Novel genetic loci regulate flowering time in the northeast soybean germplasm of China

Flowering time is a crucial agronomic trait that affects the adaptability and yield of soybeans. Despite extensive research aimed at uncovering the genetic basis of flowering time in soybean germplasm, investigations involving the soybean germplasm from Northeast China have been limited. Here, we elucidated the genetic basis of days to flowering (DTF) in the soybean germplasm grown in Northeast China by employing an integrated strategy, including association mapping, quantitative trait locus (QTL) analysis, haplotype analysis, and candidate gene analysis. Overall, the genome-wide association study (GWAS) revealed 15 single-nucleotide polymorphisms (SNPs) significantly linked with DTF across six GWAS models and four individual environments plus a combined environment (CE). Five stable QTL were identified, among which four (viz., qDTF8, qDTF12, qDTF15.1, and qDTF15.2) are reported for the first time, and the remaining one (qDTF19) was detected in previous studies. On the basis of the findings of expression and haplotype analysis, fourteen putative candidate genes were detected across the genomic intervals of these five QTL. Among these genes, Glyma.19 g197600 and Glyma.19 g200700 were confirmed through both expression and haplotype analysis. Moreover, the relationship of the haplotypes with gene expression indicates that Glyma.19 g197600 is a negative regulator of early flowering, thereby providing evidence of its role in flowering. This study reveals potential genetic loci and genes that could facilitate the expansion of soybean cultivation into regions with short growing seasons and long photoperiodic conditions across the globe.