Dissecting Genetic Architecture of Flowering and Maturity Traits in Soybean Using GWAS in Indian Environment

Background Soybean ( Glycine max [L.] Merril) is a photoperiod-sensitive crop, with traits like days to flowering, days to maturity playing crucial roles in its adaptability and yield. These traits are regulated by genetic networks controlling flowering time and environmental adaptation, making their genetic basis as an essential knowledge for breeders aiming to improve yield and adaptability. In this study, a Genome-Wide Association Study (GWAS) was conducted for Days to flowering (DTF), days to maturity (DTM) by using FarmCPU, BLINK and MLM model on 254 diverse soybean genotypes over four consecutive years (2019–2022) to dissect genetic architecture for flowering and maturity traits in an Indian Environment. Results In this study, GWAS identified 20 significant loci for days to flowering and maturity, among them 12 are new and 8 were previously reported loci. Among the 12 newly identified loci, a significant locus, Lee.Gm03-3 on chromosome 03, is associated with days to flowering and linked with SNP markers S3_46108324 and S3_46108342. We also identified key candidate genes for Lee.Gm03-3, include Glyma.03G227300 (circadian rhythm and photomorphogenesis, Phytochrome region) Glyma.03G225000 (circadian rhythm, gibberellic acid signaling, red/far-red light signaling), Glyma.03G219100 (cytokinin signaling, embryo sac development), and Glyma.03G226000 (meristem initiation). These genes are vital for light-response and developmental pathways. In addition, we also validated eight previously known genes E2, E4 , E9 , E11 , E10/FT4 , PRR7/Tof12 , Dt1 , and Dt2 that influence flowering and maturity in Indian environment. Conclusions This study advances understanding of the genetic basis underlying photoperiod sensitivity related genes for circadian rhythm and photomorphogenesis, gibberellic acid signaling, red/far-red light signaling in soybean and highlights potential targets for genetic improvement of flowering maturity duration and adaptability of soybean under Indian environment.