Identification of QTN-by-environment interactions and their candidate genes for soybean seed oil-related traits using 3VmrMLM
IntroductionAlthough seed oil content and its fatty acid compositions in soybean were affected by environment, QTN-by-environment (QEIs) and gene-by-environment interactions (GEIs) were rarely reported in genome-wide association studies.MethodsThe 3VmrMLM method was used to associate the trait pheno...
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Frontiers Media S.A.
2022-12-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.1096457/full |
| _version_ | 1811178885486739456 |
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| author | Jian-Fang Zuo Ying Chen Chao Ge Jin-Yang Liu Yuan-Ming Zhang |
| author_facet | Jian-Fang Zuo Ying Chen Chao Ge Jin-Yang Liu Yuan-Ming Zhang |
| author_sort | Jian-Fang Zuo |
| collection | DOAJ |
| description | IntroductionAlthough seed oil content and its fatty acid compositions in soybean were affected by environment, QTN-by-environment (QEIs) and gene-by-environment interactions (GEIs) were rarely reported in genome-wide association studies.MethodsThe 3VmrMLM method was used to associate the trait phenotypes, measured in five to seven environments, of 286 soybean accessions with 106,013 SNPs for detecting QTNs and QEIs.ResultsSeven oil metabolism genes (GmSACPD-A, GmSACPD-B, GmbZIP123, GmSWEET39, GmFATB1A, GmDGAT2D, and GmDGAT1B) around 598 QTNs and one oil metabolism gene GmFATB2B around 54 QEIs were verified in previous studies; 76 candidate genes and 66 candidate GEIs were predicted to be associated with these traits, in which 5 genes around QEIs were verified in other species to participate in oil metabolism, and had differential expression across environments. These genes were found to be related to soybean seed oil content in haplotype analysis. In addition, most candidate GEIs were co-expressed with drought response genes in co-expression network, and three KEGG pathways which respond to drought were enriched under drought stress rather than control condition; six candidate genes were hub genes in the co-expression networks under drought stress.DiscussionThe above results indicated that GEIs, together with drought response genes in co-expression network, may respond to drought, and play important roles in regulating seed oil-related traits together with oil metabolism genes. These results provide important information for genetic basis, molecular mechanisms, and soybean breeding for seed oil-related traits. |
| first_indexed | 2024-04-11T06:25:33Z |
| format | Article |
| id | doaj.art-c4ec6afa40a34361b42401f7f007cede |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-11T06:25:33Z |
| publishDate | 2022-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-c4ec6afa40a34361b42401f7f007cede2022-12-22T04:40:23ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-12-011310.3389/fpls.2022.10964571096457Identification of QTN-by-environment interactions and their candidate genes for soybean seed oil-related traits using 3VmrMLMJian-Fang Zuo0Ying Chen1Chao Ge2Jin-Yang Liu3Yuan-Ming Zhang4College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, ChinaCollege of Plant Science and Technology, Huazhong Agricultural University, Wuhan, ChinaCollege of Plant Science and Technology, Huazhong Agricultural University, Wuhan, ChinaJiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, ChinaCollege of Plant Science and Technology, Huazhong Agricultural University, Wuhan, ChinaIntroductionAlthough seed oil content and its fatty acid compositions in soybean were affected by environment, QTN-by-environment (QEIs) and gene-by-environment interactions (GEIs) were rarely reported in genome-wide association studies.MethodsThe 3VmrMLM method was used to associate the trait phenotypes, measured in five to seven environments, of 286 soybean accessions with 106,013 SNPs for detecting QTNs and QEIs.ResultsSeven oil metabolism genes (GmSACPD-A, GmSACPD-B, GmbZIP123, GmSWEET39, GmFATB1A, GmDGAT2D, and GmDGAT1B) around 598 QTNs and one oil metabolism gene GmFATB2B around 54 QEIs were verified in previous studies; 76 candidate genes and 66 candidate GEIs were predicted to be associated with these traits, in which 5 genes around QEIs were verified in other species to participate in oil metabolism, and had differential expression across environments. These genes were found to be related to soybean seed oil content in haplotype analysis. In addition, most candidate GEIs were co-expressed with drought response genes in co-expression network, and three KEGG pathways which respond to drought were enriched under drought stress rather than control condition; six candidate genes were hub genes in the co-expression networks under drought stress.DiscussionThe above results indicated that GEIs, together with drought response genes in co-expression network, may respond to drought, and play important roles in regulating seed oil-related traits together with oil metabolism genes. These results provide important information for genetic basis, molecular mechanisms, and soybean breeding for seed oil-related traits.https://www.frontiersin.org/articles/10.3389/fpls.2022.1096457/fullQTN-by-environment interactiongene-by-environment interaction3VmrMLMgenome-wide association studyseed oil-related traitsoybean |
| spellingShingle | Jian-Fang Zuo Ying Chen Chao Ge Jin-Yang Liu Yuan-Ming Zhang Identification of QTN-by-environment interactions and their candidate genes for soybean seed oil-related traits using 3VmrMLM Frontiers in Plant Science QTN-by-environment interaction gene-by-environment interaction 3VmrMLM genome-wide association study seed oil-related trait soybean |
| title | Identification of QTN-by-environment interactions and their candidate genes for soybean seed oil-related traits using 3VmrMLM |
| title_full | Identification of QTN-by-environment interactions and their candidate genes for soybean seed oil-related traits using 3VmrMLM |
| title_fullStr | Identification of QTN-by-environment interactions and their candidate genes for soybean seed oil-related traits using 3VmrMLM |
| title_full_unstemmed | Identification of QTN-by-environment interactions and their candidate genes for soybean seed oil-related traits using 3VmrMLM |
| title_short | Identification of QTN-by-environment interactions and their candidate genes for soybean seed oil-related traits using 3VmrMLM |
| title_sort | identification of qtn by environment interactions and their candidate genes for soybean seed oil related traits using 3vmrmlm |
| topic | QTN-by-environment interaction gene-by-environment interaction 3VmrMLM genome-wide association study seed oil-related trait soybean |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.1096457/full |
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