Constitution and function of intergenic genome regions in cultivated versus annual wild soybean in China

The subgenus Soja, including annual wild (Glycine soja) and cultivated soybean (Glycine max), is the primary germplasm source of soybeans. We analyzed the genome constitution of 750 wild and cultivated accessions from the Chinese Soybean Germplasm Population (CSGP), covering ~20.42% genic and ~79.58% intergenic regions. Most previous genomic studies focused on gene compositions and functions, with intergenic regions being non-emphasized yet. Our results showed: (i) We defined 48,465 gene blocks (2-23 alleles/gene block) in the genic region. For intergenic region partitioning, the linkage-disequilibrium (LD) confidence interval (CI) method performed the best, identifying 137,104 SNP LD blocks (SNPLDBs, 2-24 haplotypes/SNPLDB). (ii) Wild and cultivated accessions shared 98.5%/80.9% genes/alleles and 88.0%/80.8% SNPLDBs/haplotypes, indicating high wild genomic contribution to the cultivated genome; genic and intergenic regions exhibit distinct allele/haplotype dynamics during domestication. (iii) We proposed the three-case restricted two-stage multi-locus multi-allele genome-wide association study (three-case RTM-GWAS), identifying 82 day-to-flowering (DTF) main-effect genes and 47 intergenic-SNPLDB-impacted genes (by 34 SNPLDBs) (total 129 genes, 746 alleles). These explained 98.87% of phenotypic variance (PV), with main-effect and SNPLDB-impacted genes accounting for 68.61% and 30.26% PV, respectively; gene-allele(s) impacted by SNPLDB-haplotype (one/both sides) were also identified. (iv) Domestication process excluded more large-effect positive alleles that shorten DTF in cultivated accessions, enhancing DTF's transgressive recombination potential in earliness. This study provides insights into genic/intergenic genome regions, offering a novel understanding of soybean functional genomics.