Genome-wide association study of diverse soybean [Glycine max (L.) Merrill] accessions for agronomic and seed composition traits in Rwanda.

This research explored the genetic basis of adaptation for soybean to the low-latitude but high-elevation production regions in Rwanda. Soybean [Glycine max (L.) Merrill] is an increasingly important crop in Rwanda; however, production remains constrained by limited availability of high-yielding, locally adapted cultivars. The varieties introduced through Rwanda's Crop Intensification Program were developed for other regions of sub-Saharan Africa and exhibit poor adaptation, delayed maturity and low productivity in Rwanda. This study evaluated diverse germplasm to support development of a national soybean breeding program. A total of 466 accessions representing maturity groups (MG) III-X were evaluated across six environments in Rwanda during 2017 and 2018. Trials were conducted in randomized complete block designs with three or two replications. Traits evaluated included flowering (R1), beginning pod (R3), maturity (R8), reproductive periods, plant height, single-row harvest weight, 100-seed weight and seed protein and oil content. Genotype and genotype-by-environment effects were highly significant (p < 0.001) for all traits, with strong correlations among phenology, plant height, reproductive period and seed composition. MG IV-VII accessions demonstrated full season adaptation to Rwanda's high-elevation environments. Genome-wide association analysis identified significant QTNs: for R1 (30), R3 (26), R8 (33), reproductive periods from R1-R8 (25) and R3-R8 (9), plant height (31), 100-seed weight (30), single-row harvest weight (29), protein (17) and oil (8). GDD-based traits yielded 21, 19, 30, 24 and 10 QTNs for GDD_R1, GDD_R3, GDD_R8, GDD_RP and RP_3, respectively, for 222 unique and a total of 342 QTNs. These findings provide potential markers for selection and a foundation for breeding high-yielding, adapted soybean cultivars for high-elevation, low-latitude agroecosystems.