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Genome-wide association study and genomic selection of spike-related traits in bread wheat

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Abstract

Key message

Identification of 337 stable MTAs for wheat spike-related traits improved model accuracy, and favorable alleles of MTA259 and MTA64 increased grain weight and yield per plant.

Abstract

Wheat (Triticum aestivum L.) is one of the three primary global, staple crops. Improving spike-related traits in wheat is crucial for optimizing spike and plant morphology, ultimately leading to increased grain yield. Here, we performed a genome-wide association study using a dataset of 24,889 high-quality unique single-nucleotide polymorphisms (SNPs) and phenotypic data from 314 wheat accessions across eight diverse environments. In total, 337 stable and significant marker–trait associations (MTAs) related to spike-related traits were identified. MTA259 and MTA64 were consistently detected in seven and six environments, respectively. The presence of favorable alleles associated with MTA259 and MTA64 significantly reduced wheat spike exsertion length and spike length, while enhancing thousand kernel weight and yield per plant. Combined gene expression and network analyses identified TraesCS6D03G0692300 and TraesCS6D03G0692700 as candidate genes for MTA259 and TraesCS2D03G0111700 and TraesCS2D03G0112500 for MTA64. The identified MTAs significantly improved the prediction accuracy of each model compared with using all the SNPs, and the random forest model was optimal for genome selection. Additionally, the eight stable and major MTAs, including MTA259, MTA64, MTA66, MTA94, MTA110, MTA165, MTA180, and MTA164, were converted into cost-effective and efficient detection markers. This study provided valuable genetic resources and reliable molecular markers for wheat breeding programs.

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Data availability

The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

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Funding

This work was supported by the Agricultural Variety Improvement Project of Shandong Province (Grant No. 2021LZGC013), the Shandong Provincial Fund for Excellent Young Scholars (Grant No. ZR2022YQ19), the National Natural Science Foundation of China (Grant Nos. 32072051 and 32272119), the Major Basic Research Project of Natural Science Foundation of Shandong Province, China (Grant No. ZR2019ZD16), the Youth Innovation Technology Support Planning Project for Institution of Higher Education of Shandong Province, China (Grant No. 2019KJF002), and the Innovation Project for graduate students of Ludong University (Grant No. IPGS2024-093).

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  1. Huiyuan Xu and Zixu Wang have contributed equally to this work.

Authors and Affiliations

  1. College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China

    Huiyuan Xu, Zixu Wang, Faxiang Wang, Xinrong Hu, Chengxue Ma, Huijiao Jiang, Chang Xie, Yuhang Gao, Guangshuo Ding, Chunhua Zhao, Ran Qin, Han Sun, Fa Cui & Yongzhen Wu

  2. Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Research Center of Wheat and Maize/Key Laboratory of Wheat Biology and Genetics and Breeding in Northern Huang-Huai River Plain, Ministry of Agriculture and Rural Affairs/Shandong Technology Innovation Center of Wheat/Jinan Key Laboratory of Wheat Genetic Improvement, Jinan, Shandong, China

    Dezhou Cui

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  1. Huiyuan Xu
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Contributions

YW, FC, and HS designed the experiments and managed the project. HX, ZW, FW, XH, CM, HJ, CX, YG, and GD performed experiments. CZ, RQ, and DC supervised the project and provided technical assistance. YW, HX, and ZW analyzed data and wrote the manuscript. All authors have read and agreed to the final published version of the manuscript.

Corresponding authors

Correspondence to Han Sun, Fa Cui or Yongzhen Wu.

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Xu, H., Wang, Z., Wang, F. et al. Genome-wide association study and genomic selection of spike-related traits in bread wheat. Theor Appl Genet 137, 131 (2024). https://doi.org/10.1007/s00122-024-04640-x

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