Mapping the Genetic Architecture of Flowering and Maturity in Soybean [glycine Max (L.) Merr.] Using Multi-Locus Genome-Wide Association Studies under Ethiopian Conditions

Flowering and maturity time in soybean are highly sensitive to photoperiod and influence adaptation and yield potential. In Ethiopia, soybean yield remains stagnant at about 2.4 t/ha. Precocious flowering and maturity induced by tropical short-day environments are the primary contributors to the low yields. This study dissects the genetic basis of flowering and maturity under Ethiopian conditions. A diverse panel of 323 accessions, from 13 U.S. maturity groups (MG 000 to X), was evaluated across four mid-altitude production environments. A multi-locus genome-wide association study was conducted using the mrMLM framework by integrating phenotypic data with 38,281 high-quality SNPs. Analysis of variance for the phenotypic traits revealed significant differences among the genotypes. Population structure analysis clustered the accessions into four groups, and linkage disequilibrium decayed at approximately 229 kb. Eight stable quantitative trait nucleotides (QTNs) with LOD > 3 were identified across five chromosomes; six co-localized with known loci and two were novel. Several candidate genes involved in controlling flowering and maturity act as regulators of phase transitions and circadian rhythms. For instance, Glyma.13g274900 encodes an SBP-type protein Glyma.13g274300 encodes a NAM domain, Glyma.13g273300 encodes a PHD-type domain, Glyma.12g009100, a cytochrome b5 domain, and Glyma.19g206100 encodes an auxin response factor. Allelic effect analysis demonstrated that homozygous alleles significantly delay flowering and extend maturity. The identified QTNs should be considered for advanced molecular breeding applications aimed at developing high-yielding soybean lines suited to Ethiopia’s unique tropical mid-altitude environments. Future research should validate these candidate genes and their gene interactions.