Quantitative Trait Locus Mapping and Identification of Candidate Genes Controlling Sucrose and Stachyose Contents in Soybean [<scp><i>Glycine max</i></scp> (L.) Merr.]

ABSTRACT Soluble sugar contents in soybeans [ Glycine max (L.) Merr.], such as sucrose, raffinose and stachyose, are critical factors in determining the quality of soybean‐based foods. Elevated sucrose levels, in particular, positively influence the taste and flavour of these foods. This study aimed to identify quantitative trait loci (QTLs) and candidate genes associated with soluble sugar contents in soybean seeds. A recombinant inbred line (RIL) population was developed by crossing Saedanbaek (moderate sucrose and oligosaccharides) with Ilmi (high sucrose) and evaluated over two consecutive years. Using the single‐nucleotide polymorphism (SNP) marker–based linkage maps, we identified nine QTLs located on Chromosomes 6, 12, 15, 16, 19 and 20 with logarithm of odds (LOD) values ranging from 3.6 to 32.0, explaining 2.1%–30.4% of the phenotypic variance. Thirty‐eight annotated genes related to soybean seed soluble sugar metabolism, including those involved in starch, lipid and raffinose biosynthesis, were detected within these QTLs. These genes may influence the levels of sucrose, raffinose and stachyose during seed development and oil metabolism. Notably, we identified Glyma.15g221300 , a gene with a stop codon in the second exon of UDP‐glucuronosyl and UDP‐glucosyl transferase genes in Ilmi, which are implicated in sugar synthesis. This genetic variation could significantly impact sugar content in soybeans. Our findings provide valuable insights into the genetic mechanisms underlying soluble sugar accumulation in soybeans and facilitate the identification of potential candidate genes for breeding programs focused on enhancing soluble sugar content. These results will aid in marker‐assisted selection for the development of soybeans with optimized soluble sugar levels, ultimately improving the quality of soybean‐based food products.