Recombination Landscape of the Wheat Genome

The genome of the allopolyploid bread wheat (Triticum aestivum L.) is large and highly repetitive, with an estimated length of 17gb. Here, we use genotyping-by-sequencing (GBS) on two reference populations and three independent designs: a population of double haploids (SynOpDH) of 88 individuals, and two subsets of the population of recombinant inbred lines (SynOpRIL) of 179 and 993 individuals, respectively, to study the recombination landscape of the wheat genome. A total of 12492, 8250, and 8599 GBS-SNP markers passed the quality filters for each design and were used for linkage analysis across the hexaploid wheat 21 chromosomes. Three genetic maps, harboring 7832, 4074 and 5525 high-quality GBS-SNP markers were constructed with strict tests for linkage. The GBS-SNP markers and genetic maps were used to study recombination patterns and breakpoints, and recombination hotspots. In addition, our analysis will assist in validating a new assembly that the International Wheat Genome Sequencing Consortium (IWGSC) is finalizing using the NRGene DeNovoMAGIC 2.0 technology.