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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Crop Improvement and Genetics Research » Research » Publications at this Location » Publication #313315

Title: Development of a D genome specific marker resource for diploid and hexaploid wheat

item WANG, Y - University Of California
item DRADER, T - Con Agra Foods, Inc
item TIWARI, V - Kansas State University
item DONG, L - University Of California
item KUMAR, A - North Dakota State University
item HUO, N - University Of California
item GHAVAMI, F - North Dakota State University
item IQBAL, M - North Dakota State University
item Lazo, Gerard
item GILL, B - Kansas State University
item Kianian, Shahryar
item LUO, M - University Of California
item Gu, Yong

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/17/2015
Publication Date: 8/28/2015
Citation: Wang, Y., Drader, T., Tiwari, V.K., Dong, L., Kumar, A., Huo, N., Ghavami, F., Iqbal, M.J., Lazo, G.R., Gill, B., Kianian, S., Luo, M., Gu, Y.Q. 2015. Development of a D genome specific marker resource for diploid and hexaploid wheat. Biomed Central (BMC) Genomics. doi: 10.11861S12864-015-1852-2.

Interpretive Summary: Wheat accounts for approximately 30% of the global cereal consumption. However, the large size and complexity of the wheat genome presents a major hurdle in identification of genes controlling agriculturally important traits for crop improvement. In this study, we employed the available genomics resources from Aegilops tauschii, one of the diploid ancestors of the bread wheat, to develop molecular markers for mapping chromosomal locations of genes in cultivated hexaploid bread wheat. A high density NimbleGen array containing 46,221 marker probes was generated and used for mapping in various wheat genetic stocks, including those carrying deletions of chromosomes. This study allowed us to anchor thousands of molecular markers in specific defined regions of the wheat D genome, providing a great resource to the wheat research community for identification and mapping of important genes/traits in wheat. A special website was developed in the GrainGenes database to provide easy access to and efficient utilization of the data (

Technical Abstract: Mapping and map-based cloning of genes that control agriculturally and economically important traits remain great challenges for plants with complex highly repetitive genomes such as those of the grass tribe, Triticeae. Mapping limitations in the Triticeae are primarily due to low frequencies of polymorphic gene markers and genetic recombination. Although repetitive sequences may pose problems in genome analysis and sequencing of such large and complex genomes, they provide repeat junction markers (RJM) with random and unbiased distribution throughout chromosomes. Hence, development of a high-throughput mapping technology that combines gene-based and RJMs is needed to generate maps that have better coverage of the entire genome. In this study, we used the available genomics resource of the diploid Aegilops tauschii, the D genome donor of bread wheat, to develop genome specific markers that can be applied for mapping in modern hexaploid wheat. A NimbleGen array containing both gene-based and RJM probe sequences derived from Ae. tauschii was developed and used to map the Chinese Spring nullisomic-tetrasmic lines and deletion bin lines of the D genome chromosomes. Based on these mapping data, we have now anchored 5,171 RJMs and 10,892 gene probes, corresponding to 5,070 gene sequences, to the delineated deletion bins of the D genome. The order of the gene-based markers within the deletion bins of the Chinese Spring can be inferred based on their positions in the Ae. tauschii genetic map. Analysis of the marker sequences against the Chinese Spring chromosome sequence assembly database facilitated mapping of the NimbleGen probes to the sequence contigs and allowed assignment or ordering of these sequence contigs within the deletion bins. The accumulated length of anchored sequence contigs is about 155 Mb, representing ~ 3.2 % of the D genome. A specific database was developed to allow users to search or blast the marker sequence information and to directly download PCR primers for mapping specific genetic loci. In bread wheat, aneuploid stocks have been extensively used to assign markers linked with genes/traits to chromosomes, chromosome arms, and their specific bins. Through this study, we added thousands of markers to the existing wheat chromosome bin map, representing a significant step forward. The database website ( provides easy access to and efficient utilization of the data. The resources developed herein can aid map-based cloning of traits of interest in the D genome of hexaploid wheat as well as the genome sequencing.