Abstract
In wheat, a genome-wide association study (GWAS) and genomic prediction (GP) analysis were conducted for pre-harvest sprouting (PHS) tolerance and two of its related traits. For this purpose, an association panel of 190 accessions was phenotyped for PHS (using sprouting score), falling number, and grain color over two years and genotyped with 9904 DArTseq based SNP markers. GWAS for main-effect quantitative trait nucleotides (M-QTNs) using three different models (CMLM, SUPER, and FarmCPU) and epistatic QTNs (E-QTNs) using PLINK were performed. A total of 171 M-QTNs (CMLM, 47; SUPER, 70; FarmCPU, 54) for all three traits, and 15 E-QTNs involved in 20 first-order epistatic interactions were identified. Some of the above QTNs overlapped the previously reported QTLs, MTAs, and cloned genes, allowing delineating 26 PHS-responsive genomic regions that spread over 16 wheat chromosomes. As many as 20 definitive and stable QTNs were considered important for use in marker-assisted recurrent selection (MARS). The gene, TaPHS1, for PHS tolerance (PHST) associated with one of the QTNs was also validated using the KASP assay. Some of the M-QTNs were shown to have a key role in the abscisic acid pathway involved in PHST. Genomic prediction accuracies (based on the cross-validation approach) using three different models ranged from 0.41 to 0.55, which are comparable to the results of previous studies. In summary, the results of the present study improved our understanding of the genetic architecture of PHST and its related traits in wheat and provided novel genomic resources for wheat breeding based on MARS and GP.
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Acknowledgements
The present study was supported by the Science and Engineering Research Board (SERB), Department of Science and Technology (DST), Government of India, New Delhi. HSB was awarded Honorary Scientist position by the Indian National Science Academy (INSA), New Delhi. We are thankful to Professor Parveen Chhuneja, Director, School of Agricultural Biotechnology, Punjab Agricultural University (PAU), Ludhiana, Punjab for allowing us to use KASP assay facilities. The Head, Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut provided necessary facilities for this study. CIMMYT, Mexico provided the genetic materials for the present research work.
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This work was financially supported by the Science and Engineering Research Board (SERB), Department of Science and Technology (DST), Government of India, New Delhi under the Early Career Research Award (Grant No. ECR/2016/001774).
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SK and HSB conceived the idea and designed the experiment. MK, RP, AN, and HS conducted the field experiments and phenotyping. MK, GS, and TG performed GWAS analysis. KSS and NK assisted with genomic prediction analysis, interpretation, and writing. MK and SK wrote the first draft of the manuscript. SK, HSB, and PKG critically revised and edited the manuscript. All authors read and approved the final manuscript.
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Kumar, M., Kumar, S., Sandhu, K.S. et al. GWAS and genomic prediction for pre-harvest sprouting tolerance involving sprouting score and two other related traits in spring wheat. Mol Breeding 43, 14 (2023). https://doi.org/10.1007/s11032-023-01357-5
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DOI: https://doi.org/10.1007/s11032-023-01357-5