Novel genetic resources associated with sucrose and stachyose content through genome-wide association study in soybean (Glycine max (L.) Merr.)
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 a...
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| Format: | Article |
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Frontiers Media S.A.
2023-11-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1294659/full |
| _version_ | 1797643266539126784 |
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| author | Dongho Lee Dongho Lee Laura Lara David Moseley Tri D. Vuong Grover Shannon Dong Xu Henry T. Nguyen |
| author_facet | Dongho Lee Dongho Lee Laura Lara David Moseley Tri D. Vuong Grover Shannon Dong Xu Henry T. Nguyen |
| author_sort | Dongho Lee |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-11T14:12:16Z |
| format | Article |
| id | doaj.art-78cb17728abd455cb6af58baac1c093b |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-03-11T14:12:16Z |
| publishDate | 2023-11-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-78cb17728abd455cb6af58baac1c093b2023-11-01T17:27:50ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-11-011410.3389/fpls.2023.12946591294659Novel genetic resources associated with sucrose and stachyose content through genome-wide association study in soybean (Glycine max (L.) Merr.)Dongho Lee0Dongho Lee1Laura Lara2David Moseley3Tri D. Vuong4Grover Shannon5Dong Xu6Henry T. Nguyen7Fisher Delta Research, Extension, and Education Center, Division of Plant Science and Technology, University of Missouri, Portageville, MO, United StatesDivision of Plant Science and Technology, University of Missouri, Columbia, MO, United StatesAgrícola Los Alpes, Chimaltenango, GuatemalaDean Lee Research and Extension Center, LSU AgCenter, Alexandria, LA, United StatesDivision of Plant Science and Technology, University of Missouri, Columbia, MO, United StatesFisher Delta Research, Extension, and Education Center, Division of Plant Science and Technology, University of Missouri, Portageville, MO, United StatesDepartment of Electrical Engineering and Computer Sciences, Christopher S. Bond Life Science Center, University of Missouri, Columbia, MO, United StatesDivision of Plant Science and Technology, University of Missouri, Columbia, MO, United StatesThe 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.https://www.frontiersin.org/articles/10.3389/fpls.2023.1294659/fullgenome-wide association studyRNA-Seq Atlassoybeansoluble carbohydratequantitative trait loci |
| spellingShingle | Dongho Lee Dongho Lee Laura Lara David Moseley Tri D. Vuong Grover Shannon Dong Xu Henry T. Nguyen Novel genetic resources associated with sucrose and stachyose content through genome-wide association study in soybean (Glycine max (L.) Merr.) Frontiers in Plant Science genome-wide association study RNA-Seq Atlas soybean soluble carbohydrate quantitative trait loci |
| title | Novel genetic resources associated with sucrose and stachyose content through genome-wide association study in soybean (Glycine max (L.) Merr.) |
| title_full | Novel genetic resources associated with sucrose and stachyose content through genome-wide association study in soybean (Glycine max (L.) Merr.) |
| title_fullStr | Novel genetic resources associated with sucrose and stachyose content through genome-wide association study in soybean (Glycine max (L.) Merr.) |
| title_full_unstemmed | Novel genetic resources associated with sucrose and stachyose content through genome-wide association study in soybean (Glycine max (L.) Merr.) |
| title_short | Novel genetic resources associated with sucrose and stachyose content through genome-wide association study in soybean (Glycine max (L.) Merr.) |
| title_sort | novel genetic resources associated with sucrose and stachyose content through genome wide association study in soybean glycine max l merr |
| topic | genome-wide association study RNA-Seq Atlas soybean soluble carbohydrate quantitative trait loci |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1294659/full |
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