Growth period QTL-allele constitution of global soybeans and its differential evolution changes in geographic adaptation versus maturity-group extension.

Soybean has been disseminated globally as a photoperiod-temperature sensitive crop with extremely diverse days-to-flowering (DTF) and -maturity (DTM). A population with 371 global varieties covering 13 geographic regions (GRs) and 13 maturity groups (MGs) were analyzed for its DTF and DTM QTL-allele constitution using RTM-GWAS (restricted two-stage multi-locus genome-wide association study). Genotyped with 20,701 genome-wide SNPLDBs (SNP linkage-disequilibrium blocks) containing 55,404 haplotypes, 52 DTF and 59 DTM QTLs (including 29 and 21 new ones) with 241 and 246 alleles (2-13/locus) were detected, explaining phenotypic variance 84.8% and 74.4%, respectively. The QTL-allele matrix characterized with all QTL-allele information of each variety in the global population was established, and subsequently separated into geographic and MG-set submatrices. Direct comparisons among them revealed that the genetic motivation from the origin to geographic subpopulations was characterized with new-allele/new-locus emergence (mutation) but few allele-exclusion (selection), while that from the primary MG-set to emerged early and late MG-sets was allele-exclusion without allele-emergence. The evolutionary changes involved mainly 72 DTF and 71 DTM alleles on respective 28 loci, especially 10-12 loci each with 3-6 alleles showed most active. Further recombination-potential for maturity-shortening (12-21d) and maturity-extending (14-56d) supported allele-convergence (recombination) as a constant genetic motivator in addition to migration (inheritance). From the QTLs, 44 DTF and 36 DTM candidate genes were annotated and grouped respectively into 9 biological processes, indicating multi-functional DTF/DTM genes involving in a gene complex network. The key of this study was to identify QTLs-alleles relative-thoroughly using RTM-GWAS for direct matrix comparisons and subsequent analysis.