Genomic analysis and characterization of new loci associated with seed protein and oil content in soybeans

Authors: VUONG, TRI - University Of Missouri; FLOREZ-PALACIOS, LILIANA - University Of Arkansas; MOZZONI, LEANDRO - University Of Arkansas; CLUBB, MICHAEL - University Of Missouri; Quigley, Charles - Chuck; Song, Qijian; KAMAD, SHAILA - University Of Missouri; YUAN, ANDY - The Chinese University Of Hong Kong (CUHK); CHAN, TINGFUNG - The Chinese University Of Hong Kong (CUHK); Mian, Rouf; NGUYEN, HENRY - (NCE, CECR)networks Of Centres Of Exellence Of Canada, Centres Of Excellence For Commercilization A

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/2/2023
Publication Date: 11/8/2023
Citation: Vuong, T.D., Florez-Palacios, L., Mozzoni, L., Clubb, M., Quigley, C.V., Song, Q., Kamad, S., Yuan, A., Chan, T., Mian, R.M., Nguyen, H. 2023. Genomic analysis and characterization of new loci associated with seed protein and oil content in soybeans. The Plant Genome. (16)4. Article e20400. https://doi.org/10.1002/tpg2.20400.
DOI: https://doi.org/10.1002/tpg2.20400

Interpretive Summary: Soybean is a unique legume whose seeds contain high-quality vegetable protein and edible oils, providing a valuable source of nutrition for human consumption, animal feed, and many industrial applications. Among them, meal protein is the main dietary requirement of the livestock industry, accounting for 68% of the total global plant protein consumption, while soybean oil, as a by-product of meal production, accounts for more than half of the global oilseed production. Therefore, identification of germplasm and novel genes for increasing soybean seed protein and oil content has been one of the main goals of soybean breeding programs and is supported by soybean producers. In this study, the researchers identified a stable and novel major genomic region of protein and oil content on chromosome 20 after analyzing populations from the promising high-yielding and high-protein line R05-1415 in a multi-field setting. This analysis also led to the identification of candidate genes harbored in this region, laying a foundation for gene functional studies. The gene can be transferred or pyramided with other genetic resources to improve soybean protein and oil content in breeding programs once it is validated.

Technical Abstract: Breeding for increased protein without a reduction in oil content in soybeans [Glycine max (L.) Merr.] is a challenge for soybean breeders but an expected goal. Many efforts have been made to develop new soybean varieties with high yield in combinations of desirable protein and/or oil traits. An elite line, R05-1415, was reported to be high yielding, high protein, and low oil. Several significant quantitative trait loci (QTL) for protein and oil were reported in this line, but many of them were unstable across environments or genetic backgrounds. Thus, a new study under multi-field environments using the Infinium BARCSoySNP6K Beadchips was conducted to detect and confirm stable genomic loci for these traits. Genetic analyses consistently detected a single major genomic locus conveying these two traits with very high phenotypic variation (R2), varying 24.2 to 43.5%. This new genomic locus located between 25,0 and 26,7 Mb, distant from the previously reported QTL and did not overlap with other commonly reported QTL and the recently cloned gene Glyma.20G085100. Homolog analysis indicated that this QTL was not resulted from the paracentric chromosome inversion with an adjacent genomic fragment that harbors the reported QTL. Pleiotropic effect of this QTL could be a challenge for improving protein and oil simultaneously; however, a further study of four candidate genes with significant expressions in the seed developmental stages coupled with haplotype analysis could be able to pinpoint causative genes. The functionality and roles of these genes can be determined and characterized, which lay a solid foundation for the improvement of protein and oil content in soybeans.