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Haplotype diversity underlying quantitative traits in Canadian soybean breeding germplasm

Theoretical and Applied Genetics volume 133, pages 1967–1976 (2020)Cite this article

Abstract

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Identification of marker–trait associations and trait-associated haplotypes in breeding germplasm identifies regions under selection and highlights changes in haplotype diversity over decades of soybean improvement in Canada.

Abstract

Understanding marker–trait associations using genome-wide association in soybean is typically carried out in diverse germplasm groups where identified loci are often not applicable to soybean breeding efforts. To address this challenge, this study focuses on defining marker–trait associations in breeding germplasm and studying the underlying haplotypes in these regions to assess genetic change through decades of selection. Phenotype data were generated for 175 accessions across multiple environments in Ontario, Canada. A set of 76,549 SNPs were used in the association analysis. A total of 23 genomic regions were identified as significantly associated with yield (5), days to maturity (5), seed oil (3), seed protein (5) and 100-seed weight (5), of which 14 are novel. Each significant region was haplotyped to assess haplotype diversity of the underlying genomic region, identifying ten regions with trait-associated haplotypes in the breeding germplasm. The range of genomic length for these regions (7.2 kb to 6.8 Mb) indicates variation in regional LD for the trait-associated regions. Six of these regions showed changes between eras of breeding, from historical to modern and experimental soybean accessions. Continued selection on these regions may necessitate introgression of novel parental genetic diversity as some haplotypes were fixed within the breeding germplasm. This finding highlights the importance of studying associations and haplotype diversity at a breeding program scale to understand breeders’ selections and trends in soybean improvement over time. The haplotypes may also be used as a tool for selection of parental germplasm to inform breeder’s decisions on further soybean improvement.

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Acknowledgements

We would like to acknowledge funding support from the Natural Sciences and Engineering Research Council of Canada Collaborative Research and Development Grant (NSERC CRD) program and our industry partners including Grain Farmers of Ontario, Secan and Huron Commodities Inc. All of the mentioned funding is part of the NSERC CRD Grant No. CRDPJ 447948 – 13. We would also like to acknowledge Marc-André Lemay at Université Laval for his help with the HaplotypeMiner R package, the staff in Dr. Rajcan’s research program in Guelph, ON, Colbey Templeman, Yesenia Salazar, Martha Jimenez, Mei Wang and Lin Liao, as well as Bryan Stirling in Dr. Eskandari’s laboratory at Ridgetown, ON.

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Affiliations

  1. Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada

    Robert W. Bruce, Davoud Torkamaneh, Christopher M. Grainger, Milad Eskandari & Istvan Rajcan

  2. Département de Phytologie, Université Laval, Quebec City, QC, Canada

    Davoud Torkamaneh & François Belzile

  3. Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada

    Davoud Torkamaneh & François Belzile

Authors
  1. Robert W. Bruce
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  2. Davoud Torkamaneh
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  3. Christopher M. Grainger
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  4. François Belzile
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  5. Milad Eskandari
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  6. Istvan Rajcan
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Contributions

RB, CG, IR and ME performed project planning. RB, DT and FB analyzed the data. RB, DT and IR prepared the manuscript. All authors have reviewed the manuscript.

Corresponding author

Correspondence to Istvan Rajcan.

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The authors declare no conflict of interest.

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Communicated by Albrecht E. Melchinger.

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Bruce, R.W., Torkamaneh, D., Grainger, C.M. et al. Haplotype diversity underlying quantitative traits in Canadian soybean breeding germplasm. Theor Appl Genet 133, 1967–1976 (2020). https://doi.org/10.1007/s00122-020-03569-1

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  • DOI: https://doi.org/10.1007/s00122-020-03569-1