Haplotype structure in commercial maize breeding programs in relation to key founder lines

Authors: COFFMAN, STEPHANIE - Corteva Agriscience; HUFFORD, MATTHEW - Iowa State University; Andorf, Carson; LUBBERSTEDT, THOMAS - Iowa State University

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/13/2019
Publication Date: 11/20/2019
Citation: Coffman, S.M., Hufford, M.B., Andorf, C.M., Lubberstedt, T. 2019. Haplotype structure in commercial maize breeding programs in relation to key founder lines. Theoretical and Applied Genetics. 133:547-561. https://doi.org/10.1007/s00122-019-03486-y.
DOI: https://doi.org/10.1007/s00122-019-03486-y

Interpretive Summary: Development of elite proprietary inbreds among private seed industry companies has been a major driver of increased genetic gain in North American maize hybrids over the last several decades. The history of these industry inbreds can be traced back to important founder lines, some of which were key contributors to the development of heterotic groups. Pedigree-based analyses in previous studies have been used to summarize genetic diversity and population structure among inbred lines no longer under plant variety protection (ex-PVP), however, these rely on records that are sometimes unavailable or inaccurate. Marker data have been used to assess genetic diversity among ex-PVPs often as part of larger diversity studies, but less is known regarding the extent of regions within the genome that are shared between particular ex-PVPs and their founder lines. We performed a high-density analysis based on 11.3 million variations in the genomes of 212 maize inbreds including 157 ex-PVPs and 55 public lines. We focused on 12 key founders identified through literature review. Our results reveal significant regions in the genome that are shared between these ex-PVPs and founder lines, uncover source variation and quantify similarities and contrasts between heterotic groups and the major U.S. seed industry companies. These results increase the resolution of our understanding of industry germplasm breeding history, demonstrate the effectiveness of identifying shared regions as a tool to assess germplasm diversity and provide information which can help inform line selection, trait-associate haplotypes and breeding program diversity. This work will benefit public and private maize breeders in both academia and commercial seed companies.

Technical 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 U.S. 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.