Novel genetic resources associated with sucrose and stachyose content through genome-wide association study in soybean (Glycine max (L.) Merr.)

Dongho Lee; Laura Lara; David Moseley; Tri D Vuong; Grover Shannon; Dong Xu; Henry T Nguyen

doi:10.3389/fpls.2023.1294659

Novel genetic resources associated with sucrose and stachyose content through genome-wide association study in soybean (Glycine max (L.) Merr.)

Front Plant Sci. 2023 Nov 1:14:1294659. doi: 10.3389/fpls.2023.1294659. eCollection 2023.

Authors

Dongho Lee^{1

2}, Laura Lara³, David Moseley⁴, Tri D Vuong², Grover Shannon¹, Dong Xu⁵, Henry T Nguyen²

Affiliations

¹ Fisher Delta Research, Extension, and Education Center, Division of Plant Science and Technology, University of Missouri, Portageville, MO, United States.
² Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States.
³ Agrícola Los Alpes, Chimaltenango, Guatemala.
⁴ Dean Lee Research and Extension Center, LSU AgCenter, Alexandria, LA, United States.
⁵ Department of Electrical Engineering and Computer Sciences, Christopher S. Bond Life Science Center, University of Missouri, Columbia, MO, United States.

Abstract

The nutritional value of soybean [Glycine max (L.) Merr.] for animals is influenced by soluble carbohydrates, such as sucrose and stachyose. Although sucrose is nutritionally desirable, stachyose is an antinutrient causing diarrhea and flatulence in non-ruminant animals. We conducted a genome-wide association study of 220 soybean accessions using 21,317 single nucleotide polymorphisms (SNPs) from the SoySNP50K iSelect Beadchip data to identify significant SNPs associated with sucrose and stachyose content. Seven significant SNPs were identified for sucrose content across chromosomes (Chrs.) 2, 8, 12, 17, and 20, while thirteen significant SNPs were identified for stachyose content across Chrs. 2, 5, 8, 9, 10, 13, 14, and 15. Among those significant SNPs, three sucrose-related SNPs on Chrs. 8 and 17 were novel, while twelve stachyose-related SNPs on Chrs. 2, 5, 8, 9, 10, 13, 14, and 15 were novel. Based on Phytozome, STRING, and GO annotation, 17 and 24 candidate genes for sucrose and stachyose content, respectively, were highly associated with the carbohydrate metabolic pathway. Among these, the publicly available RNA-seq Atlas database highlighted four candidate genes associated with sucrose (Glyma.08g361200 and Glyma.17g258100) and stachyose (Glyma.05g025300 and Glyma.13g077900) content, which had higher gene expression levels in developing seed and multiple parts of the soybean plant. The results of this study will extend knowledge of the molecular mechanism and genetic basis underlying sucrose and stachyose content in soybean seed. Furthermore, the novel candidate genes and SNPs can be valuable genetic resources that soybean breeders may utilize to modify carbohydrate profiles for animal and human usage.

Keywords: RNA-Seq Atlas; genome-wide association study; quantitative trait loci; soluble carbohydrate; soybean.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This research was funded by the United Soybean Board (USB). This research was also funded by the Paul K. and Diane Shumaker Endowment Fund to DX.