QTL mapping and whole genome sequencing analysis for novel genetic resources associated with sucrose content in soybean [Glycine max (L.)Merr.]

Authors: LEE, DONGHO - University Of Missouri; VUONG, TRI - University Of Missouri; SHANNON, JAMES - University Of Missouri; Song, Qijian; LIN, FENG - University Of Missouri; NGUYEN, HENRY - University Of Missouri

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/20/2024
Publication Date: 2/3/2025
Citation: Lee, D., Vuong, T.D., Shannon, J.G., Song, Q., Lin, F., Nguyen, H. 2025. QTL mapping and whole genome sequencing analysis for novel genetic resources associated with sucrose content in soybean [Glycine max (L.)Merr.] . Theoretical and Applied Genetics. 138(43). https://doi.org/10.1007/s00122-024-04808-5.
DOI: https://doi.org/10.1007/s00122-024-04808-5

Interpretive Summary: Sucrose is not only the main source of digestible energy in animal feed, but also a natural source of sweetness in soy foods, popular among vegetarians. However, few variants and genes related to the high sucrose content of soybeans have been found. Researchers used two soybean populations bred from high-sucrose parents for quantitative trait loci (QTL) analysis, a genetic technique that precisely locates specific regions of chromosomes that affect sucrose content. Through QTL positioning and whole-genome sequencing, the research team located 11 sucrose-related QTLs on several chromosomes, with one major region located on chromosome 8. This region contains multiple genes with variants, some of which have significant effects on sucrose levels, making them key candidate genes for further study. The study provides insights into the genetic variation that controls soybean sucrose content. The information will help breeders understand the mechanisms that control sucrose content and can be used to develop markers for rapid detection of sucrose content in the early stages of growth of breeding lines, which will help accelerate the development of soybean varieties with optimized sucrose content.

Technical Abstract: Sucrose in soybean [Glycine max (L.) Merr.] contributes to animal feed efficiency and natural sweetness of soy products. In this study, two recombinant inbred line (RIL) populations derived from the same high sucrose donor parent, PI 506593, were used for quantitative trait loci (QTL) analysis. QTL analysis identified 11 sucrose-related regions on chromosomes (Chrs.) 4, 5, 6, 8, 10, and 13. Among them, four QTL (qSUC_08.1, qSUC_08.2, qSUC_08.3, and qSUC_08.4) were clustered in the interval of 40,597,410 – 42,861,364 bp on Chr. 8. We further identified 44 and 54 candidate genes with nonsynonymous mutations in the major QTL regions based on the annotations of Wm82.a2.v1 and Wm82.a5.v1 assemblies, respectively. Among 34 common candidate genes from both assembly annotations, 18 genes contained 34 variants that had deleterious impacts on biological functions. RNA-seq analysis highlighted five candidate genes that were highly expressed in pod and seed tissues during reproductive stage. A gene, Gm_Wm82_23219 (Glyma.08G293800, Wm82.a2.v1) encoding proline-rich protein 4-like, was highlighted in both PROVEAN and RNA-seq analyses. Additionally, a SNP substitution was identified in Gm_wm82_23224 (Glyma.08G294300, Wm82.a2.v1) encoding a galactosyltransferase family protein, which transfers galactose and regulates carbon partitioning between sucrose and raffinose. Our new findings in this study will be valuable sources in soybean breeding programs that aim to improve animal feed efficiency and human consumption.