A Fine-Scale Map of Recombination and Hotspots By Re-Sequencing Recombinant Inbred Lines Approach in Soybean

Meiosis and recombination are fundamentally important processes influencing genome structure and evolution of species. Recent advances in high-throughput genotyping and next-generation sequencing technologies offer new opportunities to analyze at a large scale genome-wide distribution of crossovers and to characterize sequence motifs around crossover hotspots. Here, we constructed two high-density linkage maps by re-sequencing two soybean recombinant inbred line (RIL) populations, MPB (246 RILs) and FW82 (499 RILs). A total of 8,166 and 7,814 breakpoints were identified in these two populations, respectively, based on 109,273 and 64,989 high quality single nucleotide polymorphism (SNP) markers. About 20% of breakpoints occurred in the genic areas. The soybean genome showed extremely contrasting genomic features with regard to the gene densities and transposable elements (TEs) distribution between the pericentromeric regions and chromosomal arms. The chromosomal arm regions exhibited five-fold higher gene density and almost three-fold higher recombination rate, also five-fold reduction in TE content. About 2,000 regions in the MPB population and 395 regions in the FW82 population were identified as recombination hotspots, in which 108 hotspots were shared. Moreover, quantitative trait loci (QTL) for six agronomically important traits were identified in both populations. About 30% of QTL were shared in both populations and more than 60% of QTL shared the region with the hotspots in both populations. Overall, the fine-scale recombination landscape and genome feature along with high density SNP markers and QTL mapping of desirable traits in this research will greatly benefit the soybean breeding programs in the future.