Genome-Wide Association Study to Identify Soybean Lodging Resistance Loci and Candidate Genes

High-density planting is crucial for maximizing the genetic potential of soybean cultivars to achieve higher yields. However, increasing the planting density can lead to the risk of plant lodging. Therefore, the identification of gene loci associated with lodging resistance is considered critical for the development of high-yielding, lodging-resistant soybean cultivars. In this study, 338 natural soybean accessions from the similar latitude were used to identify candidate genes associated with lodging resistance. Based on 9,400,987 SNPs, the soybean population was classified into three subpopulations. Genome-wide association analysis revealed that under planting densities of 300,000 and 150,000 plants/ha, a total of 20 significant SNPs were repeatedly detected under both planting densities, distributed across 14 chromosomes of soybeans. A hotspot region was identified on chromosome 19, from which seven candidate genes were detected. Based on haplotype and gene expression analyses, <i>Glyma.19g212800</i> (<i>SUS3</i>) and <i>Glyma.19g212700</i> (<i>GH9B13</i>) were found to be associated with significant phenotypic variations and were identified as candidate genes. RNA-seq analysis showed that DEGs were primarily enriched in the starch and sucrose metabolism pathways. The differential expression of <i>Glyma.19g212800</i> among soybean haplotypes was further validated by qRT-PCR. By participating in sucrose decomposition and polysaccharide metabolism processes, it regulated cellulose content, thereby affecting the soybean plant lodging. This study facilitated the dissection of genetic networks underlying lodging traits in soybean, which benefits the genetic improvement of high-yield soybean with dense planting.