-farming countries, using a new genotyping by sequencing platform known as DArT-seq technology. Our population genomic analyses using 7263 single-nucleotide polymorphisms (SNPs) after high-quality-control showed that there were two distinct populations of striped catfish in the lower Mekong river: (i) wild catfish from Thailand and (ii) catfish from Cambodia and Vietnam. The genetic diversity was greatest (0.363) in the wild stock from Thailand, but it was lower in farmed and wild stocks in other countries (0.049 to 0.088). The wild stocks were more genetically diverse than the farmed animals (0.103 vs. 0.064). The inbreeding coefficient ranged from 0.004 and 0.109, with the lowest value (−0.499) in the wild animals from Thailand. Molecular inference methods revealed high degree of historical effective population size (1043.9–1258.4), but there was considerable decline in the contemporary estimates in all populations (10.8 to 73.6). Our additional analyses calculating divergent times and migration patterns showed that the wild catfish from Thailand stand out as separate lineages, while those from Cambodia and Vietnam are genetically identical. Our results also indicated that the cultured stock in Bangladesh originated from the lower part of the Mekong river. These findings have significant practical implications in the context of genetic selection and conservation of striped catfish in the region. Collectively, they will contribute to the sustainable development of the striped catfish sector in these countries.

A incorporação de novas ferramentas biotecnológicas aos programas de melhoramento de citros oferece inúmeras possibilidades. Os marcadores DArTTM (Diversity Arrays Technology), combinados à técnica de sequenciamento de última geração, apresentam boa aplicabilidade na construção de mapas genéticos de alta resolução e no mapeamento de QTL (Quantitative Trai Loci). Assim, este estudo teve como objetivo construir um mapa genético integrado de tangor \'Murcott\' e laranja \'Pera\' usando os marcadores moleculares do tipo DArT_seqTM e localizar QTLs para doze caracteres de qualidade de frutos. A partir de um cruzamento controlado entre tangor \'Murcott\' e laranja \'Pera\', realizado no banco de germoplasma de Citros do Centro de Citricultura \"Sylvio Moreira\", Instituto Agronômico de Campinas, localizado em Cordeirópolis-SP, em 1997. Foi obtida uma família de 350 indivíduos híbridos, dos quais 278 foram selecionados para avaliação das características de fruto em 2012. No presente trabalho, esses 278 indivíduos foram genotipados usando os marcadores DArTseqTM. Para construir o mapa integrado foi utilizado o programa OneMap e foram considerados apenas os marcadores que não apresentaram desvio de segregação mendeliana. A razão de verossimilhança foi utilizada para a formação de grupos de ligação, além da informação genômica obtida a partir do genoma sequenciado de Citrus sinensis L. Osbeck disponível em (http://citrus.hzau.edu.cn/orange/index.php). O mapa parcialmente integrado foi composto de 661 marcadores, ligados em 13 grupos, que correspondem ao número haplóide de cromossomos da espécie, com cobertura genômica de 2.774 cM. De acordo com as análises de mapeamento por intervalo composto e os resultados do teste de permutação, um total 19 QTLs foram identificados, tendo em conta as características de fruto analisadas: peso (g), diâmetro (cm), altura (cm), relação diâmetro / altura, espessura da casca (cm), número de gomos, teor de sólidos solúveis (°Brix), acidez titulável (%), rendimento de suco (%), número de sementes, valor do índice tecnológico (IT) e número estimado de frutos por caixa. O mapa genético integrado foi comparado com o genoma (pseudochromosomes) de Citrus sinensis e sintenias foram claramente identificadas. A análise mais aprofundada das regiões genômicas (QTLs) apresentando os maiores valores de LOD score permitiu identificar a presença de genes candidatos que podem estar associados com as características analisadas
The incorporation of new biotechnological tools to citrus breeding programs provides many new possibilities. The DArT markers (Diversity Arrays Technology), combined with Next-Generation Sequencing presents good applicability in the construction of high resolution genetic maps and QTL mapping. This study aimed to construct an integrated genetic map of \'Murcott\' tangor and \'Pera\' sweet orange using the DArTseqTM molecular markers, and localize QTL for twelve fruit quality traits. A controlled cross between \'Murcott\' tangor and \'Pera\' sweet orange was conducted at the Citrus Germplasm Bank at the \"Sylvio Moreira\" Citrus Centre of Agronomic Institute, located in Cordeirópolis-SP in 1997.A family with 350 hybrid individuals was obtained, from which 278 were selected for evaluation of fruit traits in 2012. In this study, the 278 F1 individuals were genotyped using the DArTseqTM markers. To build the integrated map, we used the OneMap program and considered all DArT loci that showed no segregation deviation. The likelihood ratio was used for formation of linkage groups, besides the genomic information obtained from the available Citrus sinensis genome sequence (http://citrus.hzau.edu.cn/orange/index.php). The partially integrated map contained 661 markers linked in 13 linkage groups, with genomic coverage of 2,774 cM, the map is saturated and represent the species haploid chromosome number. According to the analyses using \"Composite Interval Mapping\" (CIM) and the results of the permutation test, a total of 19 QTL were identified for the 12 fruits characteristics analyzed: diameter (cm), height (cm), ratio of H/D, weight (g), rind thickness (cm), segments per fruit, total soluble solids ((°Brix), Acidity (%), Juice content (%), number of seeds, ratio of total soluble solids /acidity and number of fruits per box. The genome sequence (pseudochromosomes) of Citrus sinensis L. Osbeck was compared to the genetic map, and sinteny was clearly identified. Further analysis of the map regions with the highest LOD score enabled the identification of the presence of genes that could be associated with the characteristics. The genome sequences allowed identification of genes that may respond for phenotypic traits in Citrus

O conhecimento da diversidade genética e da estrutura populacional das variedades mantidas em bancos de germoplasma é de fundamental importância para sua efetiva utilização em programas de melhoramento. O mapeamento por associação, também conhecido como mapeamento por desequilíbrio de ligação, é um dos principais métodos para relacionar genes e alelos às características de interesse, através da co-segregação de marcadores genéticos polimórficos com os genes envolvidos na variação das características em estudo. O Banco de Germoplasma de Arroz do Departamento de Genética da ESALQ contém 192 acessos japoneses que foram estudados com o objetivo de entender sua diversidade, estruturação genética e determinar a associação genômica de caracteres agronômicos relacionados a produção de grãos. A caracterização molecular foi conduzida através da tecnologia DArT-seq, que gerou dados de marcadores SNPs (single-nucleotide polymorphism) e silico DArTs. Em seguida, após a filtragem, 5.578 SNPs de alta qualidade foram utilizados para calcular as estimativas de diversidade no pacote hierfstat e a estrutura do painel de acessos através da análise discriminante de componentes principais (DAPC), que consiste em determinar existência de cluster em um grupo de genótipos em que não há informação a priori sobre existência de grupos. A diversidade genética nos acessos foi evidenciada pelo valor de heterozigosidade esperada (HS) (0,0279) e a estruturação foi evidenciada pela formação de três subgrupos. O mapeamento associativo foi realizado com o uso do pacote GAPIT, sendo considerados seis caracteres: número de dias para florescimento (NDF), estatura de planta (EP), comprimento da panícula (CP), peso de parcela (PP), massa de mil grãos (MMG) e CICLO, bem como 24.266 marcadores silico DArTs e 1.965 marcadores SNPs. Foram detectadas um total de 113 associações significativas genótipo-fenótipo (P<0,001) quando utilizado marcadores silico DArTs em todas as seis características analisadas e, um total de 21 associações significativas genótipo-fenótipo (P<0,001) quando utilizado marcadores SNPs para apenas quatro das seis características analisadas: EP, CICLO, MMG e PP. Considerando-se os 113 silico DArTs associados significativamente na análise, 90 foram localizados em regiões intergênicas e 23 foram localizados dentro de genes. Enquanto que, dos 21 SNPs significativos, 11 foram localizados em regiões intergênicas e 10 foram localizados dentro de genes. A informação gerada neste estudo foi útil para testar associações ao longo do genoma do arroz. O modelo linear misto (MLM) empregado no mapeamento associativo acredita-se ter conseguido controlar eficientemente os falsos positivos no mapeamento utilizando os marcadores SNPs. As informações geradas neste estudo servem de base para avaliações mais aprofundadas, utilizando o conjunto de marcadores significativos como ponto de partida para determinação dos genes mais importantes para a produtividade em arroz.
The knowledge of the genetic diversity and population structure of varieties maintained in germplasm banks is crucial for their effective use in breeding programs. Association mapping, also known as linkage disequilibrium mapping, is one of the main methods for relating genes and alleles to the characteristics of interest, through the co-segregation of polymorphic genetic markers with the genes involved in the variation of the characteristics under study. The Rice Germplasm Bank of the Department of Genetics of ESALQ contains 192 Japanese accessions that were studied with the purpose of understanding its diversity, genetic structuring and determining the genomic association of agronomic traits related to grain production. The molecular characterization was conducted by DArTseq technology, which generated data of SNPs (single-nucleotide polymorphism) markers and silico DArTs. Then, after filtering, 5,578 high-quality SNPs were used to calculate the diversity estimates in hierfstat package and the accession panel structure through discriminant analysis of principal components (DAPC), which consists of determining the cluster existence in a group of genotypes where there is no a priori information about the existence of groups. The genetic diversity in the accessions was evidenced by the expected heterozygosity value (HS) (0.0279) and the population structure was evidenced by the formation of three clusters. The association mapping was performed using the GAPIT package, considering six characters: number of days for flowering (NDF), plant height (EP), panicle length (CP), plot weight (PP), mass of thousand grains (MMG) and CYCLE, as well as 24.266 silico DArTs markers and 1.965 SNPs markers. We detected a total of 113 significant associations genotype-phenotype (P <0.001) when used silico DArTs markers in all six analyzed characteristics and a total of 21 significant associations genotype-phenotype (P<0.001) when used SNPs markers for only four of the six analyzed characteristics: EP, CYCLE, MMG and PP. Considering the 113 silico DArTs significantly associated in the analysis, 90 were located in intergenic regions and 23 were localized within genes. While of the 21 significant SNPs, 11 were located in intergenic regions and 10 were located within genes. The information generated in this study was useful for testing associations throughout the rice genome. The mixed linear model (MLM) used in association mapping is believed to have been able to efficiently control false positives in the mapping using the SNPs markers. The information generated in this study serves as a basis for further evaluation using the set of significant markers as a starting point for determining the most important genes for rice yield.

Orientador: Marcos Antonio Machado
Resumo: Phytophthora nicotianae Breda de Haan (Phytophthora parasitica Dastur) e Phytophthora citrophthora (Smith & Smith), agentes causadores da gomose e podridão radicular, têm trazido graves danos em viveiros e pomares de citros no mundo inteiro. O Centro de Citricultura Sylvio Moreira/IAC vem realizando um amplo programa de melhoramento genético de citros via cruzamentos dirigidos com relação ao patossistema Phytophthora-citros, em que já foram verificadas diferenças no nível de resistência na progênie do cruzamento entre tangerina Sunki (Citrus sunki) e trifoliata Rubidoux (Poncirus trifoliata), a partir da detecção de genes diferencialmente expressos utilizando microarranjos, identificando transcritos envolvidos na resistência à Phytophthora, e do mapeamento genético. Este trabalho teve como objetivo principal mapear nos grupos de ligação dos mapas de P. trifoliata e C. sunki as regiões genômicas associadas à resistência à Phytophthora parasitica por meio de análise fenotípica (QTLs) e de expressão (eQTLs). Uma população de 110 híbridos, seus genitores e dois porta-enxertos de referência para a citricultura (limão Cravo e citrumelo Swingle), foi enxertada em limão Cravo e estabelecida em casa de vegetação. Cada híbrido foi conduzido com uma única haste e a inoculação foi realizada pelo método do disco a partir do meio de cultura contendo o micélio de P. parasitica, a 10 cm e 15 cm acima da região da enxertia, totalizando duas inoculações por genótipo. As plantas foram mantidas ... (Resumo completo, clicar acesso eletrônico abaixo)
Mestre

Malleefowl are iconic Australian birds that build large mounds to incubate their eggs using external sources of heat. Malleefowl numbers have drastically decreased since European settlement and they are now a nationally threatened species. Their decline is caused by habitat loss and fragmentation; predation by introduced species; inappropriate fire regimes and competition and habitat degradation through overabundant native and introduced herbivores. Climate change is expected to exacerbate these pressures by leading to more frequent and longer periods of high temperatures, reduced precipitation and increased frequency and intensity of wildfires. This thesis aimed to investigate how historic and recent habitat fragmentation and climatic variables influenced Malleefowl on the Eyre Peninsula and how climate change may exacerbate future impacts. The objectives were to assess population trends, investigate landscape genetics, study movement patterns and the influence of habitat variables. These objectives were addressed through a multidisciplinary approach to study discrete Malleefowl populations at study sites located on the Eyre Peninsula in South Australia. To assess population trends and the influence of environmental factors, 24 years of mound-based breeding activity data were modelled. Results showed a widespread and significant decline in Malleefowl breeding activity during the study period, driven by changes in vegetation cover and reduction in soil moisture. High throughput DNA sequencing was used to investigate past dispersal patterns and the effects of recent anthropogenic land cover changes. The results indicate that Malleefowl population structure on the Eyre Peninsula was not homogenous and that habitat fragmentation with subsequent isolation has caused the differentiation of at least two distinct populations. Further, there was preliminary genetic evidence of female dispersal. Solar-powered GPS trackers were used to determine individual movement patterns and the effects of habitat fragmentation and environmental factors. Malleefowl movement was tightly associated with breeding status, with breeding birds staying close to the mound and non-breeding birds disassociating from the mound and moving long distances. Movement was also influenced by patch size and fragmentation, with non-breeding birds in large patches moving further than birds in smaller patches, but Malleefowl were able to persist in small patches and breed successfully for many years. Malleefowl moved less with increasing temperatures. Malleefowl did not use cropping land and they avoided crossing open paddocks. Malleefowl also had high mortality rates with over 66% of tracked individuals dying within a year of trapping, mostly from cat and fox predation. Vegetation surveys were combined with GPS tracking data to investigate whether Malleefowl movement was influenced by vegetation composition or cover. Results indicate that Malleefowl seek out micropatches of tall mallee stands within a mature Eucalyptus matrix – likely as refuges from heat and predators – and that movement is less driven by a preference for plant species, reflecting the fact that Malleefowl have a highly variable and opportunistic diet. In summary, this thesis shows how anthropogenic habitat alteration and changing environmental conditions have reduced breeding activity, restricted movement, dispersal and gene flow of Malleefowl populations on the Eyre Peninsula, with noticeable long-term genetic effects. Further, we can expect climate change to exacerbate all existing pressures and possibly drive Malleefowl closer to extinction. This research provides valuable new information about Malleefowl movement ecology which supports increased efforts to protect even small patches of native vegetation in agricultural matrices and the creation of habitat corridors between patches, as well as the improvements of matrix habitat, to facilitate between-patch movement. This, combined with continued and improved predator-control efforts, may enhance the conditions for future survival of Malleefowl populations, and support biodiversity in general, which is vital when faced with increasing climate change pressures.
Thesis (Ph.D.) -- University of Adelaide, School of Biological Sciences, 2022