title: Development of a D genome specific marker resource for diploid and hexaploid wheat.
abstract: BACKGROUND
  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 within the grass tribe, Triticeae. Mapping limitations in the Triticeae are primarily due to low frequencies of polymorphic gene markers and poor genetic recombination in certain genetic regions. Although the abundance of repetitive sequence may pose common problems in genome analysis and sequence assembly of large and complex genomes, they provide repeat junction markers with random and unbiased distribution throughout chromosomes. Hence, development of a high-throughput mapping technology that combine both gene-based and repeat junction-based markers is needed to generate maps that have better coverage of the entire genome.
  
  
  RESULTS
  In this study, the available genomics resource of the diploid Aegilop tauschii, the D genome donor of bread wheat, were used to develop genome specific markers that can be applied for mapping in modern hexaploid wheat. A NimbleGen array containing both gene-based and repeat junction probe sequences derived from Ae. tauschii was developed and used to map the Chinese Spring nullisomic-tetrasomic lines and deletion bin lines of the D genome chromosomes. Based on these mapping data, we have now anchored 5,171 repeat junction probes and 10,892 gene probes, corresponding to 5,070 gene markers, 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 on the Ae. tauschii genetic map. Analysis of the probe 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 user to search or BLAST against the probe sequence information and to directly download PCR primers for mapping specific genetic loci.
  
  
  CONCLUSIONS
  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 in providing a resource to navigate the wheat genome. The database website ( http://probes.pw.usda.gov/ATRJM/ ) provides easy access and efficient utilization of the data. The resources developed herein can aid map-based cloning of traits of interest and the sequencing of the D genome of hexaploid wheat.
authors: Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA. Yi.Wang@ars.usda.gov.|Department of Plant Sciences, University of California, Davis, CA, 95616, USA. Yi.Wang@ars.usda.gov.
authors: Yi
authors: Y
authors: Wang
authors: Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA. Thomas.Drader@ars.usda.gov.
authors: Thomas
authors: T
authors: Drader
authors: Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA. vijtiwari@ksu.edu.|Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. vijtiwari@ksu.edu.
authors: Vijay K
authors: VK
authors: Tiwari
authors: Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA. lldong@genetics.ac.cn.|Department of Plant Sciences, University of California, Davis, CA, 95616, USA. lldong@genetics.ac.cn.
authors: Lingli
authors: L
authors: Dong
authors: Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA. ajay.kumar.2.@ndsu.edu.
authors: Ajay
authors: A
authors: Kumar
authors: Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA.|Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
authors: Naxin
authors: N
authors: Huo
authors: Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA.|Molecular Breeding and Genomics Technology Laboratory, BioDiagnostics Inc., River Falls, WI, 54022, USA.
authors: Farhad
authors: F
authors: Ghavami
authors: Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA.
authors: M Javed
authors: MJ
authors: Iqbal
authors: Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA. gerard.lazo@ars.usda.gov.
authors: Gerard R
authors: GR
authors: Lazo
authors: Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA. jeff.leonard@oregonstate.edu.
authors: Jeff
authors: J
authors: Leonard
authors: Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. bsgill@k-state.edu.
authors: Bikram S
authors: BS
authors: Gill
authors: Cereal Disease Laboratory, USDA-ARS, Minneapolis, MN, 55108, USA. Shahryar.Kianian@ars.usda.gov.
authors: Shahryar F
authors: SF
authors: Kianian
authors: Department of Plant Sciences, University of California, Davis, CA, 95616, USA. mcluo@ucdavis.edu.
authors: Ming-Cheng
authors: MC
authors: Luo
authors: Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA. yong.gu@ars.usda.gov.
authors: Yong Q
authors: YQ
authors: Gu
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D015342:DNA Probes; D004171:Diploidy; D019143:Evolution, Molecular; D005819:Genetic Markers; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D011123:Polyploidy; D012091:Repetitive Sequences, Nucleic Acid; D015203:Reproducibility of Results; D017384:Sequence Deletion; D014908:Triticum / Q000235:genetics*
chemical_list: D015342:DNA Probes; D005819:Genetic Markers