Abstract
Key message
High-density haplotype analysis revealed significant haplotype sharing between ex-PVPs registered from 1976 to 1992 and key maize founders, and uncovered similarities and differences in haplotype sharing patterns by company and heterotic group.
Abstract
Proprietary inbreds developed by the private seed industry have been the major source for driving genetic gain in successful North American maize hybrids for decades. Much of the history of industry germplasm can be traced back to key founder lines, some of which were pivotal in the development of prominent heterotic groups. Previous studies have summarized pedigree-based relationships, genetic diversity and population structure among commercial inbreds with expired Plant Variety Protection (ex-PVP). However, less is known about the extent of haplotype sharing between historical founders and ex-PVPs. A better understanding of the relationships between founders and ex-PVPs provides insight into the haplotype and heterotic group structure among industry germplasm. We performed high-density haplotype analysis with 11.3 million SNPs on 212 maize inbreds, which included 157 ex-PVPs registered 1976–1992 and 55 public lines relevant to PVPs. Among these lines were 12 key founders identified in literature review: 207, A632, B14, B37, B73, LH123HT, LH82, Mo17, Oh43, OH7, PHG39 and Wf9. Our results revealed that, on average, 81.6% of an ex-PVP’s genome is shared with at least 1 of these 12 founder lines and more than half when limited to B73, Mo17 and 207. Quantifiable similarities and contrasts among heterotic groups and major US seed industry companies were also observed. The results from this study provide high-resolution haplotype data on ex-PVP germplasm, confirm founder relationship trends observed in previous studies, uncover region-specific haplotype structure differences and demonstrate how haplotype sharing analysis can be used as a tool to explore germplasm diversity.
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The author SMC wishes to thank Justin Gerke and Dean Podlich for helpful discussions in preparation of this manuscript.
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SMC designed the study, designed and ran the analyses, interpreted the results and wrote the manuscript. MBH, CMA and TL assisted with the study design, interpretation of results and provided critical feedback during manuscript preparation. TL supervised the study.
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The author SMC is employed by Corteva Agriscience™, Agriculture Division of DowDuPont™. The funder provided support in the form of salary and graduate program support for author SMC, but did not have any additional role in the study design, data collection and analysis, decision to publish or preparation of the manuscript. The specific roles of this author are articulated in the author contribution statement. The authors declare that they have no conflict of interest.
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Coffman, S.M., Hufford, M.B., Andorf, C.M. et al. Haplotype structure in commercial maize breeding programs in relation to key founder lines. Theor Appl Genet 133, 547–561 (2020). https://doi.org/10.1007/s00122-019-03486-y
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DOI: https://doi.org/10.1007/s00122-019-03486-y