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GWAS for main effects and epistatic interactions for grain morphology traits in wheat

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Abstract

In the present study in wheat, GWAS was conducted for identification of marker trait associations (MTAs) for the following six grain morphology traits: (1) grain cross-sectional area (GCSA), (2) grain perimeter (GP), (3) grain length (GL), (4) grain width (GWid), (5) grain length–width ratio (GLWR) and (6) grain form-density (GFD). The data were recorded on a subset of spring wheat reference set (SWRS) comprising 225 diverse genotypes, which were genotyped using 10,904 SNPs and phenotyped for two consecutive years (2017–2018, 2018–2019). GWAS was conducted using five different models including two single-locus models (CMLM, SUPER), one multi-locus model (FarmCPU), one multi-trait model (mvLMM) and a model for Q x Q epistatic interactions. False discovery rate (FDR) [P value -log10(p) ≥ 5] and Bonferroni correction [P value -log10(p) ≥ 6] (corrected p value < 0.05) were applied to eliminate false positives due to multiple testing. This exercise gave 88 main effect and 29 epistatic MTAs after FDR and 13 main effect and 6 epistatic MTAs after Bonferroni corrections. MTAs obtained after Bonferroni corrections were further utilized for identification of 55 candidate genes (CGs). In silico expression analysis of CGs in different tissues at different parts of the seed at different developmental stages was also carried out. MTAs and CGs identified during the present study are useful addition to available resources for MAS to supplement wheat breeding programmes after due validation and also for future strategic basic research.

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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. The authors are thankful to Ch. Charan Singh University, Meerut for providing laboratory and field facilities. Harindra Singh Balyan was awarded positions of INSA Senior Scientist/Honorary Scientist during the course of the study by INSA, New Delhi.

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  1. Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, U.P, 250 004, India

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

  2. Department of Biotechnology, National Agri-Food Biotechnology Institute (NABI), Govt. of India, Sector 81 (Knowledge City), S.A.S. Nagar, Mohali, Punjab, 140306, India

    Jitendra Kumar

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

    Prabina Kumar Meher

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Shailendra Sharma conceived and conducted or directed the experiments. Parveen Malik, Jitendra Kumar and Shiveta Sharma performed the experiments. Prabina Kumar Meher, Jitendra Kumar, Parveen Malik analysed the data. Harindra Singh Balyan, Pushpendra Kumar Gupta and Shailendra Sharma participated in manuscript writing. Shailendra Sharma finalized the manuscript.

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Malik, P., Kumar, J., Sharma, S. et al. GWAS for main effects and epistatic interactions for grain morphology traits in wheat. Physiol Mol Biol Plants 28, 651–668 (2022). https://doi.org/10.1007/s12298-022-01164-w

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