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

Authors: Bellaloui, Nacer; Smith, James; RAY, JEFFERY - Retired ARS Employee; Kumar, Neeraj; Feng, Chunda; ABDELRAHEEM, ABDELRAHEEM - Oak Ridge Institute For Science And Education (ORISE); Mengistu, Alemu

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/16/2026
Publication Date: 6/18/2026
Citation: Bellaloui, N., Smith, J.R., Ray, J.D., Kumar, N.N., Feng, C., Abdelraheem, A., Mengistu, A. 2026. Identification of genomic regions and candidate genes associated with soybean seed sugars in a RIL population. Frontiers in Plant Science. 17:1-16. https://doi.org/10.3389/fpls.2026.1785097.
DOI: https://doi.org/10.3389/fpls.2026.1785097

Interpretive Summary: 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 sugars are indigestible, and therefore undesirable for humans and monogastric animals. Thus, identifying DNA regions and genes controlling sugar levels in soybean seed is desirable to develop optimal levels of each sugar. A soybean population (201 soybean genotypes), tolerant to heat, was developed, and field experiments were conducted in 2018 and 2019 at Stoneville, MS. Results showed that a total of 19 DNA regions (quantitative trait loci, QTLs), among which 12 were novel (not previously reported), were identified for sucrose, raffinose and stachyose. More than 50 candidate genes were identified and are involved in sugar metabolism. The molecular markers (single nucleotide polymorphisms, SNPs), QTLs, and candidate genes, identified in this study, provide new information that was previously unknown. The new markers and genes discovered here will assist breeders to select for higher seed sucrose, and lower seed raffinose and stachyose to increase higher soymeal nutritional qualities, enhancing farmer economic profit and minimizing the production cost.

Technical Abstract: 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 the 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 quantitative trait loci (QTLs) using a high-density linkage map with 8,445 single nucleotide polymorphism (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, 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. Two QTL (qRaf-Gm06-01-2018 and qRaf-Gm20-02-2018) were detected for raffinose on chrs 6 and 20, and two QTL were identified for stachyose (qSta-Gm06-01-2018 and qSta-Gm19-02-2018) on chrs 6 and 19. 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 assist breeders to select higher sucrose and lower stachyose to increase soymeal nutritional qualities. This will enhance farmer economic profit and minimize production costs.