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TaCKX gene family, at large, is associated with thousand-grain weight and plant height in common wheat

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Abstract

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We used SMRT sequencing and explored the haplotypes of TaCKX genes, linked with thousand-grain weight and plant height, and developed the functionally validated markers, which can be used in the marker-assisted breeding program.

Abstract

Cytokinin oxidase/dehydrogenase (CKX) enzymes catalyze the permanent degradation of cytokinins. Identification of the TaCKX alleles associated with yield traits and the development of functional markers is the first step in using these alleles in marker-assisted breeding program. To identify the alleles, we sequenced the genome fragments, containing TaCKX genes from 48 wheat genotypes, by PacBio® sequencing. Six out of 22 TaCKX genes were found polymorphic, forming 14 distinct haplotypes. Functional markers were developed and validated for all the polymorphic TaCKX genes. Four specific haplotypes, i.e., TaCKX2A_2, TaCKX4A_2, TaCKX5A_3, and TaCKX9A_2, were found significantly associated with high thousand-grain weight (TGW) and short plant height (PH) in Chinese wheat micro-core collection (MCC) and GWAS open population (GWAS-OP), whereas TaCKX1B_2 in GWAS-OP and TaCKX11A_3 in MCC were significantly associated with high TGW and short PH. The mean values of TGW and PH for cumulative favorable haplotypes from chromosome 3A, i.e., TaCKX2A_2, TaCKX4A_2, and TaCKX5A_3, were significantly higher as compared to the cumulative unfavored haplotypes, and the change was additive in manner. Frequency distribution analysis revealed that since the 1960s, the frequency of the favorable haplotypes and TGW has gradually increased in Chinese wheat cultivars. Expression profiling in the seed tissue excised at 2, 4, 6, and 8 days after anthesis depicted that the favorable haplotypes are significantly less expressive as compared to the unfavored haplotypes. We conclude that the functional markers developed in this study can be used to select the favorable haplotypes of TaCKX genes in wheat marker-assisted breeding programs.

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Acknowledgement

This work was financially supported by the National Key R&D Program of China (2016YFD0101802).

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  1. Muhammad Shoaib and Wenlong Yang have contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China

    Muhammad Shoaib, Wenlong Yang, Qiangqiang Shan, Linhe Sun, Dongzhi Wang, Muhammad Sajjad, Xin Li, Jiazhu Sun, Dongcheng Liu & Aimin Zhang

  2. University of Chinese Academy of Sciences, Beijing, 100049, China

    Muhammad Shoaib, Linhe Sun & Dongzhi Wang

  3. Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Wenlong Yang

  4. The Collaborative Innovation Center for Grain Crops in Henan, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China

    Qiangqiang Shan & Kehui Zhan

  5. Department of Biosciences, COMSATS University Islamabad, Park Road, Tarlaikalan, Islamabad, 45550, Pakistan

    Muhammad Sajjad

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Contributions

MS, WY, QS, and LS participated in experiments, drafting the manuscript, and proposal writing. DW participated in analyzing the data. DL, JS, XL, and KZ participated in material preparation. AZ and WY participated in experimental design and corrected the manuscript. MS corrected the manuscript.

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Correspondence to Wenlong Yang or Aimin Zhang.

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Communicated by Ian D Godwin.

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Shoaib, M., Yang, W., Shan, Q. et al. TaCKX gene family, at large, is associated with thousand-grain weight and plant height in common wheat. Theor Appl Genet 133, 3151–3163 (2020). https://doi.org/10.1007/s00122-020-03661-6

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