A whole-genome, radiation hybrid map of wheat

Authors: TIWARI, V - Kansas State University; HEESACKER, A - Oregon State University; RIERA-LIZARAZU, O - Dow Agro Sciences; GUNN, H - Oregon State University; WANG, S - Kansas State University; WANG, YI - University Of California; Gu, Yong; PAUX, E - Inland Northwest Research Alliance, Inra; KOO, D - Kansas State University; LUO, M - University Of California; Lazo, Gerard; AKHUNOV, E - Kansas State University; FRIEBE, B - Kansas State University; Poland, Jesse; GILL, BIKRAM - Kansas State University; Kianian, Shahryar; LEONARD, J - Oregon State University

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/22/2016
Publication Date: 3/4/2016
Citation: Tiwari, V., Heesacker, A., Riera-Lizarazu, O., Gunn, H., Wang, S., Wang, Y., Gu, Y.Q., Paux, E., Koo, D.H., Luo, M.C., Lazo, G.R., Akhunov, E., Friebe, B., Poland, J.A., Gill, B., Kianian, S., Leonard, J. 2016. A whole-genome, radiation hybrid map of wheat. Plant Journal. doi: 10.1111/tpj.13513.

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 example, conventional breeding for crop improvement is often based on genetic recombination events. However, many important regions of the chromosomes are not accessible through genetic breeding due to extremely low recombination rates in these regions. Radiation hybrid (RH) mapping technology, which relies on the frequency of physical breakage of chromosomes, often provides much better resolution in these low recombination regions. In this study, a high-throughput assay platform containing hundreds of molecular markers was used to genotype a wheat RH mapping population and to generate high resolution RH maps for the wheat genome. The utility of incorporating RH mapping data into DNA sequence assembly of large and complex plant genomes was evaluated. The results showed that RH mapping is a useful tool that can facilitate mapping and cloning of genes from low-recombination regions, providing new resources to breeders for improvement of crop traits.

Technical Abstract: Generating a reference sequence of bread wheat (Triticum aestivum L.) is a challenging task because of its large, highly repetitive and allopolyploid genome. Ordering of BAC- and NGS-based contigs in ongoing wheat genome-sequencing projects primarily uses recombination and comparative genomics-based approaches. However, recombination is suppressed within the peri-centromeric regions of wheat chromosomes and, thus, precise ordering of physical maps and sequenced contigs based on genetic maps is nearly impossible. In this study, we developed a whole-genome, radiation-hybrid (RH) resource and tested it by genotyping a randomly selected set of 115 lines on a high density SNP array. At the whole-genome level, 26,303 SNP markers were mapped on the RH panel and provided an average mapping resolution of ~248Kb/cR1500 with a total map length of 6,866 cR1500. The 7,296 unique mapping bins provided a 5-8-fold higher resolution than genetic maps used in similar studies and a mapping bin at every 2.3Mb at whole genome level. Resolution of the RH panel was validated by comparing its mapping potential with a sequenced chromosome (3B) and NGS contigs from diploid and hexaploid wheat species. Comparison of the marker order from the RH map with a sequenced physical map showed high consistency and demonstrated that RH panels developed in this study provide valuable and low-cost resource for anchoring and ordering sequenced BAC and NGS contigs. The Chinese Spring Whole-Genome Radiation-Hybrid (CS-WGRH) resource and genome mapping data generated in this study will be useful for anchoring and ordering sequenced BAC and NGS based contigs for assembling a high-quality, reference sequence of hexaploid wheat. This study provides a model for developing similar RH resource maps for other polyploid crop plants.