Journal articles: 'Diversity Array Technology (DArT)'

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Stevens, Mikel R., Shawn A. Chrisensen, Ammon B. Marshall, JoLynn J. Stevens, Peter Wenzl, Eric Hunter, Jason Carling, and Andrzej Killian. "Molecular Marker Development and High Throughput with Microarrays using Diversity Array Technology (DArT)." HortScience 40, no. 4 (July 2005): 1113D—1114. http://dx.doi.org/10.21273/hortsci.40.4.1113d.

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Recently, a technology known as DArT (diversity array technology) has been developed to increase throughput in marker assisted selection (MAS). DArT utilizes microarray technology as a method to potentially compare thousands of molecular markers in one test to a single DNA sample. We used DArT on two sets of interspecific tomato [Solanum lycopersicum (Fla 7613) × S. pennellii (LA 716 or LA 2963)] segregating populations (BC, F2, and F1). We compared over 300 segregating plants to 3840 random tomato genomic fragments. After the 3840 markers were prepared, it took about 2 weeks of laboratory time to perform the experiments. With experience, this time can be reduced. We identified a total of 654 polymorphic markers usable for developing a DArT tomato genetic map. Depending on the particular cross, 13 to 17 linkage groups were identified (LOD 3) per population. Most recently, the amplified polymorphic DNA (AFLP) technique has been used for rapid genetic mapping of large numbers of anonymous genomic fragments. Besides the additional effort and reagents using AFLPs compared to DArT, a desired AFLP polymorphic band is often difficult to clone and process into a PCR based marker, whereas in DArT all markers are already cloned and immediately available for such experiments. A drawback to DArT is that it requires specialized software and equipment and is technically demanding. However, once the equipment and software are secured, techniques are optimized, and segregating populations developed, marker throughput is increased by orders of magnitude. Although challenging, the application of DArT can dramatically increase MAS throughput, thus facilitating quantitative trait and saturated mapping research.

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Castillo, Almudena, María C. Ramírez, Azahara C. Martín, Andrzej Kilian, Antonio Martín, and Sergio G. Atienza. "High-throughput genotyping of wheat-barley amphiploids utilising diversity array technology (DArT)." BMC Plant Biology 13, no. 1 (2013): 87. http://dx.doi.org/10.1186/1471-2229-13-87.

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Whittock, S., G. Leggett, J. Jake, B. Javornik, J. Carling, A. Kilian, P. D. Matthews, et al. "USE OF DIVERSITY ARRAY TECHNOLOGY (DART) FOR GENOTYPING OF HUMULUS LUPULUS L." Acta Horticulturae, no. 848 (December 2009): 59–64. http://dx.doi.org/10.17660/actahortic.2009.848.5.

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Shaibu, Abdulwahab S., Hassan Ibrahim, Zainab L. Miko, Ibrahim B. Mohammed, Sanusi G. Mohammed, Hauwa L. Yusuf, Alpha Y. Kamara, Lucky O. Omoigui, and Benjamin Karikari. "Assessment of the Genetic Structure and Diversity of Soybean (Glycine max L.) Germplasm Using Diversity Array Technology and Single Nucleotide Polymorphism Markers." Plants 11, no. 1 (December 26, 2021): 68. http://dx.doi.org/10.3390/plants11010068.

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Knowledge of the genetic structure and diversity of germplasm collections is crucial for sustainable genetic improvement through hybridization programs and rapid adaptation to changing breeding objectives. The objective of this study was to determine the genetic diversity and population structure of 281 International Institute of Tropical Agriculture (IITA) soybean accessions using diversity array technology (DArT) and single nucleotide polymorphism (SNP) markers for the efficient utilization of these accessions. From the results, the SNP and DArT markers were well distributed across the 20 soybean chromosomes. The cluster and principal component analyses revealed the genetic diversity among the 281 accessions by grouping them into two stratifications, a grouping that was also evident from the population structure analysis, which divided the 281 accessions into two distinct groups. The analysis of molecular variance revealed that 97% and 98% of the genetic variances using SNP and DArT markers, respectively, were within the population. Genetic diversity indices such as Shannon’s diversity index, diversity and unbiased diversity revealed the diversity among the different populations of the soybean accessions. The SNP and DArT markers used provided similar information on the structure, diversity and polymorphism of the accessions, which indicates the applicability of the DArT marker in genetic diversity studies. Our study provides information about the genetic structure and diversity of the IITA soybean accessions that will allow for the efficient utilization of these accessions in soybean improvement programs, especially in Africa.

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Sohail, Quahir, Tariq Shehzad, Andrezj Kilian, Amin Elsadig Eltayeb, Hiroyuki Tanaka, and Hisashi Tsujimoto. "Development of diversity array technology (DArT) markers for assessment of population structure and diversity in Aegilops tauschii." Breeding Science 62, no. 1 (2012): 38–45. http://dx.doi.org/10.1270/jsbbs.62.38.

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Amorim, Edson P., Alberto D. Vilarinhos, Kelly O. Cohen, Vanusia B. O. Amorim, Janay A. dos Santos-Serejo, Sebastião Oliveira e. Silva, Kátia N. Pestana, et al. "Genetic diversity of carotenoid-rich bananas evaluated by Diversity Arrays Technology (DArT)." Genetics and Molecular Biology 32, no. 1 (January 30, 2009): 96–103. http://dx.doi.org/10.1590/s1415-47572009005000024.

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Wenzl, P., J. Carling, D. Kudrna, D. Jaccoud, E. Huttner, A. Kleinhofs, and A. Kilian. "Diversity Arrays Technology (DArT) for whole-genome profiling of barley." Proceedings of the National Academy of Sciences 101, no. 26 (June 10, 2004): 9915–20. http://dx.doi.org/10.1073/pnas.0401076101.

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Ovesná, J., L. Kučera, K. Vaculová, J. Milotová, J. Snape, P. Wenzl, E. Huttner, A. Kilian, G. Martelli, and L. Milella. "Analysis of the Genetic Structure of a Barley Collection Using DNA Diversity Array Technology (DArT)." Plant Molecular Biology Reporter 31, no. 2 (August 4, 2012): 280–88. http://dx.doi.org/10.1007/s11105-012-0491-x.

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Hurtado, P., K. M. Olsen, C. Buitrago, C. Ospina, J. Marin, M. Duque, C. de Vicente, et al. "Comparison of simple sequence repeat (SSR) and diversity array technology (DArT) markers for assessing genetic diversity in cassava (Manihot esculenta Crantz)." Plant Genetic Resources 6, no. 3 (August 22, 2008): 208–14. http://dx.doi.org/10.1017/s1479262108994181.

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Several molecular marker systems have been developed for assessing genetic diversity in crop germplasm collections. A trade-off often exists between the number of loci that can feasibly be sampled by a marker system and the amount of information provided by each locus. We compared the usefulness of two marker systems for revealing genetic diversity and population structure in cassava (Manihot esculenta Crantz): simple sequence repeats (SSRs) and diversity array technology (DArT) markers. DArTs survey many more loci per reaction than do SSRs; however, as bi-allelic, dominant markers, DArTs provide less polymorphism information per locus. Genetic differentiation was assessed in a randomly selected set of 436 cassava accessions, consisting of 155 African and 281 Latin American accessions. A genome-wide set of 36 SSR markers and a DArT array of approximately 1000 polymorphic clones were used to assess genetic diversity and differentiation. Cluster analyses were performed using principal coordinate analysis (PCoA). Results were compared with a priori expectations of genetic differentiation based on previous genetic analyses. Analyses of the two datasets generated broadly similar clustering patterns. However, SSRs revealed greater differentiation than DArTs, and more effectively recovered patterns of genetic differentiation observed in previous analyses (differentiation between Latin American and African accessions, and some geographical differentiation within each of these groups). These results suggest that SSR markers, while low throughput in comparison with DArTs, are relatively better at detecting genetic differentiation in cassava germplasm collections. Nonetheless, DArTs will likely prove useful in ‘orphan crop’ species, where alternative molecular markers have not been developed.

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Reddy, Umesh K., Jun-kang Rong, Padma Nimmakayala, Gopinath Vajja, Mohammad A. Rahman, John Yu, Khairy M. Soliman, Katarzyna Heller-Uszynska, Andrzej Kilian, and Andrew H. Paterson. "Use of diversity arrays technology markers for integration into a cotton reference map and anchoring to a recombinant inbred line map." Genome 54, no. 5 (May 2011): 349–59. http://dx.doi.org/10.1139/g11-001.

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A diversity array technology (DArT) marker platform was developed for the cotton genome, to evaluate the use of DArT markers compared with AFLP markers in mapping and transferability across the mapping populations. We used a reference genetic map of tetraploid Gossypium L. that already contained ∼5000 loci, which coalesced into 26 chromosomes, to anchor newly developed DArT and AFLP markers with the aim of further improving utility and map resolution. Our results indicated that the percentage of polymorphic DArT markers that could be genetically mapped (78.15%) was much higher than that of AFLP markers (22.28%). Sequence analysis of DArT markers indicated that a majority matched known expressed sequence tag (EST) sequences from tetraploid and diploid Gossypium species. A total of 794 Arabidopsis genes were homologous with various DArT marker sequences. Chromosomes 5(A), 7(A), 19(D), 23(D), and 24(D) had more Arabidopsis syntenic DArT markers than the other chromosomes. Anchoring DArT markers from the reference map to a recombinant inbred line (RIL) map indicated that DArT markers will speed the building of maps in de novo RIL populations.

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Schouten, Henk J., W. Eric van de Weg, Jason Carling, Sabaz Ali Khan, Steven J. McKay, Martijn P. W. van Kaauwen, Alexander H. J. Wittenberg, et al. "Diversity arrays technology (DArT) markers in apple for genetic linkage maps." Molecular Breeding 29, no. 3 (May 15, 2011): 645–60. http://dx.doi.org/10.1007/s11032-011-9579-5.

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Stodart, B. J., M. C. Mackay, and H. Raman. "Assessment of molecular diversity in landraces of bread wheat (Triticum aestivum L.) held in an ex situ collection with Diversity Arrays Technology (DArT™)." Australian Journal of Agricultural Research 58, no. 12 (2007): 1174. http://dx.doi.org/10.1071/ar07010.

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Diversity Arrays Technology (DArT™) was evaluated as a tool for determining molecular diversity of wheat landraces held within the Australian Winter Cereals Collection (AWCC). Initially, a set of 44 wheat landraces was evaluated with 256 DArT markers. The dataset was compared with the results obtained using 16 amplified fragment length polymorphism (AFLP) primer combinations and 63 simple sequence repeat (SSR) markers, mapped on the 21 chromosomes, from a previous study. The DArT markers exhibited a strong positive correlation with AFLP and SSR, with each marker type distinguishing similar relationships among the 44 landrace accessions. The DArT markers exhibited a higher polymorphic information content than AFLP, and were comparable with that obtained with SSR. Three hundred and fifty-five DArT markers were then used to evaluate genetic diversity among 705 wheat landrace accessions from within the AWCC, chosen to represent 5 world regions. DArT analysis was capable of distinguishing accessions from different geographic regions, and suggested that accessions originating from Nepal represent a unique gene pool within the collection. A statistical resampling of DArT loci indicated that 10–20 loci were enough to distinguish the maximum molecular diversity present within the collection. This research demonstrates the efficacy of the DArT platform as a tool for efficient examination of wheat diversity. As an ex situ germplasm repository, the AWCC contains wheat accessions of high genetic diversity, from genetically differentiated collection sites, even though diversity was under-represented in some countries represented in the repository.

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James, Karen E., Harald Schneider, Stephen W. Ansell, Margaret Evers, Lavinia Robba, Grzegorz Uszynski, Niklas Pedersen, et al. "Diversity Arrays Technology (DArT) for Pan-Genomic Evolutionary Studies of Non-Model Organisms." PLoS ONE 3, no. 2 (February 27, 2008): e1682. http://dx.doi.org/10.1371/journal.pone.0001682.

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Van Schalkwyk, A., E. Van der Walt, A. Killian, and D. K. Berger. "Genotyping Solanum lycopersicum and its related wild species using Diversity Arrays Technology (DArT)." South African Journal of Botany 74, no. 2 (April 2008): 381. http://dx.doi.org/10.1016/j.sajb.2008.01.118.

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Akbari, Mona, Peter Wenzl, Vanessa Caig, Jason Carling, Ling Xia, Shiying Yang, Grzegorz Uszynski, et al. "Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome." Theoretical and Applied Genetics 113, no. 8 (October 11, 2006): 1409–20. http://dx.doi.org/10.1007/s00122-006-0365-4.

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Howard, E. L., S. P. Whittock, J. Jakše, J. Carling, P. D. Matthews, G. Probasco, J. A. Henning, et al. "High-throughput genotyping of hop (Humulus lupulus L.) utilising diversity arrays technology (DArT)." Theoretical and Applied Genetics 122, no. 7 (January 18, 2011): 1265–80. http://dx.doi.org/10.1007/s00122-011-1529-4.

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Rungis, D. E., A. Voronova, A. Kokina, I. Veinberga, I. Skrabule, and N. Rostoks. "Assessment of genetic diversity and relatedness in the Latvian potato genetic resources collection by DArT genotyping." Plant Genetic Resources 15, no. 1 (August 14, 2015): 72–78. http://dx.doi.org/10.1017/s1479262115000398.

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Potato (Solanum tuberosumL.) has been cultivated in Latvia since the 17th century, and formal breeding programmes have been established since the start of the 20th century. The Latvian potato genetic resource collection consists of 83 accessions of Latvian origin, including landraces, old cultivars released starting from the 1930's, modern cultivars and breeding material. These are maintained in field andin vitrocollections. Pedigree information about the potato cultivars is often limited, and the use of hybrids of local cultivars as parents is common in the Latvian potato breeding programme. Ninety-four Latvian potato varieties and breeding lines and some commonly used foreign accessions were genotyped with the potato DNA diversity array technology. Analysis of the Latvian potato genetic resources collection revealed that the amount of genetic diversity has increased in the modern cultivars in comparison with the old cultivars.

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Mace, Emma S., Jean-Francois Rami, Sophie Bouchet, Patricia E. Klein, Robert R. Klein, Andrzej Kilian, Peter Wenzl, Ling Xia, Kirsten Halloran, and David R. Jordan. "A consensus genetic map of sorghum that integrates multiple component maps and high-throughput Diversity Array Technology (DArT) markers." BMC Plant Biology 9, no. 1 (2009): 13. http://dx.doi.org/10.1186/1471-2229-9-13.

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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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HONG, Yi-Huan, Ning XIAO, Chao ZHANG, Yan SU, and Jian-Min CHEN. "Principle of diversity arrays technology (DArT) and its applications in genetic research of plants." Hereditas (Beijing) 31, no. 4 (July 14, 2009): 359–64. http://dx.doi.org/10.3724/sp.j.1005.2009.00359.

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Sansaloni, Carolina P., César D. Petroli, Jason Carling, Corey J. Hudson, Dorothy A. Steane, Alexander A. Myburg, Dario Grattapaglia, René E. Vaillancourt, and Andrzej Kilian. "A high-density Diversity Arrays Technology (DArT) microarray for genome-wide genotyping in Eucalyptus." Plant Methods 6, no. 1 (2010): 16. http://dx.doi.org/10.1186/1746-4811-6-16.

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YANG, SHI YING, RACHIT K. SAXENA, PAWAN L. KULWAL, GAVIN J. ASH, ANUJA DUBEY, JOHN D. I. HARPER, HARI D. UPADHYAYA, RAGINI GOTHALWAL, ANDRZEJ KILIAN, and RAJEEV K. VARSHNEY. "The first genetic map of pigeon pea based on diversity arrays technology (DArT) markers." Journal of Genetics 90, no. 1 (April 2011): 103–9. http://dx.doi.org/10.1007/s12041-011-0050-5.

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Aitken, Karen S., Meredith D. McNeil, Scott Hermann, Peter C. Bundock, Andrzej Kilian, Katarzyna Heller-Uszynska, Robert J. Henry, and Jingchuan Li. "A comprehensive genetic map of sugarcane that provides enhanced map coverage and integrates high-throughput Diversity Array Technology (DArT) markers." BMC Genomics 15, no. 1 (2014): 152. http://dx.doi.org/10.1186/1471-2164-15-152.

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Lu, Xiu-ping, Bing-guang Xiao, Yong-ping Li, Yi-jie Gui, Yu Wang, and Long-jiang Fan. "Diversity arrays technology (DArT) for studying the genetic polymorphism of flue-cured tobacco (Nicotiana tabacum)." Journal of Zhejiang University SCIENCE B 14, no. 7 (July 2013): 570–77. http://dx.doi.org/10.1631/jzus.b1200227.

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Tyrka, M., P. T. Bednarek, A. Kilian, M. Wędzony, T. Hura, and E. Bauer. "Genetic map of triticale compiling DArT, SSR, and AFLP markers." Genome 54, no. 5 (May 2011): 391–401. http://dx.doi.org/10.1139/g11-009.

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A set of 90 doubled haploid (DH) lines derived from F1plants that originated from a cross between × Triticosecale Wittm. ‘Saka3006’ and ×Triticosecale Wittm. ‘Modus’, via wide crossing with maize, were used to create a genetic linkage map of triticale. The map has 21 linkage groups assigned to the A, B, and R genomes including 155 simple sequence repeat (SSR), 1385 diversity array technology (DArT), and 28 amplified fragment length polymorphism (AFLP) markers covering 2397 cM with a mean distance between two markers of 4.1 cM. Comparative analysis with wheat consensus maps revealed that triticale chromosomes of the A and B genomes were represented by 15 chromosomes, including combinations of 2AS.2AL#, 2AL#2BL, 6AS.6AL#, and 2BS.6AL# instead of 2A, 2B, and 6A. In respect to published maps of rye, substantial rearrangements were found also for chromosomes 1R, 2R, and 3R of the rye genome. Chromosomes 1R and 2R were truncated and the latter was linked with 3R. A nonhomogeneous distribution of markers across the triticale genome was observed with evident bias (48%) towards the rye genome. This genetic map may serve as a reference linkage map of triticale for efficient studies of structural rearrangements, gene mapping, and marker-assisted selection.

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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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Tanhuanpää, Pirjo, Outi Manninen, Aaron Beattie, Peter Eckstein, Graham Scoles, Brian Rossnagel, and Elina Kiviharju. "An updated doubled haploid oat linkage map and QTL mapping of agronomic and grain quality traits from Canadian field trials." Genome 55, no. 4 (April 2012): 289–301. http://dx.doi.org/10.1139/g2012-017.

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The first doubled haploid oat linkage map constructed at MTT Agrifood Research Finland was supplemented with additional microsatellites and Diversity Array Technology (DArT) markers to produce a map containing 1058 DNA markers and 34 linkage groups. The map was used to locate quantitative trait loci (QTLs) for 11 important breeding traits analyzed from Finnish and Canadian field trials. The new markers enabled most of the linkage groups to be anchored to the ‘Kanota’ × ‘Ogle’ oat ( Avena sativa L.) reference map and allowed comparison of the QTLs located in this study with those found previously. Two to 12 QTLs for each trait were discovered, of which several were expressed consistently across several environments.

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Thant, Aye Aye, Hein Zaw, Marie Kalousova, Rakesh Kumar Singh, and Bohdan Lojka. "Genetic Diversity and Population Structure of Myanmar Rice (Oryza sativa L.) Varieties Using DArTseq-Based SNP and SilicoDArT Markers." Plants 10, no. 12 (November 24, 2021): 2564. http://dx.doi.org/10.3390/plants10122564.

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Myanmar is well known as a primary center of plant genetic resources for rice. A considerable number of genetic diversity studies have been conducted in Myanmar using various DNA markers. However, this is the first report using DArTseq technology for exploring the genetic diversity of Myanmar rice. In our study, two ultra-high-throughput diversity array technology markers were employed to investigate the genetic diversity and population structure of local rice varieties in the Ayeyarwady delta, the major region of rice cultivation. The study was performed using 117 rice genotypes with 7643 SNP and 4064 silicoDArT markers derived from the DArT platform. Genetic variance among the genotypes ranged from 0 to 0.753 in SNPs, and from 0.001 to 0.954 in silicoDArT. Two distinct population groups were identified from SNP data analysis. Cluster analysis with both markers clearly separated traditional Pawsan varieties and modern high-yielding varieties. A significant divergence was found between populations according to the Fst values (0.737) obtained from the analysis of molecular variance, which revealed 74% genetic variation at the population level. These findings support rice researchers in identifying useful DNA polymorphisms in genes and pinpointing specific genes conferring desirable phenotypic traits for further genome-wide association studies and parental selection for recombination breeding to enhance rice varietal development and release.

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Semagn, Kassa, Åsmund Bjørnstad, Helge Skinnes, Anne Guri Marøy, Yalew Tarkegne, and Manilal William. "Distribution of DArT, AFLP, and SSR markers in a genetic linkage map of a doubled-haploid hexaploid wheat population." Genome 49, no. 5 (May 1, 2006): 545–55. http://dx.doi.org/10.1139/g06-002.

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A genetic linkage mapping study was conducted in 93 doubled-haploid lines derived from a cross between Triticum aestivum L. em. Thell 'Arina' and a Norwegian spring wheat breeding line, NK93604, using diversity arrays technology (DArT), amplified fragment length polymorphism (AFLP), and simple sequence repeat (SSR) markers. The objective of this study was to understand the distribution, redundancy, and segregation distortion of DArT markers in comparison with AFLP and SSR markers. The map contains a total of 624 markers with 189 DArTs, 165 AFLPs and 270 SSRs, and spans 2595.5 cM. All 3 marker types showed significant (p < 0.01) segregation distortion, but it was higher for AFLPs (24.2%) and SSRs (22.6%) than for DArTs (13.8%). The overall segregation distortion was 20.4%. DArTs showed the highest frequency of clustering (27.0%) at < 0.5 cM intervals between consecutive markers, which is 3 and 15 times higher than SSRs (8.9%) and AFLPs (1.8%), respectively. This high proportion of clustering of DArT markers may be indicative of gene-rich regions and (or) the result of inclusion of redundant clones in the genomic representations, which was supported by the presence of very high correlation coefficients (r > 0.98) and multicollinearity among the clustered markers. The present study is the first to compare the utility of DArT with AFLP and SSR markers, and the present map has been successfully used to identify novel QTLs for resistance to Fusarium head blight and powdery mildew and for anther extrusion, leaf segment incubation, and latency.Key words: 'Arina', diversity arrays technology, double haploid, genetic map, marker clustering, microsatellite.

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Gbedevi, Kodjo M., Ousmane Boukar, Haruki Ishikawa, Ayodeji Abe, Patrick O. Ongom, Nnanna Unachukwu, Ismail Rabbi, and Christian Fatokun. "Genetic Diversity and Population Structure of Cowpea [Vigna unguiculata (L.) Walp.] Germplasm Collected from Togo Based on DArT Markers." Genes 12, no. 9 (September 20, 2021): 1451. http://dx.doi.org/10.3390/genes12091451.

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Crop genetic diversity is a sine qua non for continuous progress in the development of improved varieties, hence the need for germplasm collection, conservation and characterization. Over the years, cowpea has contributed immensely to the nutrition and economic life of the people in Togo. However, the bulk of varieties grown by farmers are landraces due to the absence of any serious genetic improvement activity on cowpea in the country. In this study, the genetic diversity and population structure of 255 cowpea accessions collected from five administrative regions and the agricultural research institute of Togo were assessed using 4600 informative diversity array technology (DArT) markers. Among the regions, the polymorphic information content (PIC) ranged from 0.19 to 0.27 with a mean value of 0.25. The expected heterozygosity (He) varied from 0.22 to 0.34 with a mean value of 0.31, while the observed heterozygosity (Ho) varied from 0.03 to 0.07 with an average of 0.05. The average inbreeding coefficient (FIS) varied from 0.78 to 0.89 with a mean value of 0.83, suggesting that most of the accessions are inbred. Cluster analysis and population structure identified four groups with each comprising accessions from the six different sources. Weak to moderate differentiation was observed among the populations with a genetic differentiation index varying from 0.014 to 0.117. Variation was highest (78%) among accessions within populations and lowest between populations (7%). These results revealed a moderate level of diversity among the Togo cowpea germplasm. The findings of this study constitute a foundation for genetic improvement of cowpea in Togo.

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Traini, Alessandra, Massimo Iorizzo, Harpartap Mann, James M. Bradeen, Domenico Carputo, Luigi Frusciante, and Maria Luisa Chiusano. "Genome Microscale Heterogeneity among Wild Potatoes Revealed by Diversity Arrays Technology Marker Sequences." International Journal of Genomics 2013 (2013): 1–9. http://dx.doi.org/10.1155/2013/257218.

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Tuber-bearing potato species possess several genes that can be exploited to improve the genetic background of the cultivated potatoSolanum tuberosum. Among them,S. bulbocastanumandS. commersoniiare well known for their strong resistance to environmental stresses. However, scant information is available for these species in terms of genome organization, gene function, and regulatory networks. Consequently, genomic tools to assist breeding are meager, and efficient exploitation of these species has been limited so far. In this paper, we employed the reference genome sequences from cultivated potato and tomato and a collection of sequences of 1,423 potato Diversity Arrays Technology (DArT) markers that show polymorphic representation across the genomes ofS. bulbocastanumand/orS. commersoniigenotypes. Our results highlighted microscale genome sequence heterogeneity that may play a significant role in functional and structural divergence between related species. Our analytical approach provides knowledge of genome structural and sequence variability that could not be detected by transcriptome and proteome approaches.

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Grzebelus, Dariusz, Massimo Iorizzo, Douglas Senalik, Shelby Ellison, Pablo Cavagnaro, Alicja Macko-Podgorni, Kasia Heller-Uszynska, et al. "Diversity, genetic mapping, and signatures of domestication in the carrot (Daucus carota L.) genome, as revealed by Diversity Arrays Technology (DArT) markers." Molecular Breeding 33, no. 3 (October 26, 2013): 625–37. http://dx.doi.org/10.1007/s11032-013-9979-9.

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Sánchez-Sevilla, José F., Aniko Horvath, Miguel A. Botella, Amèlia Gaston, Kevin Folta, Andrzej Kilian, Beatrice Denoyes, and Iraida Amaya. "Diversity Arrays Technology (DArT) Marker Platforms for Diversity Analysis and Linkage Mapping in a Complex Crop, the Octoploid Cultivated Strawberry (Fragaria × ananassa)." PLOS ONE 10, no. 12 (December 16, 2015): e0144960. http://dx.doi.org/10.1371/journal.pone.0144960.

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Upadhyaya, Hari D., Mahendar Thudi, Naresh Dronavalli, Neha Gujaria, Sube Singh, Shivali Sharma, and Rajeev K. Varshney. "Genomic tools and germplasm diversity for chickpea improvement." Plant Genetic Resources 9, no. 01 (January 14, 2011): 45–58. http://dx.doi.org/10.1017/s1479262110000468.

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Chickpea is the third most important grain legume grown in the arid and semi-arid regions of the world. In spite of vast germplasm accessions available in different genebanks, there has been very limited use of these accessions in genetic enhancement of chickpea. However, in recent years, specialized germplasm subsets such as global composite collection, core collection, mini core collection and reference set have been developed. In parallel, significant genomic resources such as molecular markers including simple sequence repeats (SSRs), single nucleotide polymorphisms (SNPs), diversity arrays technology (DArT) and transcript sequences, e.g. expressed sequence tags, short transcript reads, have been developed. By using SSR, SNP and DArT markers, integrated genetic maps have been developed. It is anticipated that the use of genomic resources and specialized germplasm subsets such as mini core collection and reference set will facilitate identification of trait-specific germplasm, trait mapping and allele mining for resistance to biotic and abiotic stresses and for agronomic traits. Advent of the next generation sequencing technologies coupled with advances in bioinformatics offers the possibility of undertaking large-scale sequencing of germplasm accessions so that modern breeding approaches such as genomic selection and breeding by design can be realized in near future for chickpea improvement.

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Adhikari, Tika B., Eric W. Jackson, Suraj Gurung, Jana M. Hansen, and J. Michael Bonman. "Association Mapping of Quantitative Resistance to Phaeosphaeria nodorum in Spring Wheat Landraces from the USDA National Small Grains Collection." Phytopathology® 101, no. 11 (November 2011): 1301–10. http://dx.doi.org/10.1094/phyto-03-11-0076.

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Stagonospora nodorum blotch (SNB), caused by Phaeosphaeria nodorum, is a destructive disease of wheat (Triticum aestivum) found throughout the United States. Host resistance is the only economically feasible option for managing the disease; however, few SNB-resistant wheat cultivars are known to exist. In this study, we report findings from an association mapping (AM) of resistance to P. nodorum in 567 spring wheat landraces of diverse geographic origin. The accessions were evaluated for seedling resistance to P. nodorum in a greenhouse. Phenotypic data and 625 polymorphic diversity array technology (DArT) markers have been used for linkage disequilibrium (LD) and association analyses. The results showed that seven DArT markers on five chromosomes (2D, 3B, 5B, 6A, and 7A) were significantly associated with resistance to P. nodorum. Genetic regions on 2D, 3B, and 5B correspond to previously mapped quantitative trait loci (QTL) conferring resistance to P. nodorum whereas the remaining QTL appeared to be novel. These results demonstrate that the use of AM is an effective method for identifying new genomic regions associated with resistance to P. nodorum in spring wheat landraces. Additionally, the novel resistance found in this study could be useful in wheat breeding aimed at controlling SNB.

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Mourad, Amira M. I., Mohamed A. Abou-Zeid, Shamseldeen Eltaher, P. Stephen Baenziger, and Andreas Börner. "Identification of Candidate Genes and Genomic Regions Associated with Adult Plant Resistance to Stripe Rust in Spring Wheat." Agronomy 11, no. 12 (December 19, 2021): 2585. http://dx.doi.org/10.3390/agronomy11122585.

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Wheat stripe rust (caused by Puccinia striiformis f. sp. tritici) is a major disease that damages wheat plants and affects wheat yield all over the world. In recent years, stripe rust became a major problem that affects wheat yield in Egypt. New races appeared and caused breakdowns in the resistant genotypes. To improve resistance in the Egyptian genotypes, new sources of resistance are urgently needed. In the recent research, a set of 95 wheat genotypes collected from 19 countries, including Egypt, were evaluated for their resistance against the Egyptian race(s) of stripe rust under field conditions in the two growing seasons 2018/2019 and 2019/2020. A high genetic variation was found among the tested genotypes. Single marker analysis was conducted using a subset of 71 genotypes and 424 diversity array technology (DArT) markers, well distributed across the genome. Out of the tested markers, 13 stable markers were identified that were significantly associated with resistance in both years (p-value ≤ 0.05). By using the sequence of the DArT markers, the chromosomal position of the significant DArT markers was detected, and nearby gene models were identified. Two markers on chromosomes 5A and 5B were found to be located within gene models functionally annotated with disease resistance in plants. These two markers could be used in marker-assisted selection for stripe rust resistance under Egyptian conditions. Two German genotypes were carrying the targeted allele of all the significant DArT markers associated with stripe rust resistance and could be used to improve resistance under Egyptian conditions.

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Góralska, Magdalena, Jan Bińkowski, Natalia Lenarczyk, Anna Bienias, Agnieszka Grądzielewska, Ilona Czyczyło-Mysza, Kamila Kapłoniak, Stefan Stojałowski, and Beata Myśków. "How Machine Learning Methods Helped Find Putative Rye Wax Genes Among GBS Data." International Journal of Molecular Sciences 21, no. 20 (October 12, 2020): 7501. http://dx.doi.org/10.3390/ijms21207501.

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The standard approach to genetic mapping was supplemented by machine learning (ML) to establish the location of the rye gene associated with epicuticular wax formation (glaucous phenotype). Over 180 plants of the biparental F2 population were genotyped with the DArTseq (sequencing-based diversity array technology). A maximum likelihood (MLH) algorithm (JoinMap 5.0) and three ML algorithms: logistic regression (LR), random forest and extreme gradient boosted trees (XGBoost), were used to select markers closely linked to the gene encoding wax layer. The allele conditioning the nonglaucous appearance of plants, derived from the cultivar Karlikovaja Zelenostebelnaja, was mapped at the chromosome 2R, which is the first report on this localization. The DNA sequence of DArT-Silico 3585843, closely linked to wax segregation detected by using ML methods, was indicated as one of the candidates controlling the studied trait. The putative gene encodes the ABCG11 transporter.

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Onley, Isabelle R., Jeremy J. Austin, and Kieren J. Mitchell. "Sex assignment in a non-model organism in the absence of field records using Diversity Arrays Technology (DArT) data." Conservation Genetics Resources 13, no. 3 (March 9, 2021): 255–60. http://dx.doi.org/10.1007/s12686-021-01203-w.

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Niedziela, Agnieszka, and Piotr Bednarek. "CHARACTERIZATION OF DART SEQUENCES REFLECTING GENOMICREGIONS INVOLVED IN ALUMINUM TOLERANCE IN TRITICALE (X TRITICOSECALE WITTMACK)." Plant Breeding and Seed Science, no. 79 (June 30, 2020): 39–48. http://dx.doi.org/10.37317/pbss-2019-0005.

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Aluminum toxicity is the major growth-limiting factor for crop cultivation on acid soils. Tolerance mecha-nisms for Al stress in triticale have not been systematically investigated so far. It is presumed, that in the case of this species they may be a function of the interaction between wheat and rye genes. In this study the se-quences of forty-six Diversity Arrays Technology markers associated with aluminum tolerance in triticale and under selection pressure were blasted against BLAST database for the identification of possible functions of the respective genome regions in Al-stress response. The analysis has showed sequences similarity to the domains involved in signaling, disease response and DNA repair mechanisms.

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Zhang, Mian, Man-Man Fu, Cheng-Wei Qiu, Fangbin Cao, Zhong-Hua Chen, Guoping Zhang, and Feibo Wu. "Response of Tibetan Wild Barley Genotypes to Drought Stress and Identification of Quantitative Trait Loci by Genome-Wide Association Analysis." International Journal of Molecular Sciences 20, no. 3 (February 12, 2019): 791. http://dx.doi.org/10.3390/ijms20030791.

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Tibetan wild barley has been identified to show large genetic variation and stress tolerance. A genome-wide association (GWA) analysis was performed to detect quantitative trait loci (QTLs) for drought tolerance using 777 Diversity Array Technology (DArT) markers and morphological and physiological traits of 166 Tibetan wild barley accessions in both hydroponic and pot experiments. Large genotypic variation for these traits was found; and population structure and kinship analysis identified three subpopulations among these barley genotypes. The average LD (linkage disequilibrium) decay distance was 5.16 cM, with the minimum on 6H (0.03 cM) and the maximum on 4H (23.48 cM). A total of 91 DArT markers were identified to be associated with drought tolerance-related traits, with 33, 26, 16, 1, 3, and 12 associations for morphological traits, H+K+-ATPase activity, antioxidant enzyme activities, malondialdehyde (MDA) content, soluble protein content, and potassium concentration, respectively. Furthermore, 7 and 24 putative candidate genes were identified based on the reference Meta-QTL map and by searching the Barleymap. The present study implicated that Tibetan annual wild barley from Qinghai–Tibet Plateau is rich in genetic variation for drought stress. The QTLs detected by genome-wide association analysis could be used in marker-assisting breeding for drought-tolerant barley genotypes and provide useful information for discovery and functional analysis of key genes in the future.

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Adu, Bright Gyamfi, Richard Akromah, Stephen Amoah, Daniel Nyadanu, Alex Yeboah, Lawrence Missah Aboagye, Richard Adu Amoah, and Eva Gyamfuaa Owusu. "High-density DArT-based SilicoDArT and SNP markers for genetic diversity and population structure studies in cassava (Manihot esculenta Crantz)." PLOS ONE 16, no. 7 (July 27, 2021): e0255290. http://dx.doi.org/10.1371/journal.pone.0255290.

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Cassava (Manihot esculenta Crantz) is an important industrial and staple crop due to its high starch content, low input requirement, and resilience which makes it an ideal crop for sustainable agricultural systems and marginal lands in the tropics. However, the lack of genomic information on local genetic resources has impeded efficient conservation and improvement of the crop and the exploration of its full agronomic and breeding potential. This work was carried out to obtain information on population structure and extent of genetic variability among some local landraces conserved at the Plant Genetic Resources Research Institute, Ghana and exotic cassava accessions with Diversity Array Technology based SilicoDArT and SNP markers to infer how the relatedness in the genetic materials can be used to enhance germplasm curation and future breeding efforts. A total of 10521 SilicoDArT and 10808 SNP markers were used with varying polymorphic information content (PIC) values. The average PIC was 0.36 and 0.28 for the SilicoDArT and SNPs respectively. Population structure and average linkage hierarchical clustering based on SNPs revealed two distinct subpopulations and a large number of admixtures. Both DArT platforms identified 22 landraces as potential duplicates based on Gower’s genetic dissimilarity. The expected heterozygosity which defines the genetic variation within each subpopulation was 0.008 for subpop1 which were mainly landraces and 0.391 for subpop2 indicating the homogeneous and admixture nature of the two subpopulations. Further analysis upon removal of the duplicates increased the expected heterozygosity of subpop1 from 0.008 to 0.357. A mantel test indicated strong interdependence (r = 0.970; P < 0.001) between SilicoDArT and DArTSeq SNP genotypic data suggesting both marker platforms as a robust system for genomic studies in cassava. These findings provide important information for efficient ex-situ conservation of cassava, future heterosis breeding, and marker-assisted selection (MAS) to enhance cassava improvement.

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Hackl, Evelyn, Marianne Konrad-Köszler, Andrzej Kilian, Peter Wenzl, Christian Kornschober, and Angela Sessitsch. "Phage-type specific markers identified by Diversity Arrays Technology (DArT) analysis of Salmonella enterica ssp. enterica serovars Enteritidis and Typhimurium." Journal of Microbiological Methods 80, no. 1 (January 2010): 100–105. http://dx.doi.org/10.1016/j.mimet.2009.10.008.

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Berger, Jens D., Jon C. Clements, Matthew N. Nelson, Lars G. Kamphuis, Karam B. Singh, and Bevan Buirchell. "The essential role of genetic resources in narrow-leafed lupin improvement." Crop and Pasture Science 64, no. 4 (2013): 361. http://dx.doi.org/10.1071/cp13092.

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The narrow-leafed lupin (Lupinus angustifolius L.) is a legume with much to offer to agriculture and human wellbeing through its adaptation to nitrogen- and phosphorus-deficient, acid, sandy soils, and production of nutritious, very low glycemic index grain with manifold health benefits. However, the industry has exploited only a small fraction of the genetic and adaptive diversity of the species, reflecting a short and fragmented domestication history. Given declining global production, unlocking the potential residing in untapped sources of genetic diversity to maximise yield and value is critical for the future of the crop. To this end, a wide range of genetic resources is under evaluation. The Australian Lupin Collection comprises almost 4600 diverse, mostly wild accessions, many of which have been genotyped using DArT (Diversity Array Technology) markers, and collection sites characterised to facilitate ecophysiology of contrasting material. Additional exotic genetic resources include recombinant inbred line and mutant populations, as well as inter-specific crosses. These resources are being used to investigate specific adaptation and genetic and molecular control of key traits, all of which will be expedited by current efforts to provide a reference genome sequence for L. angustifolius. Genetic base broadening is the current breeding focus, combining distantly related wild and domestic material with elite cultivars in double-backcrosses or topcrosses, with dramatic effects on yield. In future this will be complemented by marker-based, targeted trait introgression to improve narrow-leafed lupin adaptation, quality/value, and fit into the farming system.

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Vu, Hang T. T., A. Kilian, A. T. James, L. M. Bielig, and R. J. Lawn. "Use of DArT molecular markers for QTL analysis of drought-stress responses in soybean. II. Marker identification and QTL analyses." Crop and Pasture Science 66, no. 8 (2015): 817. http://dx.doi.org/10.1071/cp14304.

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This study applied newly developed Diversity Arrays Technology (DArT) and soybean and mungbean DArT libraries for quantitative trait locus (QTL) linkage analysis in recombinant inbred lines (RILs) from three soybean crosses that had previously been assessed for physiological response to severe drought stress. The phenotypic assessments had identified statistically significant genetic variation among and within the RIL populations and their parents for three drought-related responses: epidermal conductance (ge) and relative water content (RWC) during stress, and plant recovery after stress. The new linkage maps containing only DArT markers for the three populations individually contained 196–409 markers and 15–22 linkage groups (LGs), with an aggregate length ranging from 409.4 to 516.7 cM. An integrated map constructed by using the marker data from all three RIL populations comprised 759 DArT markers, 27 LGs and an expanded length of 762.2 cM. Two populations with the landrace accession G2120 as a parent, CPI 26671 × G2120 (CG) and Valder × G2120 (VG), respectively contained 106 and 34 QTLs. In each of these populations, 10 LGs harboured QTLs associated with RWC, ge and recovery ability, of which six similar LGs were associated with drought tolerance. A BLAST (Basic Local Alignment Search Tool) search for sequences of 19 selected DArT markers linked to QTLs conditioning the drought-response traits indicated that 18 DArT markers were unique and aligned to 12 soybean chromosomes. Comparison of these sequenced DArT markers with other markers associated with drought-related QTLs in previously reported studies using other marker types confirmed that five of them overlapped, whereas the remaining 13 were new. Except for chromosome 15, the chromosomes with which the DArT QTLs in the CG and VG populations were associated were those that had been shown to harbour drought-related QTLs in previous studies. A BLASTx protein database search identified soPt-856602 as being associated with the gene for a probable glycosyltransferase At5g03795-like isoform X1 on chromosome 6. Although the several QTLs identified in the study were all of relatively minor effect, it was concluded that, because the DArT technology involves large numbers of markers and enables many lines to be genotyped simultaneously, it should help the process of manipulating multiple QTLs and so enhance their likely cumulative effect.

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Eberhard, Friederike S., Peng Zhang, Anke Lehmensiek, Ray A. Hare, Steven Simpfendorfer, and Mark W. Sutherland. "Chromosome composition of an F2 Triticum aestivum×T. turgidum spp. durum cross analysed by DArT markers and MCFISH." Crop and Pasture Science 61, no. 8 (2010): 619. http://dx.doi.org/10.1071/cp10131.

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This study has employed multicolour fluorescence in situ hybridisation (MCFISH) and Diversity Arrays Technology (DArT) markers to determine the segregation of parental A, B and D genome material into the progeny of a cross between a hexaploid bread wheat (Triticum aestivum L. var. 2-49) and a tetraploid durum wheat [T. turgidum L. spp. durum (Desf.) var. Bellaroi]. In the F2 progeny from a 2-49/Bellaroi cross, 82 out of 83 F2 plants investigated with DArT analysis carried some D genome material, principally as entire chromosomes, while 40 plants included at least one complete copy of all seven D genome chromosomes. Twelve plants containing partial D chromosomes were identified. MCFISH analysis of 26 additional F2 plants of the same cross showed that all 26 plants contained varying amounts of D genome material of which three carried single A-D translocations. In addition two telocentric D genome chromosomes were detected. The D genome content of each line and the breakpoint positions of the three A-D translocations were confirmed with DArT marker analysis. Overall results indicate a random recombination of A and B genome loci from the hexaploid female parent and the tetraploid male parent in this F2 population and a significant retention of the maternal D genome material. This study illustrates that the combined application of the MCFISH and DArT techniques provides a powerful approach for the analysis of crosses between cereal genotypes of different ploidy.

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Steffan, Philipp Matthias, Anders Borgen, Anna Maria Torp, Gunter Backes, and Søren K. Rasmussen. "Association Mapping for Common Bunt Resistance in Wheat Landraces and Cultivars." Agronomy 12, no. 3 (March 5, 2022): 642. http://dx.doi.org/10.3390/agronomy12030642.

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Common bunt is a seed borne disease of wheat whose importance is likely to increase due to the growing organic seed market, which, in addition to seed phytosanitary measures, relies on genetic resistances towards the disease. Genome wide association studies in wheat have been proven to be a useful tool in the detection of genetic polymorphisms underlying phenotypic trait variation in wheat. Here 248 wheat landraces and cultivars representing 130 years of breeding history were screened for two years in the field for their resistance reactions towards common bunt. The majority of lines exhibited high levels of susceptibility towards common bunt, while 25 accessions had less than 10% infection. Using Diversity Array Technology (DArT) markers for genotyping and correcting for population stratification by using a compressed mixed linear model, we identified two significant marker trait associations (MTA) for common bunt resistance, designated QCbt.cph-2B and QCbt.cph-7A, located on wheat chromosomes 2B and 7A, respectively. This shows that genome wide association studies (GWAS) are applicable in the search for genetic polymorphisms for resistance towards less studied plant diseases such as common bunt in the context of an under representation of resistant lines.

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Nantongo, Judith Ssali, Juventine Boaz Odoi, Hillary Agaba, and Samson Gwali. "SilicoDArT and SNP markers for genetic diversity and population structure analysis of Trema orientalis; a fodder species." PLOS ONE 17, no. 8 (August 22, 2022): e0267464. http://dx.doi.org/10.1371/journal.pone.0267464.

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Establishing the genetic diversity and population structure of a species can guide the selection of appropriate conservation and sustainable utilization strategies. Next-generation sequencing (NGS) approaches are increasingly being used to generate multi-locus data for genetic structure determination. This study presents the genetic structure of a fodder species -Trema orientalis based on two genome-wide high-throughput diversity array technology (DArT) markers; silicoDArT and single nucleotide polymorphisms (SNPs). Genotyping of 119 individuals generated 40,650 silicoDArT and 4767 SNP markers. Both marker types had a high average scoring reproducibility (>99%). Genetic relationships explored by principal coordinates analysis (PCoA) showed that the first principal coordinate axis explained most of the variation in both the SilicoDArT (34.2%) and SNP (89.6%) marker data. The average polymorphic information content did not highly differ between silicoDArT (0.22) and SNPs (0.17) suggesting minimal differences in informativeness in the two groups of markers. The, mean observed (Ho) and expected (He) heterozygosity were low and differed between the silicoDArT and SNPs respectively, estimated at Ho = 0.08 and He = 0.05 for silicoDArT and Ho = 0.23 and He = 0.19 for SNPs. The population of T. orientalis was moderately differentiated (FST = 0.20–0.53) and formed 2 distinct clusters based on maximum likelihood and principal coordinates analysis. Analysis of molecular variance revealed that clusters contributed more to the variation (46.3–60.8%) than individuals (32.9–31.2%). Overall, the results suggest a high relatedness of the individuals sampled and a threatened genetic potential of T. orientalis in the wild. Therefore, genetic management activities such as ex-situ germplasm management are required for the sustainability of the species. Ex-situ conservation efforts should involve core collection of individuals from different populations to capture efficient diversity. This study demonstrates the importance of silicoDArT and SNP makers in population structure and genetic diversity analysis of Trema orientalis, useful for future genome wide studies in the species.

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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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Olivera, P. D., A. Kilian, P. Wenzl, and B. J. Steffenson. "Development of a genetic linkage map for Sharon goatgrass (Aegilops sharonensis) and mapping of a leaf rust resistance gene." Genome 56, no. 7 (July 2013): 367–76. http://dx.doi.org/10.1139/gen-2013-0065.

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Aegilops sharonensis (Sharon goatgrass), a diploid wheat relative, is known to be a rich source of disease resistance genes for wheat improvement. To facilitate the transfer of these genes into wheat, information on their chromosomal location is important. A genetic linkage map of Ae. sharonensis was constructed based on 179 F2 plants derived from a cross between accessions resistant (1644) and susceptible (1193) to wheat leaf rust. The linkage map was based on 389 markers (377 Diversity Arrays Technology (DArT) and 12 simple sequence repeat (SSR) loci) and was comprised of 10 linkage groups, ranging from 2.3 to 124.6 cM. The total genetic length of the map was 818.0 cM, with an average interval distance between markers of 3.63 cM. Based on the chromosomal location of 115 markers previously mapped in wheat, the four linkage groups of A, B, C, and E were assigned to Ae. sharonensis (Ssh) and homoeologous wheat chromosomes 6, 1, 3, and 2. The single dominant gene (designated LrAeSh1644) conferring resistance to leaf rust race THBJ in accession 1644 was positioned on linkage group A (chromosome 6Ssh) and was flanked by DArT markers wpt-9881 (at 1.9 cM distal from the gene) and wpt-6925 (4.5 cM proximal). This study clearly demonstrates the utility of DArT for genotyping uncharacterized species and tagging resistance genes where pertinent genomic information is lacking.

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Lex, Jeannette, Jutta Ahlemeyer, Wolfgang Friedt, and Frank Ordon. "Genome-wide association studies of agronomic and quality traits in a set of German winter barley (Hordeum vulgare L.) cultivars using Diversity Arrays Technology (DArT)." Journal of Applied Genetics 55, no. 3 (May 1, 2014): 295–305. http://dx.doi.org/10.1007/s13353-014-0214-0.

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Journal articles on the topic 'Diversity Array Technology (DArT)'

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