Genetic architecture of shade tolerance in soybean (Glycine max L. Merr.) revealed by genome-wide association study

Shade tolerance is a critical trait for soybean [Glycine max (L.) Merr.] adaptation to intercropping systems. This study investigated the genetic architecture of shade response in soybean through genome-wide association analysis of 461 diverse accessions evaluated under both normal and shade conditions across two distinct environments in China (Heilongjiang and Inner Mongolia) in the 2022 season. Plant height (PH), main stem node number (MSNN), and pod number per plant (PODn) were assessed to characterize morphological responses to shade stress. Principal component analysis revealed that geographic location was the primary driver of phenotypic variation, explaining 57.4% of total variance. Shade treatment significantly increased PH while reducing MSNN and PODn across both locations, demonstrating classic shade avoidance syndrome traits. Genome-wide association study using 82,208 high-quality single-nucleotide polymorphisms (SNPs) identified 31 significant marker-trait associations (p < 6.0E-4) distributed across 14 chromosomes. Six SNPs were associated with MSNN, 20 with PODn, and five with PH. Notable stable associations included SNP Gm16_9640074 for pod number under normal conditions and Gm08_2576632 for PH under shade stress across both environments. The identification of both environment-specific and stable genetic loci demonstrates the complex genetic architecture underlying shade response in soybean. These findings provide valuable insights into the molecular mechanisms of shade tolerance and identify promising genetic markers for developing soybean varieties better adapted to intercropping systems, potentially enhancing sustainable agricultural practices in diverse agroecological zones.