Association mapping for canopy temperature under irrigated and rainfed conditions at 12 environments identified both known and novel genetic loci.

Soybean (Glycine max (L.) Merrill) is the most widely cultivated oilseed crop and faces significant yield challenges due to drought stress. Canopy temperature has been proposed as an effective proxy for evaluation of differences in genotypic responses to water limitation, as well as indirectly assessing transpiration and stomatal conductance. Cooler canopy temperatures are associated with higher transpiration and open stomata, whereas warmer canopy temperatures are associated with reduced transpiration and stomatal closure. This study evaluated a diverse group of 205 soybean maturity group IV genotypes across six irrigated and six rainfed environments. Genome-wide association mapping identified 111 loci associated with normalized canopy temperature (nCT). Among these, only three loci overlapped with previously identified nCT loci, while 63 loci were aligned with other drought-associated traits, and the remaining 45 loci were novel. Additionally, we identified 542 putative candidate genes in close proximity to significant single nucleotide polymorphisms, which have gene ontology annotations related to drought response mechanisms such as water transport, stomata regulation, response to temperature, and root development. Our findings were substantially consistent with previous studies on other drought tolerance traits, underscoring the interconnected nature of drought-tolerance responses, as well as highlighting common genetic resources for breeding programs to develop more drought tolerant soybean cultivars. These confirmed genomic loci offer a valuable resource for enhancing soybean resilience to drought by pyramiding favorable alleles for nCT, thereby expediting breeding for cooler canopies.