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A whole-genome, radiation hybrid mapping resource of hexaploid wheat

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  • 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.
  • Keywords: gamma radiation, physical mapping, Radiation hybrid mapping, genome assembly, wheat resource, Triticum aestivum
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  • Tiwari, V. K., Heesacker, A., Riera‐Lizarazu, O., Gunn, H., Wang, S., Wang, Y., ... & Leonard, J. M. (2016). A Whole‐Genome, Radiation Hybrid Mapping Resource of Hexaploid Wheat. The Plant Journal, 86(2), 195-207. doi:10.1111/tpj.13153
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  • 86
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  • 2
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  • This work was supported by funding from the National Science Foundation, Plant Genome Research Program (NSF-PGRP) grant no. IOS-082210. A part of research was also supported by Oregon Wheat Commission. VKT was supported by WGRC I/UCRC partially funded by an NSF grant contract (IIP-1338897). Computational support for this project was provided by the Beocat High-performance Computing Cluster at Kansas State University, which is funded in part by NSF grants CNS-1006860, EPS-1006860, and EPS-0919443. This work represents contribution number from Kansas Agricultural Experiment Station, Kansas State University, Manhattan KS 66506-502, USA.
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