Journal articles: 'DArT-seq'

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Meyer, Kate D. "DART-seq: an antibody-free method for global m6A detection." Nature Methods 16, no. 12 (September 23, 2019): 1275–80. http://dx.doi.org/10.1038/s41592-019-0570-0.

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Mostert, Diane, Emmanuel Wicker, Mignon M. de Jager, Saif M. Al Kaabi, Wayne T. O’Neill, Suzy Perry, Chunyu Li, et al. "A Polyphasic Approach Reveals Novel Genotypes and Updates the Genetic Structure of the Banana Fusarium Wilt Pathogen." Microorganisms 10, no. 2 (January 25, 2022): 269. http://dx.doi.org/10.3390/microorganisms10020269.

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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.

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Ziems, Laura A., Lee T. Hickey, Gregory J. Platz, Jerome D. Franckowiak, Peter M. Dracatos, Davinder Singh, and Robert F. Park. "Characterization of Rph24: A Gene Conferring Adult Plant Resistance to Puccinia hordei in Barley." Phytopathology® 107, no. 7 (July 2017): 834–41. http://dx.doi.org/10.1094/phyto-08-16-0295-r.

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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.

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Lin, Hsin-Nan, and Wen-Lian Hsu. "DART: a fast and accurate RNA-seq mapper with a partitioning strategy." Bioinformatics 34, no. 2 (September 5, 2017): 190–97. http://dx.doi.org/10.1093/bioinformatics/btx558.

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Ren, Y., R. P. Singh, B. R. Basnet, C. X. Lan, J. Huerta-Espino, E. S. Lagudah, and L. J. Ponce-Molina. "Identification and Mapping of Adult Plant Resistance Loci to Leaf Rust and Stripe Rust in Common Wheat Cultivar Kundan." Plant Disease 101, no. 3 (March 2017): 456–63. http://dx.doi.org/10.1094/pdis-06-16-0890-re.

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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.

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Boczkowska, Maja, Katarzyna Bączek, Olga Kosakowska, Anna Rucińska, Wiesław Podyma, and Zenon Węglarz. "Genome-Wide Diversity Analysis of Valeriana officinalis L. Using DArT-seq Derived SNP Markers." Agronomy 10, no. 9 (September 7, 2020): 1346. http://dx.doi.org/10.3390/agronomy10091346.

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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.

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Dadjo, Colombe, Aggrey B. Nyende, Nasser Yao, Ngeno Kiplangat, and Achille E. Assogbadjo. "Genome-wide genetic diversity and population structure of Garcinia kola (Heckel) in Benin using DArT-Seq technology." PLOS ONE 15, no. 9 (September 23, 2020): e0238984. http://dx.doi.org/10.1371/journal.pone.0238984.

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Vu, Sang V., Cedric Gondro, Ngoc T. H. Nguyen, Arthur R. Gilmour, Rick Tearle, Wayne Knibb, Michael Dove, In Van Vu, Le Duy Khuong, and Wayne O’Connor. "Prediction Accuracies of Genomic Selection for Nine Commercially Important Traits in the Portuguese Oyster (Crassostrea angulata) Using DArT-Seq Technology." Genes 12, no. 2 (February 1, 2021): 210. http://dx.doi.org/10.3390/genes12020210.

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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.

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Shams, Foyez, Fiona Dyer, Ross Thompson, Richard P. Duncan, Jason D. Thiem, Andrzej Kilian, and Tariq Ezaz. "Application of DArT seq derived SNP tags for comparative genome analysis in fishes; An alternative pipeline using sequence data from a non-traditional model species, Macquaria ambigua." PLOS ONE 14, no. 12 (December 12, 2019): e0226365. http://dx.doi.org/10.1371/journal.pone.0226365.

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Vu, Nguyen Thanh, Tran Thi Thuy Ha, Vo Thi Bich Thuy, Vu Thi Trang, and Nguyen Hong Nguyen. "Population Genomic Analyses of Wild and Farmed Striped Catfish Pangasianodon Hypophthalmus in the Lower Mekong River." Journal of Marine Science and Engineering 8, no. 6 (June 25, 2020): 471. http://dx.doi.org/10.3390/jmse8060471.

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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.

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Bączek, Katarzyna Barbara, Olga Kosakowska, Maja Boczkowska, Paulina Bolc, Rafał Chmielecki, Ewelina Pióro-Jabrucka, Kavana Raj, and Zenon Węglarz. "Intraspecific Variability of Wild-Growing Common Valerian (Valeriana officinalis L.)." Plants 11, no. 24 (December 9, 2022): 3455. http://dx.doi.org/10.3390/plants11243455.

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Common valerian (Valeriana officinalis L.) is an important medicinal plant revealing sedative, hypotensive, anti-spasmodic and anxiolytic activity. The purpose of the study was to determine the intraspecific variability of the common valerian growing wild in Poland and the ‘Lubelski’ landrace, as to their developmental traits, chemical composition and selected genetic parameters. Both wild-growing populations (19) and the landrace (1) were evaluated under ex situ conditions. Observations of the underground organs parameters, both developmental and chemical (according to the European Pharmacopoeia) were carried out in the first year of the plant’s development, while the characteristics of the aboveground organs, followed by the sowing value of seeds (according to the International Seed Testing Association)—in the second year. The genetic analyses were performed using the NGS-DArT-seq method. Results indicate the presence of five different gene pools covering the regions of population’s origin, with a gene flow within and between them. A high level of developmental and chemical variabilities among the wild-growing populations was noticed, however without a clear relation to the region of the origin. The mass of underground organs ranged from 107.4 to 403.6 g FW × plant−1 with the content of sesquiterpenic acids at the level of 0.004–0.094%. Population no 18 was distinguished by the highest content of sesquiterpenic acids and the relatively high mass of underground organs, followed by the admixture of the gene pool, typical for the ‘Lubelski’ landrace. Unlike the ‘Lubelski’ landrace, the wild-growing populations were characterized by a high amount of an essential oils (3.90 to 10.04 mL/kg), which may be promising from the perspective of their potential use. In turn, the sowing value of the seeds obtained from the populations, expressed as the germinability, was rather low (25.25–62.25%).

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Marone, Daniela, Monica Rodriguez, Sergio Saia, Roberto Papa, Domenico Rau, Ivano Pecorella, Giovanni Laidò, et al. "Genome-Wide Association Mapping of Prostrate/Erect Growth Habit in Winter Durum Wheat." International Journal of Molecular Sciences 21, no. 2 (January 8, 2020): 394. http://dx.doi.org/10.3390/ijms21020394.

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By selecting for prostrate growth habit of the juvenile phase of the cycle, durum wheat cultivars could be developed with improved competitive ability against weeds, and better soil coverage to reduce the soil water lost by evaporation. A panel of 184 durum wheat (Triticum turgidum subsp. durum) genotypes, previously genotyped with DArT-seq markers, was used to perform association mapping analysis of prostrate/erect growth habit trait and to identify candidate genes. Phenotypic data of plant growth habit were recorded during three consecutive growing seasons (2014–2016), two different growth conditions (field trial and greenhouse) and two sowing periods (autumn and spring). Genome-wide association study revealed significant marker-trait associations, twelve of which were specific for a single environment/year, 4 consistent in two environments, and two MTAs for the LSmeans were identified across all environments, on chromosomes 2B and 5A. The co-localization of some MTAs identified in this study with known vernalization and photoperiod genes demonstrated that the sensitivity to vernalization and photoperiod response are actually not only key components of spring/winter growth habit, but they play also an important role in defining the magnitude of the tiller angle during the tillering stage. Many zinc-finger transcription factors, such as C2H2 or CCCH-domain zinc finger proteins, known to be involved in plant growth habit and in leaf angle regulation were found as among the most likely candidate genes. The highest numbers of candidate genes putatively related to the trait were found on chromosomes 3A, 4B, 5A and 6A. Moreover, a bioinformatic approach has been considered to search for functional ortholog genes in wheat by using the sequence of rice and barley tiller angle-related genes. The information generated could be used to improve the understanding of the mechanisms that regulate the prostrate/erect growth habit in wheat and the adaptive potential of durum wheat under resource-limited environmental conditions.

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De Vlaminck, Iwijn, Mridusmita Saikia, Philip Burnham, Sara Keshavjee, Michael Wang, Michael Heyang, Pablo Moral-Lopez, Meleana Hinchman, Charles Danko, and John Parker. "DART-seq." Protocol Exchange, 2019. http://dx.doi.org/10.1038/protex.2018.118.

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Zhang, Ao, Shan Chen, Zhenhai Cui, Yubo Liu, Yuan Guan, Shuang Yang, Jingtao Qu, et al. "Genomic prediction of drought tolerance during seedling stage in maize using low-cost molecular markers." Euphytica 218, no. 11 (October 8, 2022). http://dx.doi.org/10.1007/s10681-022-03103-y.

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AbstractDrought tolerance in maize is a complex and polygenic trait, especially in the seedling stage. In plant breeding, complex genetic traits can be improved by genomic selection (GS), which has become a practical and effective breeding tool. In the present study, a natural maize population named Northeast China core population (NCCP) consisting of 379 inbred lines were genotyped with diversity arrays technology (DArT) and genotyping-by-sequencing (GBS) platforms. Target traits of seedling emergence rate (ER), seedling plant height (SPH), and grain yield (GY) were evaluated under two natural drought stress environments in northeast China. Adequate genetic variations were observed for all the target traits, but they were divergent across environments. Similarly, the heritability of the target trait also varied across years and environments, the heritabilities in 2019 (0.88, 0.82, 0.85 for ER, SPH, GY) were higher than those in 2020 (0.65, 0.53, 0.33) and cross-2-years (0.32, 0.26, 0.33). In total, three marker datasets, 11,865 SilicoDArT markers obtained from the DArT-seq platform, 7837 SNPs obtained from the DArT-seq platform, and 91,003 SNPs obtained from the GBS platform, were used for GS analysis after quality control. The results of phylogenetic trees showed that broad genetic diversity existed in the NCCP population. Genomic prediction results showed that the average prediction accuracies estimated using the DArT SNP dataset under the two-fold cross-validation scheme were 0.27, 0.19, and 0.33, for ER, SPH, and GY, respectively. The result of SilicoDArT is close to the SNPs from DArT-seq, those were 0.26, 0.22, and 0.33. For the trait with lower heritability, the prediction accuracy can be improved using the dataset filtered by linkage disequilibrium. For the same trait, the prediction accuracies estimated with two DArT marker datasets were consistently higher than that estimated with the GBS SNP dataset under the same genotyping cost. The prediction accuracy was improved by controlling population structure and marker quality, even though the marker density was reduced. The prediction accuracies were improved by more than 30% using the significant-associated SNPs. Due to the complexity of drought tolerance under the natural stress environments, multiple years of data need to be accumulated to improve prediction accuracy by reducing genotype-by-environment interaction. Modeling genotype-by-environment interaction into genomic prediction needs to be further developed for improving drought tolerance in maize. The results obtained from the present study provides valuable pathway for improving drought tolerance in maize using GS.

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Nguyen, Nguyen H., H. K. A. Premachandra, Andrzej Kilian, and Wayne Knibb. "Genomic prediction using DArT-Seq technology for yellowtail kingfish Seriola lalandi." BMC Genomics 19, no. 1 (January 30, 2018). http://dx.doi.org/10.1186/s12864-018-4493-4.

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Chen, Tianqing, Piyada Alisha Tantasawat, Wei Wang, Xu Gao, and Liyi Zhang. "Population structure of Chinese southwest wheat germplasms resistant to stripe rust and powdery mildew using the DArT-seq technique." Ciência Rural 48, no. 4 (April 16, 2018). http://dx.doi.org/10.1590/0103-8478cr20160066.

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ABSTRACT: Understanding genetic variability in existing wheat accessions is critical for collection, conservation and use of wheat germplasms. In this study, 138 Chinese southwest wheat accessions were investigated by genotyping using two resistance gene makers (Pm21 and Yr26) and DArT-seq technique. Finally, about 50% cultivars (lines) amplified the specific allele for the Yr26 gene (Gwm11) and 40.6% for the Pm21 gene (SCAR1265). By DArT-seq analysis, 30,485 markers (6486 SNPs and 23999 DArTs) were obtained with mean polymorphic information content (PIC) value 0.33 and 0.28 for DArT and SNP marker, respectively. The mean Dice genetic similarity coefficient (GS) was 0.72. Two consistent groups of wheat varieties were identified using principal coordinate analysis (PCoA) at the level of both the chromosome 6AS and the whole-genome, respectively. Group I was composed of non-6VS/6AL translocation lines of different origins, while Group II was composed of 6VS/6AL translocation (T6VS/6AL) lines, most of which carried the Yr26 and Pm21 genes and originated from Guizhou. Besides, a model-based population structure analysis revealed extensive admixture and further divided these wheat accessions into six subgroups (SG1, SG2, SG3, SG4, SG5 and SG6), based on their origin, pedigree or disease resistance. This information is useful for wheat breeding in southwestern China and association mapping for disease resistance using these wheat germplasms in future.

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Dracatos, Peter M., Rouja Haghdoust, Ravi P. Singh, Julio Huerta Espino, Charles W. Barnes, Kerrie Forrest, Matthew Hayden, Rients E. Niks, Robert F. Park, and Davinder Singh. "High-Density Mapping of Triple Rust Resistance in Barley Using DArT-Seq Markers." Frontiers in Plant Science 10 (April 26, 2019). http://dx.doi.org/10.3389/fpls.2019.00467.

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Bükücü, Şakir Burak, Mehmet Sütyemez, Sina Kefayati, Aibibula Paizila, Abdulqader Jighly, and Salih Kafkas. "Major QTL with pleiotropic effects controlling time of leaf budburst and flowering-related traits in walnut (Juglans regia L.)." Scientific Reports 10, no. 1 (September 16, 2020). http://dx.doi.org/10.1038/s41598-020-71809-x.

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Abstract Breeding studies in walnut (Juglans regia L.) are usually time consuming due to the long juvenile period and therefore, this study aimed to determine markers associated with time of leaf budburst and flowering-related traits by performing a genome-wide association study (GWAS). We investigated genotypic variation and its association with time of leaf budburst and flowering-related traits in 188 walnut accessions. Phenotypic data was obtained from 13 different traits during 3 consecutive years. We used DArT-seq for genotyping with a total of 33,519 (14,761 SNP and 18,758 DArT) markers for genome-wide associations to identify marker underlying these traits. Significant correlations were determined among the 13 different traits. Linkage disequilibrium decayed very quickly in walnut in comparison with other plants. Sixteen quantitative trait loci (QTL) with major effects (R2 between 0.08 and 0.23) were found to be associated with a minimum of two phenotypic traits each. Of these QTL, QTL05 had the maximum number of associated traits (seven). Our study is GWAS for time of leaf budburst and flowering-related traits in Juglans regia L. and has a strong potential to efficiently implement the identified QTL in walnut breeding programs.

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Malebe, MP, NIK Mphangwe, AA Myburg, and Z. Apostolides. "Assessment of genome-wide DArT-seq markers for tea Camellia sinensis (L.) O. Kuntze germplasm analysis." Tree Genetics & Genomes 15, no. 4 (June 4, 2019). http://dx.doi.org/10.1007/s11295-019-1358-1.

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Muchira, Nicoleta, Kahiu Ngugi, Lydia N. Wamalwa, Millicent Avosa, Wiliter Chepkorir, Eric Manyasa, Desterio Nyamongo, and Damaris A. Odeny. "Genotypic Variation in Cultivated and Wild Sorghum Genotypes in Response to Striga hermonthica Infestation." Frontiers in Plant Science 12 (July 8, 2021). http://dx.doi.org/10.3389/fpls.2021.671984.

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Striga hermonthica is the most important parasitic weed in sub-Saharan Africa and remains one of the most devastating biotic factors affecting sorghum production in the western regions of Kenya. Farmers have traditionally managed Striga using cultural methods, but the most effective and practical solution to poor smallholder farmers is to develop Striga-resistant varieties. This study was undertaken with the aim of identifying new sources of resistance to Striga in comparison with the conventional sources as standard checks. We evaluated 64 sorghum genotypes consisting of wild relatives, landraces, improved varieties, and fourth filial generation (F4) progenies in both a field trial and a pot trial. Data were collected for days to 50% flowering (DTF), dry panicle weight (DPW, g), plant height (PH, cm), yield (YLD, t ha−1), 100-grain weight (HGW, g), overall disease score (ODS), overall pest score (OPS), area under Striga number progress curve (ASNPC), maximum above-ground Striga (NSmax), and number of Striga-forming capsules (NSFC) at relevant stages. Genetic diversity and hybridity confirmation was determined using Diversity Arrays Technology sequencing (DArT-seq). Residual heterosis for HGW and NSmax was calculated as the percent increase or decrease in performance of F4 crossover midparent (MP). The top 10 best yielding genotypes were predominantly F4 crosses in both experiments, all of which yielded better than resistant checks, except FRAMIDA in the field trial and HAKIKA in the pot trial. Five F4 progenies (ICSVIII IN × E36-1, LANDIWHITE × B35, B35 × E36-1, F6YQ212 × B35, and ICSVIII IN × LODOKA) recorded some of the highest HGW in both trials revealing their stability in good performance. Three genotypes (F6YQ212, GBK045827, and F6YQ212xB35) and one check (SRN39) were among the most resistant to Striga in both trials. SNPs generated from DArT-seq grouped the genotypes into three major clusters, with all resistant checks grouping in the same cluster except N13. We identified more resistant and high-yielding genotypes than the conventional checks, especially among the F4 crosses, which should be promoted for adoption by farmers. Future studies will need to look for more diverse sources of Striga resistance and pyramid different mechanisms of resistance into farmer-preferred varieties to enhance the durability of Striga resistance in the fields of farmers.

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Vikram, Prashant, Cynthia Ortiz, S. Singh, and Sukhwinder Singh. "Genetic analysis revealed a quantitative trait loci (QTL2A.K) on short arm of chromosome 2A associated with yellow rust resistance in wheat (Triticum aestivum L.)." Indian Journal of Genetics and Plant Breeding (The) 80, no. 03 (September 22, 2020). http://dx.doi.org/10.31742/ijgpb.80.3.1.

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Yellow rust, caused by Puccinia striiformis, is one of the most devastating diseases in wheat. A synthetic by elite recombinant inbred line (RIL) population derived from a cross, Botnol/Aegilops squarrosa (666)//Kachu was evaluated for yellow rust resistance in two different environments in Mexico. The population was subjected to DArT-seq analysis for an in-depth genetic characterization. A major effect rust resistance QTL (QTL2A.K) explaining up to 45% phenotypic variance was found to be contributed by Kachee, an elite line of International Maize and Wheat Improvement Center (CIMMYT) Mexico. The QTL2A.K was found to be contributed by a segment of 2NS Chromosome of Triticum ventricosum translocated into the short arm of bread wheat chromosome 2A (QTL2A.K). The position of QTL2A.K was confirmed using T. ventricosum specific primer VENTRIUP-LN2. Identified genomic regions are being introgressed in to the popular but susceptible wheat varieties through marker-assisted breeding for enhancing yellow rust resistance.

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Malebe, M. P., R. K. Koech, E. G. N. Mbanjo, S. M. Kamunya, A. A. Myburg, and Z. Apostolides. "Construction of a DArT-seq marker–based genetic linkage map and identification of QTLs for yield in tea (Camellia sinensis (L.) O. Kuntze)." Tree Genetics & Genomes 17, no. 1 (January 27, 2021). http://dx.doi.org/10.1007/s11295-021-01491-1.

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Nguyen, Dung Ho My, Jatupong Ponjarat, Nararat Laopichienpong, Thitipong Panthum, Worapong Singchat, Syed Farhan Ahmad, Ekaphan Kraichak, et al. "Genome-Wide SNP Analysis of Hybrid Clariid Fish Reflects the Existence of Polygenic Sex-Determination in the Lineage." Frontiers in Genetics 13 (February 3, 2022). http://dx.doi.org/10.3389/fgene.2022.789573.

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The African catfish (Clarias gariepinus) may exhibit the co-existence of XX/XY and ZZ/ZW sex-determination systems (SDSs). However, the SDS of African catfish might be influenced by a polygenic sex-determination (PSD) system, comprising multiple independently segregating sex “switch” loci to determine sex within a species. Here, we aimed to detect the existence of PSD using hybrid. The hybrid produced by crossing male African catfish with female bighead catfish (C. macrocephalus, XX/XY) is a good animal model to study SDSs. Determining the SDS of hybrid catfish can help in understanding the interactions between these two complex SDS systems. Using the genotyping-by-sequencing “DART-seq” approach, we detected seven moderately male-linked loci and seventeen female-linked loci across all the examined hybrid specimens. Most of these loci were not sex-linked in the parental species, suggesting that the hybrid exhibits a combination of different alleles. Annotation of the identified sex-linked loci revealed the presence of one female-linked locus homologous with the B4GALNT1 gene, which is involved in the spermatogenesis pathway and hatchability. However, this locus was not sex-linked in the parental species, and the African catfish might also exhibit PSD.

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Singh, Sahadev, Shailendra Singh Gaurav, Neeraj Kumar Vasistha, Uttam Kumar, Arun Kumar Joshi, Vinod Kumar Mishra, Ramesh Chand, and Pushpendra Kumar Gupta. "Genetics of spot blotch resistance in bread wheat (Triticum aestivum L.) using five models for GWAS." Frontiers in Plant Science 13 (January 18, 2023). http://dx.doi.org/10.3389/fpls.2022.1036064.

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Genetic architecture of resistance to spot blotch in wheat was examined using a Genome-Wide Association Study (GWAS) involving an association panel comprising 303 diverse genotypes. The association panel was evaluated at two different locations in India including Banaras Hindu University (BHU), Varanasi (Uttar Pradesh), and Borlaug Institute for South Asia (BISA), Pusa, Samastipur (Bihar) for two consecutive years (2017-2018 and 2018-2019), thus making four environments (E1, BHU 2017-18; E2, BHU 2018-19; E3, PUSA, 2017-18; E4, PUSA, 2018-19). The panel was genotyped for 12,196 SNPs based on DArT-seq (outsourced to DArT Ltd by CIMMYT); these SNPs included 5,400 SNPs, which could not be assigned to individual chromosomes and were therefore, described as unassigned by the vendor. Phenotypic data was recorded on the following three disease-related traits: (i) Area Under Disease Progress Curve (AUDPC), (ii) Incubation Period (IP), and (iii) Lesion Number (LN). GWAS was conducted using each of five different models, which included two single-locus models (CMLM and SUPER) and three multi-locus models (MLMM, FarmCPU, and BLINK). This exercise gave 306 MTAs, but only 89 MTAs (33 for AUDPC, 30 for IP and 26 for LN) including a solitary MTA detected using all the five models and 88 identified using four of the five models (barring SUPER) were considered to be important. These were used for further analysis, which included identification of candidate genes (CGs) and their annotation. A majority of these MTAs were novel. Only 70 of the 89 MTAs were assigned to individual chromosomes; the remaining 19 MTAs belonged to unassigned SNPs, for which chromosomes were not known. Seven MTAs were selected on the basis of minimum P value, number of models, number of environments and location on chromosomes with respect to QTLs reported earlier. These 7 MTAs, which included five main effect MTAs and two for epistatic interactions, were considered to be important for marker-assisted selection (MAS). The present study thus improved our understanding of the genetics of resistance against spot blotch in wheat and provided seven MTAs, which may be used for MAS after due validation.

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Khan, Rao Waqar Ahmad, Rao Sohail Ahmad Khan, Faisal Saeed Awan, Ahmed Akrem, Arslan Iftikhar, Farhana Naureen Anwar, Hind A. S. Alzahrani, Hameed Alsamadany, and Rana Khalid Iqbal. "Genome-wide association studies of seedling quantitative trait loci against salt tolerance in wheat." Frontiers in Genetics 13 (September 7, 2022). http://dx.doi.org/10.3389/fgene.2022.946869.

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Salinity is one of the significant factors in decreasing wheat yield and quality. To counter this, it is necessary to develop salt-tolerant wheat varieties through conventional and advanced molecular techniques. The current study identified quantitative trait loci in response to salt stress among worldwide landraces and improved varieties of wheat at the seedling stage. A total of 125 landraces and wheat varieties were subjected to salt treatment (50, 100, and 150 mM) with control. Morphological seedling traits, i.e., shoot length, root length, and fresh and dry shoot and root weights for salinity tolerance were observed to assess salt tolerance and genetic analysis using SNP data through DArT-seq. The results showed that, at the seedling stage, 150 mM NaCl treatment decreased shoot length, root length, and fresh and dry weights of the shoot and root. The root length and dry root weight were the most affected traits at the seedling stage. Effective 4417 SNPs encompassing all the chromosomes of the wheat genome with marker density, i.e., 37%, fall in genome B, genome D (32%), and genome A (31%). Five loci were found on four chromosomes 6B, 6D, 7A, and 7D, showing strong associations with the root length, fresh shoot weight, fresh root weight, and dry root weight at the p < 0.03 significance level. The positive correlation was found among all morphological traits under study.

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Pujar, Mahesh, S. Gangaprasad, Mahalingam Govindaraj, Sunil S. Gangurde, A. Kanatti, and Himabindu Kudapa. "Genome-wide association study uncovers genomic regions associated with grain iron, zinc and protein content in pearl millet." Scientific Reports 10, no. 1 (November 10, 2020). http://dx.doi.org/10.1038/s41598-020-76230-y.

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Abstract Pearl millet hybrids biofortified with iron (Fe) and zinc (Zn) promise to be part of a long-term strategy to combat micronutrient malnutrition in the arid and semi-arid tropical (SAT) regions of the world. Biofortification through molecular breeding is the way forward to achieving a rapid trait-based breeding strategy. This genome-wide association study (GWAS) was conducted to identify significant marker-trait associations (MTAs) for Fe, Zn, and protein content (PC) for enhanced biofortification breeding. A diverse panel of 281 advanced inbred lines was evaluated for Fe, Zn, and PC over two seasons. Phenotypic evaluation revealed high variability (Fe: 32–120 mg kg−1, Zn: 19–87 mg kg−1, PC: 8–16%), heritability (hbs2 ≥ 90%) and significantly positive correlation among Fe, Zn and PC (P = 0.01), implying concurrent improvement. Based on the Diversity Arrays Technology (DArT) seq assay, 58,719 highly informative SNPs were filtered for association mapping. Population structure analysis showed six major genetic groups (K = 6). A total of 78 MTAs were identified, of which 18 were associated with Fe, 43 with Zn, and 17 with PC. Four SNPs viz., Pgl04_64673688, Pgl05_135500493, Pgl05_144482656, and Pgl07_101483782 located on chromosomes Pgl04 (1), Pgl05 (2) and Pgl07 (1), respectively were co-segregated for Fe and Zn. Promising genes, ‘Late embryogenesis abundant protein’, ‘Myb domain’, ‘pentatricopeptide repeat’, and ‘iron ion binding’ coded by 8 SNPs were identified. The SNPs/genes identified in the present study presents prospects for genomics assisted biofortification breeding in pearl millet.

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Dang, Viet Hoang, Camilla Beate Hill, Xiao-Qi Zhang, Tefera Tolera Angessa, Lee-Anne McFawn, and Chengdao Li. "Multi-locus genome-wide association studies reveal novel alleles for flowering time under vernalisation and extended photoperiod in a barley MAGIC population." Theoretical and Applied Genetics, July 25, 2022. http://dx.doi.org/10.1007/s00122-022-04169-x.

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Abstract Key message Key genes controlling flowering and interactions of different photoperiod alleles with various environments were identified in a barley MAGIC population. A new candidate gene for vernalisation requirements was also detected. Abstract Optimal flowering time has a major impact on grain yield in crop species, including the globally important temperate cereal crop barley (Hordeum vulgare L.). Understanding the genetics of flowering is a key avenue to enhancing yield potential. Although bi-parental populations were used intensively to map genes controlling flowering, their lack of genetic diversity requires additional work to obtain desired gene combinations in the selected lines, especially when the two parental cultivars did not carry the genes. Multi-parent mapping populations, which use a combination of four or eight parental cultivars, have higher genetic and phenotypic diversity and can provide novel genetic combinations that cannot be achieved using bi-parental populations. This study uses a Multi-parent advanced generation intercross (MAGIC) population from four commercial barley cultivars to identify genes controlling flowering time in different environmental conditions. Genome-wide association studies (GWAS) were performed using 5,112 high-quality markers from Diversity Arrays Technology sequencing (DArT-seq), and Kompetitive allele-specific polymerase chain reaction (KASP) genetic markers were developed. Phenotypic data were collected from fifteen different field trials for three consecutive years. Planting was conducted at various sowing times, and plants were grown with/without additional vernalisation and extended photoperiod treatments. This study detected fourteen stable regions associated with flowering time across multiple environments. GWAS combined with pangenome data highlighted the role of CEN gene in flowering and enabled the prediction of different CEN alleles from parental lines. As the founder lines of the multi-parental population are elite germplasm, the favourable alleles identified in this study are directly relevant to breeding, increasing the efficiency of subsequent breeding strategies and offering better grain yield and adaptation to growing conditions.

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Zhang, Peipei, Caixia Lan, Ravi P. Singh, Julio Huerta-Espino, Zaifeng Li, Evans Lagudah, and Sridhar Bhavani. "Identification and Characterization of Resistance Loci to Wheat Leaf Rust and Stripe Rust in Afghan Landrace “KU3067”." Frontiers in Plant Science 13 (June 28, 2022). http://dx.doi.org/10.3389/fpls.2022.894528.

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Leaf rust and stripe rust are important wheat diseases worldwide causing significant losses where susceptible varieties are grown. Resistant cultivars offer long-term control and reduce the use of hazardous chemicals, which can be detrimental to both human health and the environment. Land races have been a valuable resource for mining new genes for various abiotic and biotic stresses including wheat rusts. Afghan wheat landrace “KU3067” displayed high seedling infection type (IT) for leaf rust and low IT for stripe rust; however, it displayed high levels of field resistance for both rusts when tested for multiple seasons against the Mexican rust isolates. This study focused on identifying loci-conferring seedling resistance to stripe rust, and also loci-conferring adult plant resistance (APR) against the Mexican races of leaf rust and stripe rust. A backcrossed inbred line (BIL) population advanced to the BC1F5 generation derived from the cross of KU3067 and Apav (triple rust susceptible line) was used for both, inheritance and QTL mapping studies. The population and parents were genotyped with Diversity Arrays Technology-genotyping-by-sequencing (DArT-Seq) and phenotyped for leaf rust and stripe rust response at both seedling and adult plant stages during multiple seasons in Mexico with relevant pathotypes. Mapping results identified an all-stage resistance gene for stripe rust, temporarily designated as YrKU, on chromosome 7BL. In total, six QTL-conferring APR to leaf rust on 1AS, 2AL, 4DL, 6BL, 7AL, and 7BL, and four QTL for stripe rust resistance on 1BS, 2AL, 4DL, and 7BL were detected in the analyses. Among these, pleiotropic gene Lr67/Yr46 on 4DL with a significantly large effect is the first report in an Afghan landrace-conferring resistance to both leaf and stripe rusts. QLr.cim-7BL/YrKU showed pleiotropic resistance to both rusts and explained 7.5–17.2 and 12.6–19.3% of the phenotypic variance for leaf and stripe rusts, respectively. QYr.cim-1BS and QYr.cim-2AL detected in all stripe environments with phenotypic variance explained (PVE) 12.9–20.5 and 5.4–12.5%, and QLr.cim-6BL are likely to be new. These QTL and their closely linked markers will be useful for fine mapping and marker-assisted selection (MAS) in breeding for durable resistance to multiple rust diseases.

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Journal articles on the topic 'DArT-seq'

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