Genome-wide detection of quantitative trait loci and prediction of candidate genes for seed sugar composition in early mature soybean

Authors: HU, LI - Yunnan University; WANG, XIANZHI - Yunnan University; ZHANG, JIAOPING - Nanjing Agricultural University; FLORZ-PALACIOS, LILIANA - University Of Arkansas; Song, Qijian; JIANG, GOULIANG - Virginia State University

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/1/2023
Publication Date: 2/5/2023
Citation: Hu, L., Wang, X., Zhang, J., Florz-Palacios, L., Song, Q., Jiang, G. 2023. Genome-wide detection of quantitative trait loci and prediction of candidate genes for seed sugar composition in early mature soybean. International Journal of Molecular Sciences. 24:3167. https://doi.org/10.3390/ijms24043167.
DOI: https://doi.org/10.3390/ijms24043167

Interpretive Summary: Soybean seeds consist of approximately 33% carbohydrates by dry seed weight. Soluble sugars are an important part of carbohydrates, mainly including sucrose, stachyose, raffinose, glucose and fructose in soybean seeds. The proportion of sugar components in soybean seeds significantly affects the quality, digestibility and nutritional value of soybean foods. For soy foods, higher levels of sucrose, glucose, and fructose are preferred because they help provide a sweet taste and are easily digested, while raffinose and stachyose are less digestible and can cause unwanted flatulence and diarrhea. However, to date, only a limited number of studies have been performed to investigate the genetic factors controlling sugar composition. The researchers analyzed the sugar profiles of 323 soybean accessions and identified loci associated with sugar components and loci associated with total sugars. They also identified candidate genes controlling sugar traits through pathway and gene function characterization. This study will enhance our understanding of the genetic structure of sugar composition and expedite the identification of genes that regulate soybean sugar composition. It will also help in the development of markers that can be used to improve the soybean sugar composition.

Technical Abstract: Seed sugar composition, mainly including fructose, glucose, sucrose, raffinose, and stachyose, is an important indicator of soybean [Glycine max (L.) Merr.] seed quality. However, research on soybean sugar composition is limited. To better understand the genetic architecture underlying the sugar composition in soybean seeds, we conducted a genome-wide association study (GWAS) using a population of 323 soybean germplasm accessions which were grown and evaluated under three different environments. A total of 31,245 single-nucleotide polymorphisms (SNPs) with minor allele frequencies (MAFs) = 5% and missing data = 10% were selected and used in the GWAS. The analysis identified 72 quantitative trait loci (QTLs) associated with individual sugars and 14 with total sugar. Ten candidate genes within the 100 Kb flanking regions of the lead SNPs across six chromosomes were significantly associated with sugar contents. According to GO and KEGG classification, eight genes were involved in the sugar metabolism in soybean and showed similar functions in Arabidopsis. The other two located in known QTL regions associated with sugar composition may play a role in sugar metabolism in soybean. This study advances our understanding of the genetic basis of soybean sugar composition and facilitates the identification of genes controlling this trait. The identified candidate genes will help improve seed sugar composition in soybean.