QTLs Mapping and Identification of Candidate Genes Associated with Stachyose and Sucrose in Soybean (<i>Glycine max</i> L.)

Soluble sugars are essential components in the physiology and metabolism of soybeans (<i>Glycine max</i>), playing a critical role in regulating key processes such as development, germination, and flavor formation. The soluble sugar content in soybean seeds is primarily composed of stachyose, raffinose, sucrose, and glucose. This study aims to elucidate the genetic mechanisms underlying variation in the composition of soluble sugars in soybean seeds. A 128 recombinant inbred line (RIL) population was used, and concentrations of these four sugars were quantified across three years (2015, 2016, and 2017 in Shanxi). The analysis revealed that Jin Da 53 exhibited significantly higher sucrose and total sugar contents compared to Ping Nan, while stachyose levels were notably elevated in Ping Nan. Except for glucose content in 2017 and 2019, the RIL population’s traits all exhibited a normal distribution, making it suitable for QTL analyses. A total of twenty QTLs were identified for the four sugar components: five for glucose, four for raffinose, four for sucrose, three for stachyose, and four for total sugar, all with LOD > 2.5. Notably, three QTLs located on chromosome 10 (S10_37101443-S10_38298307, S10_38681635-S10_39134900, and S10_36697685-S10_36697916) were found to be associated with stachyose content, identifying one candidate gene, <i>Glyma.10g154400</i>, which was implicated in carbohydrate metabolic processes; a QTL located on chromosome 11 (96.881–105.5 cM) was identified in 2019 as a significant locus influencing sucrose content, identifying another candidate gene, <i>Glyma.11g136200</i>, which was linked to sugar/inositol transporter activity. Expression analysis of these candidate genes demonstrated the <i>Glyma.10g154400</i> gene exhibited higher expression levels in varieties with lower stachyose content, whereas <i>Glyma.11g136200</i> showed increased expression in lines with elevated sucrose levels. This study provides an important genetic basis for the breeding of soybean varieties with increased sugar content.