Xin Ma, Lei Fan, Zhifang Zhang, Xia Yang, Yucheng Liu, Yanming Ma, Yi Pan, Guoan Zhou, Min Zhang, Hailong Ning, Fanjiang Kong, Junkui Ma, Shulin Liu, Zhixi Tian²

Plant Biotechnol J.; 2023 Mar;21(3):606-620. doi: 10.1111/pbi.13975

Abstract

Recombination is crucial for crop breeding because it can break linkage drag and generate novel allele combinations. However, the high-resolution recombination landscape and its driving forces in soybean are largely unknown. Here, we constructed eight recombinant inbred line (RIL) populations and genotyped individual lines using the high-density 600K SoySNP array, which yielded a high-resolution recombination map with 5636 recombination sites at a resolution of 1.37 kb. The recombination rate was negatively correlated with transposable element density and GC content but positively correlated with gene density. Interestingly, we found that meiotic recombination was enriched at the promoters of active genes. Further investigations revealed that chromatin accessibility and active epigenetic modifications promoted recombination. Our findings provide important insights into the control of homologous recombination and thus will increase our ability to accelerate soybean breeding by manipulating meiotic recombination rate.

See https://pubmed.ncbi.nlm.nih.gov/36458856/

Figure 1 Construction of the high‐density 600K SoySNP array and its characteristics. (a) The design process of the 600K SoySNP array in soybean. MAF, minor allele frequency. (b) The distribution of SNPs along the 20 chromosomes. The number of SNPs in the non‐overlapping window with the size of 1 Mb was counted along the chromosome. (c) The distribution of SNP intervals. (d) The proportions of SNPs in intergenic and intragenic regions. (e) The classification of SNPs in intragenic regions. According to the genome annotation, SNPs in intragenic regions were classed in exonic regions (locating in a coding exon), splicing sites (within 2 bp of a splicing junction), 5′ untranslated regions (UTRs) and 3′ UTRs, intronic regions (overlapping with an intron), upstream (within a 1 kb region upstream from the transcription start site) and downstream regions (locating in a 1 kb region downstream from the transcription termination site). (f) Impacts of high‐quality SNPs in coding regions. (g) The distribution of SNPs with different minor allele frequency (MAF) in the natural soybean populations. Red lines represent the number of SNPs in various intervals for MAF.