In soybeans (Glycine max (L.) Merr.), their growth periods, DSF (days of sowing-to-flowering), and DFM (days of flowering-to-maturity) are determined by their required accumulative day-length (ADL) and active temperature (AAT). A sample of 354 soybean varieties from five world eco-regions was tested in four seasons in Nanjing, China. The ADL and AAT of DSF and DFM were calculated from daily day-lengths and temperatures provided by the Nanjing Meteorological Bureau. The improved restricted two-stage multi-locus genome-wide association study using gene–allele sequences as markers (coded GASM-RTM-GWAS) was performed. (i) For DSF and its related ADL_DSF and AAT_DSF, 130–141 genes with 384–406 alleles were explored, and for DFM and its related ADL_DFM and AAT_DFM, 124–135 genes with 362–384 alleles were explored, in a total of six gene–allele systems. DSF shared more ADL and AAT contributions than DFM. (ii) Comparisons between the eco-region gene–allele submatrices indicated that the genetic adaptation from the origin to the geographic sub-regions was characterized by allele emergence (mutation), while genetic expansion from primary maturity group (MG)-sets to early/late MG-sets featured allele exclusion (selection) without allele emergence in addition to inheritance (migration). (iii) Optimal crosses with transgressive segregations in both directions were predicted and recommended for breeding purposes, indicating that allele recombination in soybean is an important evolutionary drive. (iv) Genes of the six traits were mostly trait-specific involved in four categories of 10 groups of biological functions. GASM-RTM-GWAS showed potential in detecting directly causal genes with their alleles, identifying differential trait evolutionary drives, predicting recombination breeding potentials, and revealing population gene networks.

Soybean (Glycine max (L.) Merr.) is a typical short-day and thermophilic crop. This study aimed to reveal the required accumulative day length (ADL) and accumulative active temperature (AAT) for DSF (days of sowing to flowering) and DFM (days of flowering to maturity) in global soybeans. A sample consisted of 354 varieties from 27 countries in five geographic regions, which were tested in Nanjing, China in two spring-sowing and two summer-sowing seasons. The ADL and AAT were calculated from the climatological data provided by the Public Service of Nanjing Meteorological Bureau. The results showed that the average DSF and DFM of global soybeans were 41.0 d and 83.3 d, which required ADL_DSF of 606.6 d·h and AAT_DSF of 1185.9 d·°C, ADL_DFM of 1126.7 d·h and AAT_DFM of 2145.1 d·°C, respectively, all with a wide variation among/within geographic and MG(maturity-group)-set subpopulations. From the multiple regression of DSF and DFM on required ADL and AAT, the ADL, AAT and ADL×AAT contributed 38.5%, 44.79% and 17.10% to DSF variation and 86.98%, 11.42% and 0.54% to DFM variation, respectively, and their relative importance to DSF and DFM varied among the geographic and MG subpopulations. The geographic subpopulations matched only partially with the genomic marker clusters, indicating multiple genetic sources of each subpopulation and that genetic exchange happened among subpopulations.