Selecting Drought-Tolerance Markers: An Exploratory Analysis in Contrasting Soybeans

Identifying high-yield genotypes under low water availability is an important goal for soybean breeding. However, a major bottleneck lies in phenotyping, particularly in selecting cost-efficient markers associated with stress tolerance and yield stabilization. Here, we conducted in-depth phenotyping experiments using two soybean genotypes with contrasting drought tolerance, MUNASQA (tolerant) and TJ2049 (susceptible), aiming to identify and statistically validate stress tolerance and yield stabilization markers. Firstly, at the R5 critical reproductive stage, the molecular differences between the genotypes responses to mild water deficit were explored through massive analysis of cDNA ends (MACE)-transcriptomic and gene ontology. MUNASQA transcriptional profile, compared to TJ2049, revealed significant differences when responding to drought. Next, both genotypes were phenotyped under mild water deficit, imposed in vegetative (V3) and R5 stages, by evaluating 22 stress-response, growth and water-use markers, which were subsequently correlated between phenological stages and with yield. Several markers showed high consistency, independent of the phenological stage, demonstrating the effectiveness of the phenotyping methodology and its possible use for early selection. Finally, these markers were classified and selected according to their cost-feasibility, statistical weight and correlation with yield. Here, pubescence, stomatal density and canopy temperature depression emerged as promising markers for early selection of drought-tolerant soybeans.