Molecular-assisted breeding for improved carbohydrate profiles in soybean seed

Authors: HAGELY, KATHERINE - University Of Missouri; JO, HYUN - Kyungpook National University; KIM, JEONGHWA - University Of Missouri; Hudson, Karen; BILYEU, KRISTIN - US Department Of Agriculture (USDA)

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/7/2020
Publication Date: 1/20/2020
Citation: Hagely, K., Jo, H., Kim, J., Hudson, K.A., Bilyeu, K. 2020. Molecular-assisted breeding for improved carbohydrate profiles in soybean seed. Theoretical and Applied Genetics. 133:1189-1200. https://doi.org/10.1007/s00122-020-03541-z.
DOI: https://doi.org/10.1007/s00122-020-03541-z

Interpretive Summary: Soybean is a major protein meal crop, however soybean meal contains compounds called raffinose family oligosaccharides (RFOs) that prevent optimal digestion of soybean meal in non-ruminant animals. There are few varieties of soybeans with lower levels of RFOs available to growers and breeders, and geneticists are still working to understand which genes control this trait. It was found in this study that plants that have mutations inactivating two genes (RAFFINOSE SYNTHASE2 and RAFFINOSE SYNTHASE3) in the RFO biosynthesis pathway contain very low levels of the antinutritional RFOs and provide increased levels of sucrose. This trait shows promise for improved soybean meal with enhanced energy content.

Technical Abstract: Soybean is an important crop because the processed seed is utilized as a vegetable oil and a high protein meal typically used in livestock feeds. Raffinose and stachyose, the raffinose family of oligosaccharides (RFO) carbohydrate components of the seed, are synthesized in developing soybean seeds from sucrose and galactinol. Sucrose is considered positive for metabolizable energy while RFO are anti-nutritional factors in diets of monogastric animals such as humans, poultry and swine. To increase metabolizable energy available in soybean seed meal, prior research has been successful in deploying variant alleles of key soybean raffinose synthase (RS) genes leading to reductions or near elimination of seed RFO, with significant increases in seed sucrose. The objective of this research was to investigate the specific role of variants of the RS3 gene in a genomic context and improve molecular marker assisted selection for the ultra-low RFO phenotype in soybean seeds. The results revealed a haplotype-specific variant RS3 allele could contribute to the ultra-low RFO phenotype when mutant alleles of RS2 were present. The variant RS3 allele identified was present in about 15% of a small set of soybean cultivars released in North America. In addition, a novel missense allele of the RS3 gene was found that also produced the ultra-low RFO seed carbohydrate phenotype when combined with mutant alleles of RS2. The discoveries reported here enable direct marker assisted selection for an improved soybean meal trait that has the potential to add value to soybean by improving the metabolizable energy of the meal.