Genome-wide detection of superior haplotypes for seed oil and protein content in Northeast China soybean (Glycine max L.) germplasm

Seed oil content (SOC) and seed protein content (SPC) are the crucial traits determining the economic importance of soybeans. However, the molecular mechanism underlying the high SOC and low SPC of Northeast China soybeans is still limited. To address this, we elucidated the genetic basis of SOC and SPC in soybean germplasm adapted to Northeast China by employing an integrated genomic analysis. The genome-wide association study (GWAS) detected 105 and 59 significant SNPs associated with the SOC and SPC, respectively across four environments plus combined environment (CE). The haplotype allele number in the 15 identified haplotype blocks varied from 2-4 regulating the SOC and SPC in the range of 16.68-21.15% and 38.63-42.69%, respectively. Five quantitative trait loci (QTLs) among the total 17 identified QTLs were novel that include <i>qSOC1</i>, <i>qSPC1</i>, <i>qSOC9</i>, <i>qSOC_SPC15.1</i> and <i>qSOC_SPC15.2</i> associated with SOC or/and SPC. Based on the <i>in-silico</i>, variant annotation and haplotype analysis, the 80 genes were prioritized as potential candidates. The haplotype alleles of these genes varied from 2-8 regulating SOC and SPC in the range of 15.98-21.23% and 37.69%-43.30%, respectively. Twelve of 80 genes showed distinct selection signatures between the two populations, suggesting their key roles in shaping the specific seed quality profiles of soybean germplasm in Northeast China. Hence, the current study provides novel insights on divergent breeding influencing the local adaptation and seed quality difference between different regional soybean populations. Besides, the stable QTLs, superior haplotypes and candidate genes identified can be used for soybean improvement.