title: A whole-genome, radiation hybrid mapping resource of hexaploid wheat.
abstract: Generating a contiguous, ordered reference sequence of a complex genome such as hexaploid wheat (2n = 6x = 42; approximately 17 GB) is a challenging task due to its large, highly repetitive, and allopolyploid genome. In wheat, ordering of whole-genome or hierarchical shotgun sequencing contigs is primarily based on recombination and comparative genomics-based approaches. However, comparative genomics approaches are limited to syntenic inference and recombination is suppressed within the pericentromeric regions of wheat chromosomes, thus, precise ordering of physical maps and sequenced contigs across the whole-genome using these approaches is nearly impossible. We developed a whole-genome radiation hybrid (WGRH) resource and tested it by genotyping a set of 115 randomly selected lines on a high-density single nucleotide polymorphism (SNP) array. At the whole-genome level, 26 299 SNP markers were mapped on the RH panel and provided an average mapping resolution of approximately 248 Kb/cR1500 with a total map length of 6866 cR1500 . The 7296 unique mapping bins provided a five- to eight-fold higher resolution than genetic maps used in similar studies. Most strikingly, the RH map had uniform bin resolution across the entire chromosome(s), including pericentromeric regions. Our research provides a valuable and low-cost resource for anchoring and ordering sequenced BAC and next generation sequencing (NGS) contigs. The WGRH developed for reference wheat line Chinese Spring (CS-WGRH), will be useful for anchoring and ordering sequenced BAC and NGS based contigs for assembling a high-quality, reference sequence of hexaploid wheat. Additionally, this study provides an excellent model for developing similar resources for other polyploid species.
authors.affiliation: Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA.
authors.forename: Vijay K
authors.initials: VK
authors.lastname: Tiwari
authors.affiliation: Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA.
authors.forename: Adam
authors.initials: A
authors.lastname: Heesacker
authors.affiliation: Dow AgroSciences, Pullman, WA, USA.
authors.forename: Oscar
authors.initials: O
authors.lastname: Riera-Lizarazu
authors.affiliation: Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA.
authors.forename: Hilary
authors.initials: H
authors.lastname: Gunn
authors.affiliation: Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA.
authors.forename: Shichen
authors.initials: S
authors.lastname: Wang
authors.affiliation: Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, NY, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, NY, USA.
authors.forename: Young Q
authors.initials: YQ
authors.lastname: Gu
authors.affiliation: Diversité et Ecophysiologie des Céréales, INRA, UMR 1095 Génétique, 5 chemin de Beaulieu, F-63039, Clermont-Ferrand, France.|Diversité et Ecophysiologie des Céréales, UMR 1095 Génétique, Université Blaise Pascal, F-63177, Aubière Cedex, France.
authors.forename: Etienne
authors.initials: E
authors.lastname: Paux
authors.affiliation: Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA.
authors.forename: Dal-Hoe
authors.initials: DH
authors.lastname: Koo
authors.affiliation: Department of Plant Sciences, North Dakota State University, Fargo, ND, USA.
authors.forename: Ajay
authors.initials: A
authors.lastname: Kumar
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, USA.
authors.forename: Ming-Cheng
authors.initials: MC
authors.lastname: Luo
authors.affiliation: Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, NY, USA.
authors.forename: Gerard
authors.initials: G
authors.lastname: Lazo
authors.affiliation: Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Zemetra
authors.affiliation: Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA.
authors.forename: Eduard
authors.initials: E
authors.lastname: Akhunov
authors.affiliation: Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA.
authors.forename: Bernd
authors.initials: B
authors.lastname: Friebe
authors.affiliation: Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA.
authors.forename: Jesse
authors.initials: J
authors.lastname: Poland
authors.affiliation: Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA.
authors.forename: Bikram S
authors.initials: BS
authors.lastname: Gill
authors.affiliation: Cereal Disease Laboratory, University of Minnesota, Saint Paul, MN, USA.
authors.forename: Shahryar
authors.initials: S
authors.lastname: Kianian
authors.affiliation: Department of Crop and Soil Science, Oregon State University, Corvallis, OR, USA.
authors.forename: Jeffrey M
authors.initials: JM
authors.lastname: Leonard
mesh_terms: D002874:Chromosome Mapping; D020451:Contig Mapping; D059014:High-Throughput Nucleotide Sequencing; D020641:Polymorphism, Single Nucleotide; D021101:Radiation Hybrid Mapping; D017422:Sequence Analysis, DNA; D014908:Triticum / Q000235:genetics*
keywords: Radiation hybrid mapping; Triticum aestivum; gamma radiation; genome assembly; physical mapping; wheat resource