Performing whole-genome association analysis of winter wheat plant height using the 55K chip
Plant height is a critical agronomic that affects both plant architecture and yield. To decipher the genetic mechanisms underlying winter wheat plant height and identify candidate genes associated with this trait, we conducted phenotypic analysis on 239 wheat varieties (lines) collected from around...
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Frontiers Media S.A.
2025-01-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2024.1471636/full |
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| author | Yindeng Ding Guiqiang Fan Yonghong Gao Tianrong Huang Anding Zhou Shan Yu Lianjia Zhao Xiaolei Shi Sunlei Ding Jiahao Hao Wei Wang Jikun Song Na Sun Hui Fang |
| author_facet | Yindeng Ding Guiqiang Fan Yonghong Gao Tianrong Huang Anding Zhou Shan Yu Lianjia Zhao Xiaolei Shi Sunlei Ding Jiahao Hao Wei Wang Jikun Song Na Sun Hui Fang |
| author_sort | Yindeng Ding |
| collection | DOAJ |
| description | Plant height is a critical agronomic that affects both plant architecture and yield. To decipher the genetic mechanisms underlying winter wheat plant height and identify candidate genes associated with this trait, we conducted phenotypic analysis on 239 wheat varieties (lines) collected from around the world. This analysis was complemented by genotyping using the wheat 55K SNP chip. A Wholegenome association analysis (GWAS) of wheat plant height was conducted utilizing the MLM (Q+K) model within TASSLE software. The results revealed significant phenotypic variation in wheat plant height across different years, with coefficients of variation ranging from 0.96% to 1.97%. Additionally, there was a strong correlation in plant height measurements between different years. GWAS identified 44 SNP markers significantly associated with wheat plant height across various environments (P ≤ 0.00001), predominantly distributed on chromosomes 1B, 1D, 2A, 2B, 2D, 3B, 3D, 4A, 4B, 6B, 6D, and 7D, explaining individual phenotypic variance rates ranging from 5.00% to 11.11%. Further, by mining association loci with substantial phenotypic effects and stability across multiple environments, seven candidate genes related to wheat plant height have been identified. This study provides new genetic markers and resources for improving wheat plant height. |
| format | Article |
| id | doaj-art-b9bda603014a46069d3b4470f426f372 |
| institution | Kabale University |
| issn | 1664-462X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj-art-b9bda603014a46069d3b4470f426f3722025-01-17T06:51:00ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2025-01-011510.3389/fpls.2024.14716361471636Performing whole-genome association analysis of winter wheat plant height using the 55K chipYindeng Ding0Guiqiang Fan1Yonghong Gao2Tianrong Huang3Anding Zhou4Shan Yu5Lianjia Zhao6Xiaolei Shi7Sunlei Ding8Jiahao Hao9Wei Wang10Jikun Song11Na Sun12Hui Fang13Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Xinjiang, ChinaInstitute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Xinjiang, ChinaInstitute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Xinjiang, ChinaInstitute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Xinjiang, ChinaInstitute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Xinjiang, ChinaCollege of Agriculture, Xinjiang Agricultural University, Xinjiang, ChinaInstitute of Crop Variety Resources, Xinjiang Academy of Agricultural Sciences, Xinjiang, ChinaInstitute of Crop Variety Resources, Xinjiang Academy of Agricultural Sciences, Xinjiang, ChinaInstitute of Crop Variety Resources, Xinjiang Academy of Agricultural Sciences, Xinjiang, ChinaDepartment of Computer Science and Information Engineering, Anyang Institute of Technology, Anyang, ChinaDepartment of Computer Science and Information Engineering, Anyang Institute of Technology, Anyang, ChinaCotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, ChinaYili Prefecture Institute of Agricultural Sciences/Yili Prefecture Key Laboratory of Crop Breeding and Quality Detection, Yining, ChinaInstitute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Xinjiang, ChinaPlant height is a critical agronomic that affects both plant architecture and yield. To decipher the genetic mechanisms underlying winter wheat plant height and identify candidate genes associated with this trait, we conducted phenotypic analysis on 239 wheat varieties (lines) collected from around the world. This analysis was complemented by genotyping using the wheat 55K SNP chip. A Wholegenome association analysis (GWAS) of wheat plant height was conducted utilizing the MLM (Q+K) model within TASSLE software. The results revealed significant phenotypic variation in wheat plant height across different years, with coefficients of variation ranging from 0.96% to 1.97%. Additionally, there was a strong correlation in plant height measurements between different years. GWAS identified 44 SNP markers significantly associated with wheat plant height across various environments (P ≤ 0.00001), predominantly distributed on chromosomes 1B, 1D, 2A, 2B, 2D, 3B, 3D, 4A, 4B, 6B, 6D, and 7D, explaining individual phenotypic variance rates ranging from 5.00% to 11.11%. Further, by mining association loci with substantial phenotypic effects and stability across multiple environments, seven candidate genes related to wheat plant height have been identified. This study provides new genetic markers and resources for improving wheat plant height.https://www.frontiersin.org/articles/10.3389/fpls.2024.1471636/fullwinter wheatplant height55K SNP arrayGWAScandidate genes |
| spellingShingle | Yindeng Ding Guiqiang Fan Yonghong Gao Tianrong Huang Anding Zhou Shan Yu Lianjia Zhao Xiaolei Shi Sunlei Ding Jiahao Hao Wei Wang Jikun Song Na Sun Hui Fang Performing whole-genome association analysis of winter wheat plant height using the 55K chip Frontiers in Plant Science winter wheat plant height 55K SNP array GWAS candidate genes |
| title | Performing whole-genome association analysis of winter wheat plant height using the 55K chip |
| title_full | Performing whole-genome association analysis of winter wheat plant height using the 55K chip |
| title_fullStr | Performing whole-genome association analysis of winter wheat plant height using the 55K chip |
| title_full_unstemmed | Performing whole-genome association analysis of winter wheat plant height using the 55K chip |
| title_short | Performing whole-genome association analysis of winter wheat plant height using the 55K chip |
| title_sort | performing whole genome association analysis of winter wheat plant height using the 55k chip |
| topic | winter wheat plant height 55K SNP array GWAS candidate genes |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2024.1471636/full |
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