Haplotype diversity underlying quantitative traits in Canadian soybean breeding germplasm
- 19 March 2020
- journal article
- research article
- Published by Springer Science and Business Media LLC in Theoretical and Applied Genetics
- Vol. 133 (6), 1967-1976
- https://doi.org/10.1007/s00122-020-03569-1
Abstract
Key message Identification of markerâtrait 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 markerâtrait 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 markerâtrait 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 breedersâ selections and trends in soybean improvement over time. The haplotypes may also be used as a tool for selection of parental germplasm to inform breederâs decisions on further soybean improvement.Funding Information
- National Science and Engineering Research Council of Canada (CRDPJ 447948 - 13)
- Grain Farmers of Ontario (CRDPJ 447948 - 13)
- SeCan (CRDPJ 447948 - 13)
- Huron Commodities Inc. (CRDPJ 447948 - 13)
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