Genome-Wide Identification of Candidate Genes Underlying Soluble Sugar Content in Vegetable Soybean ( L.) Association and Expression Analysis.

Soluble sugar is a major indicator of the intrinsic quality of vegetable soybean [ (L.) Merr. ]. The improvement of soluble sugar content in soybean is very important due to its healthcare functions for humans. The genetic mechanism of soluble sugar in soybean is unclear. In this study, 278 diverse soybean accessions were utilized to identify the quantitative trait nucleotides (QTNs) for total soluble sugar content in soybean seeds based on a genome-wide association study (GWAS). A total of 25,921 single-nucleotide polymorphisms (SNPs) with minor allele frequencies (MAFs) ≥ 5% and missing data ≤ 10% were selected for GWAS. Totally, thirteen QTNs associated with total soluble sugar content were identified, which were distributed on ten chromosomes. One hundred and fifteen genes near the 200-kb flanking region of these identified QTNs were considered candidate genes associated with total soluble sugar content in soybean seed. Gene-based association analysis and haplotype analysis were utilized to further identify the effect of candidate genes on total soluble sugar content. Totally, 84 SNPs from seventeen genes across four chromosomes were significantly associated with the total soluble sugar content. Among them, three SNPs from were identified at two locations, and other eighty-one SNPs from sixteen genes were detected at three locations. Furthermore, expression level analysis of candidate genes revealed that and were significantly positively associated with soluble sugar content and was significantly negatively associated with soluble sugar content. Six genes (i.e., , and ) identified by GWAS were also detected by the analysis of differential expression genes based on soybean germplasms with higher and lower soluble sugar content. Among them, is the only gene that was identified by gene-based association analysis with total soluble sugar content and was considered an important candidate gene for soluble sugar content. These candidate genes and beneficial alleles would be useful for improving the soluble sugar content of soybean.