Genetic dissection of heat stress tolerance in soybean through genome-wide association studies and use of genomic prediction to enhance breeding applications

Rising temperatures and associated heat stress threaten soybean [Glycine max (L.) Merr.] productivity. With few mitigation options, improving genetic tolerance is key. However, the genetics of heat tolerance in soybean remain understudied. We evaluated 450 accessions (maturity groups 0–IV) under optimal and heat stress conditions to characterize physiological and growth traits, explore trait relationships, and assess genomic prediction. We identified 37 significant marker–trait associations (MTAs): 20 unique MTAs in optimal conditions, 16 under heat stress, and one MTA for a heat tolerance index. Only one MTA was consistent across temperatures, indicating genetic divergence in responses. Genomic prediction had moderate predictive ability for biomass traits but less accurate for physiological traits related to photosynthetic parameters. Several heat-tolerant accessions were identified for use in breeding. These results provide insights into the genetic architecture of heat tolerance, supporting marker-assisted and genomic selection to develop heat-tolerant soybean varieties.