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Single-trait, multi-locus and multi-trait GWAS using four different models for yield traits in bread wheat

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Abstract

A genome-wide association study (GWAS) for 10 yield and yield component traits was conducted using an association panel comprising 225 diverse spring wheat genotypes. The panel was genotyped using 10,904 SNPs and evaluated for three years (2016–2019), which constituted three environments (E1, E2 and E3). Heritability for different traits ranged from 29.21 to 97.69%. Marker-trait associations (MTAs) were identified for each trait using data from each environment separately and also using BLUP values. Four different models were used, which included three single trait models (CMLM, FarmCPU, SUPER) and one multi-trait model (mvLMM). Hundreds of MTAs were obtained using each model, but after Bonferroni correction, only 6 MTAs for 3 traits were available using CMLM, and 21 MTAs for 4 traits were available using FarmCPU; none of the 525 MTAs obtained using SUPER could qualify after Bonferroni correction. Using BLUP, 20 MTAs were available, five of which also figured among MTAs identified for individual environments. Using mvLMM model, after Bonferroni correction, 38 multi-trait MTAs, for 15 different trait combinations were available. Epistatic interactions involving 28 pairs of MTAs were also available for seven of the 10 traits; no epistatic interactions were available for GNPS, PH, and BYPP. As many as 164 putative candidate genes (CGs) were identified using all the 50 MTAs (CMLM, 3; FarmCPU, 9; mvLMM, 6, epistasis, 21 and BLUP, 11 MTAs), which ranged from 20 (CMLM) to 66 (epistasis) CGs. In-silico expression analysis of CGs was also conducted in different tissues at different developmental stages. The information generated through the present study proved useful for developing a better understanding of the genetics of each of the 10 traits; the study also provided novel markers for marker-assisted selection (MAS) to be utilized for the development of wheat cultivars with improved agronomic traits.

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Acknowledgements

The material for association panel and the genotypic data for this work was received from CIMMYT, Mexico. Thanks are due to the Department of Biotechnology (DBT), Govt of India for providing funds in the form of research projects awarded to Shailendra Sharma (SS). The authors are thankful to Ch. Charan Singh University, Meerut for providing laboratory and field facilities. HSB was awarded positions of INSA Senior Scientist/Honorary Scientist during the course of the study by INSA, New Delhi.

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  1. Parveen Malik and Jitendra Kumar equal contribution

Authors and Affiliations

  1. Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India

    Parveen Malik, Jitendra Kumar, Sahadev Singh, Shiveta Sharma, Pradeep Kumar Sharma, Harindra Singh Balyan, Pushpendra Kumar Gupta & Shailendra Sharma

  2. National Agri-Food Biotechnology Institute (NABI), Sector 81, Sahibzada Ajit Singh Nagar, 140306, Punjab, India

    Jitendra Kumar & Joy Kumar Roy

  3. Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India

    Prabina Kumar Meher

  4. Department of Mathematics, Chaudhary Charan Singh University, Meerut 250004, India

    Mukesh Kumar Sharma

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  1. Parveen Malik
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  2. Jitendra Kumar
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  3. Sahadev Singh
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Contributions

SS (Shailendra Sharma) conceived and conducted or directed the experiments. PM, JK, SS1(SahadevSingh), SS2 (Shiveta Sharma) performed the experiments. JK, PKM, MS analysed the data. JKR, PKS, HSB, PKG and SS participated in manuscript writing. SS finalized the manuscript.

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Correspondence to Shailendra Sharma.

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Malik, P., Kumar, J., Singh, S. et al. Single-trait, multi-locus and multi-trait GWAS using four different models for yield traits in bread wheat. Mol Breeding 41, 46 (2021). https://doi.org/10.1007/s11032-021-01240-1

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