Identification of genomic regions and candidate genes associated with soybean seed sugars in a RIL population

Soybean seed sugar profiling determines the quality of soymeal for humans and livestock nutrition. Seed sucrose is desirable for taste and flavor, whereas raffinose and stachyose are indigestible, and therefore undesirable for humans and monogastric animals. Thus, identifying the genomic regions and genes controlling sugar type and level in the seed is desirable for developing optimal levels of each sugar. The objective of this research was to locate the genomic regions for seed sugars content and further identify potential candidate genes involved in sugar metabolism. A segregating mapping population (recombinant inbred lines, RILs) for heat tolerance was developed from a cross between DS25-1 (heat-tolerant parent) and DT97-4290. Both DS25-1 and DT97-4290 are maturity group IV. 201 RILs, parents, and checks were planted in field experiments conducted in 2018 and 2019 without irrigation at Stoneville, MS. Composite interval mapping (CIM) was performed to identify QTLs using a high-density linkage map with 8,445 polymorphic SNP markers. A logarithm of odds (LOD) value of ≥ 2.5 was used as the QTL significance level. Results showed that a total of 19 QTL for seed sugars, among which 12 were novel, were identified. A total of 8 QTL was identified for sugars in 2018. Four QTL (qSu-Gm03-01-2018, qSu-Gm05-02-2018, qSu-Gm11-03-2018, and qSu-Gm19-04-2018) were identified for sucrose on chromosomes (chrs) 3, 5, 11, and 19, respectively. Two QTL (qRaf-Gm06-01-2018 and qRaf-Gm20-02-2018) were detected for raffinose on chrs 6 and 20, respectively, and two QTL were identified for stachyose (qSta-Gm06-01-2018 and qSta-Gm19-02-2018) on chrs 6 and 19, respectively. In 2019, four QTL on chrs 5, 9, 17, 19; four QTL on chrs 6, 14, 19, and 20; and three QTL on chrs 3, 13, 19, were identified for sucrose, raffinose and stachyose, respectively. More than 50 candidate genes within each QTL interval were identified that are involved in sugar metabolic pathways. The SNP markers, QTLs, and candidate genes identified in this study provide new information that was previously unknown. The molecular markers will potentially assist breeders to select higher sucrose and lower stachyose that will increase soymeal nutritional qualities, enhancing farmer economic profit and minimizing production cost.