GWAS and WGCNA Analysis Uncover Candidate Genes Associated with Oil Content in Soybean

• Published in: Plants (Basel) Vol. 13; no. 10; p. 1351
• Main Authors: Zhao, Xunchao, Zhang, Yan, Wang, Jie, Zhao, Xue, Li, Yongguang, Teng, Weili, Han, Yingpeng, Zhan, Yuhang
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 01-05-2024
• Subjects: Analysis; Biosynthesis; Biotechnology industry; Fatty acids; Gene expression; Gene mapping; Genes; Genetic analysis; Genetic aspects; Genome-wide association studies; genome-wide association study (GWAS); Genomes; Germplasm; Haplotypes; Linolenic acids; Metabolism; Methods; Monounsaturated fatty acids; Network analysis; Nucleotides; oil content; Photosynthesis; Phylogenetics; Physiological aspects; Piperidine; Polymorphism; Protein transport; Proteins; Quantitative trait loci; Regulatory mechanisms (biology); Saturated fatty acids; Seeds; Single-nucleotide polymorphism; Soybean; Soybean oil; Soybeans; Tropane; Vegetable oils; WGCNA; United States; China; soybean; genome-wide association study (GWAS); WGCNA; oil content
• ISSN: 2223-7747; 2223-7747
• DOI: 10.3390/plants13101351

Soybean vegetable oil is an important source of the human diet. However, the analysis of the genetic mechanism leading to changes in soybean oil content is still incomplete. In this study, a total of 227 soybean materials were applied and analyzed by a genome-wide association study (GWAS). There are 44 quantitative trait nucleotides (QTNs) that were identified as associated with oil content. A total of six, four, and 34 significant QTN loci were identified in Xiangyang, Hulan, and Acheng, respectively. Of those, 26 QTNs overlapped with or were near the known oil content quantitative trait locus (QTL), and 18 new QTNs related to oil content were identified. A total of 594 genes were located near the peak single nucleotide polymorphism (SNP) from three tested environments. These candidate genes exhibited significant enrichment in tropane, piperidine, and pyridine alkaloid biosynthesiss (ko00960), ABC transporters (ko02010), photosynthesis-antenna proteins (ko00196), and betalain biosynthesis (ko00965). Combined with the GWAS and weighted gene co-expression network analysis (WGCNA), four candidate genes (
,
,
, and
) that may regulate oil content were identified. In addition,
was divided into two main haplotypes in the studied accessions. The oil content of haplotype 1 is significantly lower than that of haplotype 2. Our research findings provide a theoretical basis for improving the regulatory mechanism of soybean oil content.