Novel comparative genomics of cultivated soybeans

Accurate definition of recombination blocks is necessary for efficient molecular breeding and screening trait-related locus. Yet, the linkage disequilibrium block-based analysis has made it hardly applicable to these purposes because of its limitation for detecting recombination blocks. Here, by high-depth sequencing of five cultivated soybean genomes, we developed novel method determining accurate recombination blocks, called CRB (Core Recombination Block) based on SNV density information, and found that soybean genomes are the assembly of very long-length of distinct CRBs, up to 10Mb, like LEGO. These CRB-based comparative genomics enabled accurate identification of all recombination blocks at the whole chromosome level and successfully utilized to analyze publically available 31 soybean genomes. We also identified new Ih locus determining yellow hilum color of soybean using small InDel markers representing dense mutation blocks. Therefore, CRB is a promising platform for molecular breeding and for map-based cloning.