Soluble carbohydrates in soybean - discovery of novel genetic resources and evaluation of known mutations
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Soybean [Glycine max (L.) Merr.] is the leading protein meal source, primarily used to feed non-ruminant animals, such as poultry and swine. Additionally, soy products have garnered huge popularity as a high-quality plant-based protein source in vegetarian diets worldwide. Among soluble carbohydrates, sucrose positively impacts feed efficiency and the natural sweetness of soy products. In contrast, raffinose and stachyose (RFOs) create unpleasant intestinal conditions and reduce feed efficiency in non-ruminant animals. Therefore, this research focused on three main topics, including i) the identification of novel genetic resources for high sucrose and low stachyose content via genome-wide association study (GWAS), ii) the discovery of novel quantitative trait loci (QTL) and variants for high sucrose content via QTL mapping, and iii) the evaluation of environmental stability and genetic effect of soybean lines differing in allele combinations between raffinose synthase (RS) and D-myo-inositol-3-phosphate synthase 1 (MIPS1) mutations for soluble carbohydrates. Through GWAS, seven significant single nucleotide polymorphisms (SNPs) for sucrose content were identified across chromosomes (Chrs.) 2, 8, 12, 17, and 20, whereas 13 significant SNPs for stachyose content were identified across Chrs. 2, 5, 8, 9, 10, 13, 14, and 15. Among the candidate genes, Glyma.08g361200 and Glyma.17g258100 for sucrose content and Glyma.05g025300 and Glyma.13g077900 for stachyose content were highlighted based on functional annotations, protein-protein interactions, and RNA-seq Atlas database. For QTL mapping, a high sucrose germplasm, PI 506593, was selected from the previous GWAS analysis and used as a donor parent in two bi-parental mapping populations. The QTL mapping pinpointed a major QTL region on Chr. 8 at the physical interval of 40,597,410 -- 42,861,364 bp. The whole-genome sequencing (WGS) analysis using parental lines identified unique variants in 31 candidate genes within the major QTL region based on Wm82.a2.v1 and Wm82.a5.v1 reference genomes. Among those candidate genes, Glyma.08g294300, Glyma.08g297000, and Glyma.08g300400 were closely associated with sucrose metabolism. Lastly, the environmental stability test and overall genetic effects of known mutant lines for high sucrose and low RFOs demonstrated that the mips1 mutant lines had significantly higher sucrose and lower RFOs content than other lines with rs2 and rs3 mutations across the environments. The three different germination tests showed that the germination rates of mutant lines with rs2W331- and mips1 mutations were either statistically similar or significantly greater than the check. Given the limited genetic resources and functional germplasms for desirable soluble carbohydrate profiles, this research provided valuable genetic information to maximize animal feed efficiency and market preference for soy products.
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Ph. D.