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Genomic selection for agronomic traits in a winter wheat breeding program

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Abstract

Key message

rAMP-seq based genomic selection for agronomic traits has been shown to be a useful tool for winter wheat breeding programs by increasing the rate of genetic gain.

Abstract

Genomic selection (GS) is an effective strategy to employ in a breeding program that focuses on optimizing quantitative traits, which results in the ability for breeders to select the best genotypes. GS was incorporated into a breeding program to determine the potential for implementation on an annual basis, with emphasis on selecting optimal parents and decreasing the time and costs associated with phenotyping large numbers of genotypes. The design options for applying repeat amplification sequencing (rAMP-seq) in bread wheat were explored, and a low-cost single primer pair strategy was implemented. A total of 1870 winter wheat genotypes were phenotyped and genotyped using rAMP-seq. The optimization of training to testing population size showed that the 70:30 ratio provided the most consistent prediction accuracy. Three GS models were tested, rrBLUP, RKHS and feed-forward neural networks using the University of Guelph Winter Wheat Breeding Program (UGWWBP) and Elite-UGWWBP populations. The models performed equally well for both populations and did not differ in prediction accuracy (r) for most agronomic traits, with the exception of yield, where RKHS performed the best with an r = 0.34 and 0.39 for each population, respectively. The ability to operate a breeding program where multiple selection strategies, including GS, are utilized will lead to higher efficiency in the program and ultimately lead to a higher rate of genetic gain.

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Data that are not included in the manuscript or supplementary files are available upon request.

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Acknowledgements

This work was supported by the National Research Council of Canada’s Canadian Wheat Improvement Flagship Program. We thank Janet Condie and Yasmina Bekkaoui from the National Research Council’s Nucleic Acid Solutions (NAS) facility for assistance with library preparation and sequencing. The authors would also like to thank the late Dr. Ali Navabi, who initiated and developed this project and received funding for it from the Ontario Genomics.

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Authors and Affiliations

  1. Department of Plant Agriculture, University of Guelph, Crop Science Building, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada

    Alexandra Ficht & Istvan Rajcan

  2. Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, Canada

    David J. Konkin, Dustin Cram, Christine Sidebottom & Yifang Tan

  3. Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Room 2E64, Agriculture Building, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada

    Curtis Pozniak

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  1. Alexandra Ficht
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Contributions

AF conceptualized the study, carried out all the experiments, wrote and edited the manuscript. IR provided guidance and co-advised AF during her Ph.D. and helped with data interpretation, presentation, manuscript writing and editing. CP co-advised AF and helped with data interpretation and editing of the manuscript. DJK led the rAMP-seq design, implementation and genotyping. DC performed the rAMP-seq design space analysis. CS implemented the rAMP-seq method. YT implemented the variant calling approach.

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Correspondence to Istvan Rajcan.

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Communicated by Mark E. Sorrells.

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Ficht, A., Konkin, D.J., Cram, D. et al. Genomic selection for agronomic traits in a winter wheat breeding program. Theor Appl Genet 136, 38 (2023). https://doi.org/10.1007/s00122-023-04294-1

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