Genome-Wide Association Study of Kernel Traits Using a 35K SNP Array in Bread Wheat (Triticum aestivum L.)
Kernel size and weight are crucial components of grain yield in wheat. Deciphering their genetic basis is essential for improving yield potential in wheat breeding. In this study, five kernel traits, including kernel length (KL), kernel width (KW), kernel diameter ratio (KDR), kernel perimeter (KP),...
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Frontiers Media S.A.
2022-06-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.905660/full |
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| author | Peng Wang Peng Wang Tian Tian Tian Tian Jingfu Ma Jingfu Ma Yuan Liu Yuan Liu Peipei Zhang Tao Chen Tao Chen Fahimeh Shahinnia Delong Yang Delong Yang |
| author_facet | Peng Wang Peng Wang Tian Tian Tian Tian Jingfu Ma Jingfu Ma Yuan Liu Yuan Liu Peipei Zhang Tao Chen Tao Chen Fahimeh Shahinnia Delong Yang Delong Yang |
| author_sort | Peng Wang |
| collection | DOAJ |
| description | Kernel size and weight are crucial components of grain yield in wheat. Deciphering their genetic basis is essential for improving yield potential in wheat breeding. In this study, five kernel traits, including kernel length (KL), kernel width (KW), kernel diameter ratio (KDR), kernel perimeter (KP), and thousand-kernel weight (TKW), were evaluated in a panel consisting of 198 wheat accessions under six environments. Wheat accessions were genotyped using the 35K SNP iSelect chip array, resulting in a set of 13,228 polymorphic SNP markers that were used for genome-wide association study (GWAS). A total of 146 significant marker-trait associations (MTAs) were identified for five kernel traits on 21 chromosomes [–log10(P) ≥ 3], which explained 5.91–15.02% of the phenotypic variation. Of these, 12 stable MTAs were identified in multiple environments, and six superior alleles showed positive effects on KL, KP, and KDR. Four potential candidate genes underlying the associated SNP markers were predicted for encoding ML protein, F-box protein, ethylene-responsive transcription factor, and 1,4-α-glucan branching enzyme. These genes were strongly expressed in grain development at different growth stages. The results will provide new insights into the genetic basis of kernel traits in wheat. The associated SNP markers and predicted candidate genes will facilitate marker-assisted selection in wheat breeding. |
| first_indexed | 2024-12-12T08:30:21Z |
| format | Article |
| id | doaj.art-48d5937a7aa74cdd883a1fa16b19478a |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-12T08:30:21Z |
| publishDate | 2022-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-48d5937a7aa74cdd883a1fa16b19478a2022-12-22T00:31:07ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-06-011310.3389/fpls.2022.905660905660Genome-Wide Association Study of Kernel Traits Using a 35K SNP Array in Bread Wheat (Triticum aestivum L.)Peng Wang0Peng Wang1Tian Tian2Tian Tian3Jingfu Ma4Jingfu Ma5Yuan Liu6Yuan Liu7Peipei Zhang8Tao Chen9Tao Chen10Fahimeh Shahinnia11Delong Yang12Delong Yang13State Key Laboratory of Aridland Crop Science, Lanzhou, ChinaCollege of Life Science and Technology, Gansu Agricultural University, Lanzhou, ChinaState Key Laboratory of Aridland Crop Science, Lanzhou, ChinaCollege of Life Science and Technology, Gansu Agricultural University, Lanzhou, ChinaState Key Laboratory of Aridland Crop Science, Lanzhou, ChinaCollege of Agronomy, Gansu Agricultural University, Lanzhou, ChinaState Key Laboratory of Aridland Crop Science, Lanzhou, ChinaCollege of Life Science and Technology, Gansu Agricultural University, Lanzhou, ChinaState Key Laboratory of Aridland Crop Science, Lanzhou, ChinaState Key Laboratory of Aridland Crop Science, Lanzhou, ChinaCollege of Life Science and Technology, Gansu Agricultural University, Lanzhou, ChinaBavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Freising, GermanyState Key Laboratory of Aridland Crop Science, Lanzhou, ChinaCollege of Life Science and Technology, Gansu Agricultural University, Lanzhou, ChinaKernel size and weight are crucial components of grain yield in wheat. Deciphering their genetic basis is essential for improving yield potential in wheat breeding. In this study, five kernel traits, including kernel length (KL), kernel width (KW), kernel diameter ratio (KDR), kernel perimeter (KP), and thousand-kernel weight (TKW), were evaluated in a panel consisting of 198 wheat accessions under six environments. Wheat accessions were genotyped using the 35K SNP iSelect chip array, resulting in a set of 13,228 polymorphic SNP markers that were used for genome-wide association study (GWAS). A total of 146 significant marker-trait associations (MTAs) were identified for five kernel traits on 21 chromosomes [–log10(P) ≥ 3], which explained 5.91–15.02% of the phenotypic variation. Of these, 12 stable MTAs were identified in multiple environments, and six superior alleles showed positive effects on KL, KP, and KDR. Four potential candidate genes underlying the associated SNP markers were predicted for encoding ML protein, F-box protein, ethylene-responsive transcription factor, and 1,4-α-glucan branching enzyme. These genes were strongly expressed in grain development at different growth stages. The results will provide new insights into the genetic basis of kernel traits in wheat. The associated SNP markers and predicted candidate genes will facilitate marker-assisted selection in wheat breeding.https://www.frontiersin.org/articles/10.3389/fpls.2022.905660/fullbread wheatkernel traitsSNP arrayGWAScandidate genes |
| spellingShingle | Peng Wang Peng Wang Tian Tian Tian Tian Jingfu Ma Jingfu Ma Yuan Liu Yuan Liu Peipei Zhang Tao Chen Tao Chen Fahimeh Shahinnia Delong Yang Delong Yang Genome-Wide Association Study of Kernel Traits Using a 35K SNP Array in Bread Wheat (Triticum aestivum L.) Frontiers in Plant Science bread wheat kernel traits SNP array GWAS candidate genes |
| title | Genome-Wide Association Study of Kernel Traits Using a 35K SNP Array in Bread Wheat (Triticum aestivum L.) |
| title_full | Genome-Wide Association Study of Kernel Traits Using a 35K SNP Array in Bread Wheat (Triticum aestivum L.) |
| title_fullStr | Genome-Wide Association Study of Kernel Traits Using a 35K SNP Array in Bread Wheat (Triticum aestivum L.) |
| title_full_unstemmed | Genome-Wide Association Study of Kernel Traits Using a 35K SNP Array in Bread Wheat (Triticum aestivum L.) |
| title_short | Genome-Wide Association Study of Kernel Traits Using a 35K SNP Array in Bread Wheat (Triticum aestivum L.) |
| title_sort | genome wide association study of kernel traits using a 35k snp array in bread wheat triticum aestivum l |
| topic | bread wheat kernel traits SNP array GWAS candidate genes |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.905660/full |
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