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ORIGINAL RESEARCH article

Front. Plant Sci.
Sec. Plant Breeding
Volume 15 - 2024 | doi: 10.3389/fpls.2024.1471636
This article is part of the Research Topic Utilizing Machine Learning with Phenotypic and Genotypic Data to enhance Effective Breeding in Agricultural and Horticultural Crops View all 11 articles

Performing whole-genome association analysis of winter wheat plant height using the 55K chip

Provisionally accepted
Yindeng Ding Yindeng Ding 1Guiqiang Fan Guiqiang Fan 1Yonghong Gao Yonghong Gao 1*Tianrong Huang Tianrong Huang 1*Anding Zhou Anding Zhou 1*Shan Yu Shan Yu 2*Lianjia Zhao Lianjia Zhao 3*Xiaolei Shi Xiaolei Shi 3*Sunlei Ding Sunlei Ding 3*Jiahao Hao Jiahao Hao 4Wei Wang Wei Wang 4*Jikun Song Jikun Song 5Na Sun Na Sun 6*Hui Fang Hui Fang 1*
  • 1 Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
  • 2 College of Agriculture, Xinjiang Agricultural University, Urumqi, Xinjiang, China
  • 3 Xinjiang Academy of Agricultural Sciences, Urumqi, China
  • 4 Anyang Institute of Technology, Anyang, Henan, China
  • 5 Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
  • 6 Yili Prefecture Institute of Agricultural Science, Yining, China

The final, formatted version of the article will be published soon.

    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.

    Keywords: winter wheat, Plant height, 55K SNP array, GWAS, candidate genes

    Received: 28 Jul 2024; Accepted: 19 Dec 2024.

    Copyright: © 2024 Ding, Fan, Gao, Huang, Zhou, Yu, Zhao, Shi, Ding, Hao, Wang, Song, Sun and Fang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Yonghong Gao, Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830000, China
    Tianrong Huang, Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830000, China
    Anding Zhou, Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830000, China
    Shan Yu, College of Agriculture, Xinjiang Agricultural University, Urumqi, Xinjiang, China
    Lianjia Zhao, Xinjiang Academy of Agricultural Sciences, Urumqi, 830000, China
    Xiaolei Shi, Xinjiang Academy of Agricultural Sciences, Urumqi, 830000, China
    Sunlei Ding, Xinjiang Academy of Agricultural Sciences, Urumqi, 830000, China
    Wei Wang, Anyang Institute of Technology, Anyang, 455000, Henan, China
    Na Sun, Yili Prefecture Institute of Agricultural Science, Yining, China
    Hui Fang, Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830000, China

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.