GmCP5 positively regulates seed total purine content in soybean

Purine content in soybean seeds is an important nutritional trait with direct relevance to human health, as excessive dietary purine intake is associated with gout and hyperuricemia. To investigate the genetic basis of total purine content (TPC) in soybean seeds, 264 accessions were evaluated across five environments. TPC showed high heritability and relatively limited environmental variation, with coefficients of variation ranging from 6.80% to 9.75%. Genome-wide association study (GWAS) using high-density SNP markers identified 1,266 SNPs significantly associated with TPC (-log ₁₀ ( p)  ≥ 5), including 78 loci that were consistently detected across at least two environments. A Kompetitive Allele-Specific PCR (KASP) marker was developed for the stable SNP S20_45300484 and enabled reliable discrimination between high-purine and low-purine genotypes. Four candidate genes were identified within the associated regions, representing diverse biological functions related to RNA regulation, energy metabolism, and stress responses. Functional analysis of an EMS-induced mutant demonstrated that GmCP5 positively regulates seed purine accumulation in soybean seeds. In addition, haplotype analysis identified a favorable haplotype (Hap1), associated with lower TPC and more frequent in cultivar accessions. Together, these results provide insight into the genetic control of seed purine content and offer practical gene and marker resources for the development of low-purine soybean varieties.