Biparental resequencing coupled with SNP genotyping of a segregating population offers insights into the landscape of recombination and fixed genomic regions in elite soybean

Identification of genes underlying agronomic traits is dependent on the segregation of quantitative trait loci (QTL). A popular hypothesis is that elite lines are becoming increasingly similar to each other, resulting in large genomic regions with fixed genes. Here, we resequenced two parental modern elite soybean lines [ZhongHuang13 (ZH) and ZhongPin03-5373 (ZP)] and discovered 794,876 SNPs with reference to the published Williams82 genome. SNPs were distributed unevenly across the chromosomes, with 87.1% of SNPs clustering in 4.9% of the soybean reference genome. Most of the regions with a high density of SNP polymorphisms were located in the chromosome arms. Moreover, seven large regions that were highly similar between parental lines were identified. A GoldenGate SNP genotyping array was designed using 384 SNPs and the 254 recombinant inbred lines (F₈) derived from the cross of ZP × ZH were genotyped. We constructed a genetic linkage map using a total of 485 molecular markers, including 313 SNPs from the array, 167 simple sequence repeats (SSRs), 4 expressed sequence tag-derived SSRs, and 1 insertion/deletion marker. The total length of the genetic map was 2594.34 cM, with an average marker spacing of 5.58 cM. Comparing physical and genetic distances, we found 20 hotspot and 14 coldspot regions of recombination. Our results suggest that the technology of resequencing of parental lines coupled with high-throughput SNP genotyping could efficiently bridge the genotyping gap and provide deep insights into the landscape of recombination and fixed genomic regions in biparental segregating populations of soybean with implications for fine mapping of QTL.