Genome-wide association studies reveal novel QTLs, QTL-by-environment interactions and their candidate genes for tocopherol content in soybean seed
Genome-wide association studies (GWAS) is an efficient method to detect quantitative trait locus (QTL), and has dissected many complex traits in soybean [Glycine max (L.) Merr.]. Although these results have undoubtedly played a far-reaching role in the study of soybean biology, environmental interac...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-10-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.1026581/full |
| _version_ | 1811329539482058752 |
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| author | Kuanwei Yu Huanran Miao Hongliang Liu Jinghang Zhou Meinan Sui Yuhang Zhan Ning Xia Xue Zhao Yingpeng Han |
| author_facet | Kuanwei Yu Huanran Miao Hongliang Liu Jinghang Zhou Meinan Sui Yuhang Zhan Ning Xia Xue Zhao Yingpeng Han |
| author_sort | Kuanwei Yu |
| collection | DOAJ |
| description | Genome-wide association studies (GWAS) is an efficient method to detect quantitative trait locus (QTL), and has dissected many complex traits in soybean [Glycine max (L.) Merr.]. Although these results have undoubtedly played a far-reaching role in the study of soybean biology, environmental interactions for complex traits in traditional GWAS models are frequently overlooked. Recently, a new GWAS model, 3VmrMLM, was established to identify QTLs and QTL-by-environment interactions (QEIs) for complex traits. In this study, the GLM, MLM, CMLM, FarmCPU, BLINK, and 3VmrMLM models were used to identify QTLs and QEIs for tocopherol (Toc) content in soybean seed, including δ‐Tocotrienol (δ‐Toc) content, γ‐Tocotrienol (γ‐Toc) content, α‐Tocopherol (α‐Toc) content, and total Tocopherol (T-Toc) content. As a result, 101 QTLs were detected by the above methods in single-environment analysis, and 57 QTLs and 13 QEIs were detected by 3VmrMLM in multi-environment analysis. Among these QTLs, some QTLs (Group I) were repeatedly detected three times or by at least two models, and some QTLs (Group II) were repeatedly detected only by 3VmrMLM. In the two Groups, 3VmrMLM was able to correctly detect all known QTLs in group I, while good results were achieved in Group II, for example, 8 novel QTLs were detected in Group II. In addition, comparative genomic analysis revealed that the proportion of Glyma_max specific genes near QEIs was higher, in other words, these QEIs nearby genes are more susceptible to environmental influences. Finally, around the 8 novel QTLs, 11 important candidate genes were identified using haplotype, and validated by RNA-Seq data and qRT-PCR analysis. In summary, we used phenotypic data of Toc content in soybean, and tested the accuracy and reliability of 3VmrMLM, and then revealed novel QTLs, QEIs and candidate genes for these traits. Hence, the 3VmrMLM model has broad prospects and potential for analyzing the genetic structure of complex quantitative traits in soybean. |
| first_indexed | 2024-04-13T15:45:41Z |
| format | Article |
| id | doaj.art-b018a76b46be418f978dcefc324a3b17 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-13T15:45:41Z |
| publishDate | 2022-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-b018a76b46be418f978dcefc324a3b172022-12-22T02:40:59ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-10-011310.3389/fpls.2022.10265811026581Genome-wide association studies reveal novel QTLs, QTL-by-environment interactions and their candidate genes for tocopherol content in soybean seedKuanwei YuHuanran MiaoHongliang LiuJinghang ZhouMeinan SuiYuhang ZhanNing XiaXue ZhaoYingpeng HanGenome-wide association studies (GWAS) is an efficient method to detect quantitative trait locus (QTL), and has dissected many complex traits in soybean [Glycine max (L.) Merr.]. Although these results have undoubtedly played a far-reaching role in the study of soybean biology, environmental interactions for complex traits in traditional GWAS models are frequently overlooked. Recently, a new GWAS model, 3VmrMLM, was established to identify QTLs and QTL-by-environment interactions (QEIs) for complex traits. In this study, the GLM, MLM, CMLM, FarmCPU, BLINK, and 3VmrMLM models were used to identify QTLs and QEIs for tocopherol (Toc) content in soybean seed, including δ‐Tocotrienol (δ‐Toc) content, γ‐Tocotrienol (γ‐Toc) content, α‐Tocopherol (α‐Toc) content, and total Tocopherol (T-Toc) content. As a result, 101 QTLs were detected by the above methods in single-environment analysis, and 57 QTLs and 13 QEIs were detected by 3VmrMLM in multi-environment analysis. Among these QTLs, some QTLs (Group I) were repeatedly detected three times or by at least two models, and some QTLs (Group II) were repeatedly detected only by 3VmrMLM. In the two Groups, 3VmrMLM was able to correctly detect all known QTLs in group I, while good results were achieved in Group II, for example, 8 novel QTLs were detected in Group II. In addition, comparative genomic analysis revealed that the proportion of Glyma_max specific genes near QEIs was higher, in other words, these QEIs nearby genes are more susceptible to environmental influences. Finally, around the 8 novel QTLs, 11 important candidate genes were identified using haplotype, and validated by RNA-Seq data and qRT-PCR analysis. In summary, we used phenotypic data of Toc content in soybean, and tested the accuracy and reliability of 3VmrMLM, and then revealed novel QTLs, QEIs and candidate genes for these traits. Hence, the 3VmrMLM model has broad prospects and potential for analyzing the genetic structure of complex quantitative traits in soybean.https://www.frontiersin.org/articles/10.3389/fpls.2022.1026581/fullGWAS3VmrMLMsoybeantocopherol contentQTLcandidate genes |
| spellingShingle | Kuanwei Yu Huanran Miao Hongliang Liu Jinghang Zhou Meinan Sui Yuhang Zhan Ning Xia Xue Zhao Yingpeng Han Genome-wide association studies reveal novel QTLs, QTL-by-environment interactions and their candidate genes for tocopherol content in soybean seed Frontiers in Plant Science GWAS 3VmrMLM soybean tocopherol content QTL candidate genes |
| title | Genome-wide association studies reveal novel QTLs, QTL-by-environment interactions and their candidate genes for tocopherol content in soybean seed |
| title_full | Genome-wide association studies reveal novel QTLs, QTL-by-environment interactions and their candidate genes for tocopherol content in soybean seed |
| title_fullStr | Genome-wide association studies reveal novel QTLs, QTL-by-environment interactions and their candidate genes for tocopherol content in soybean seed |
| title_full_unstemmed | Genome-wide association studies reveal novel QTLs, QTL-by-environment interactions and their candidate genes for tocopherol content in soybean seed |
| title_short | Genome-wide association studies reveal novel QTLs, QTL-by-environment interactions and their candidate genes for tocopherol content in soybean seed |
| title_sort | genome wide association studies reveal novel qtls qtl by environment interactions and their candidate genes for tocopherol content in soybean seed |
| topic | GWAS 3VmrMLM soybean tocopherol content QTL candidate genes |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.1026581/full |
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