Genome-Wide Dissection of Shade Tolerance in Soybean at Seedling Stage
2025
Linfang Hu | Kamran Arshad | Meiying Zheng | Ran Ou | Yinmeng Song | Mengyan Xie | Yazhi Wei | Luyi Ling | Weiying Zeng | Jiaoping Zhang
Dense planting and intercropping are the main ways to improve soybean production. However, both confront inter- and intra-crop shading stress. This leads to stem elongation, resulting in lodging and yield losses. Most previous studies have focused on the later growth stages for shade tolerance. However, it has been found that the seedling stage is crucial, and understanding the genetic basis of shade tolerance at this stage is pivotal for yield improvement. In this study, 310 soybean accessions were used to evaluate shade tolerance under greenhouse conditions. Plant height (PH), main stem length (MSL), and hypocotyl length (HL) were examined at seedling stage, and their treatment/control ratios (PH_r, MSL_r, HL_r) were used for genetic dissection of shade tolerance. Their overall phenotypic variation and heritability (H<sup>2</sup>) ranged 22.97–36.85% and 31.66–83.81%, respectively. RTM-GWAS identified 12, 10, and 6 QTLs associated with PH_r, MSL_r, and HL_r, respectively. Among these, <i>Block_17_11907536_11926235</i> was associated with both PH_r and MSL_r, and <i>Block_1_55630414_55715065</i> associated with the HL_r trait showed the highest contribution (R<sup>2</sup> = 10.38%). Additionally, seven promising candidate genes, primarily linked to ethylene-responsive transcription factors, were proposed, supported by their established roles in plant development and stress responses, as evidenced in prior studies. The germplasm, QTLs, and candidate genes identified in this study improve our understanding of shade tolerance and have the potential to accelerate the breeding of shade-resilient soybeans.
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