The advent of double cross hybrids and eventually single cross hybrids in maize stimulated formation of private breeding programs to develop elite inbred parents. Maize breeding programs in North America have progressed over the last century, driving the formation and evolution of heterotic groups. Modern day maize hybrids are exclusively developed using proprietary inbreds. The Plant Variety Protection Act was passed in 1970 by the U.S. Congress and provides 20 years of legal protection for inbreds and varieties developed for many species. Maize lines with expired Plant Variety Protection (ex-PVP) represent germplasm that is the foundation of many industry seed industry companies. The genetic content of these inbreds can be related back to founder lines through pedigree, molecular data or a combination of the two. Seed companies started with similar genetics from founder lines and have independently used these to evolve their own proprietary germplasm. The structure of this germplasm continues to evolve as breeding programs experiment with different line crosses within each company. Understanding the relationships between ex-PVPs and founder lines will provide insight into the haplotype and heterotic group structure of industry germplasm.

In this study, we utilize high-density SNP data to generate high resolution identity-by-state haplotypes (IBS) haplotypes for 212 maize inbred lines. Among these 212 inbred lines are 157 ex-PVPs registered 1976-1992 and 55 public inbreds relevant for PVP germplasm. These lines include ex-PVPs from the major seed industry companies DowDuPont, Monsanto and Syngenta as well as 12 key founders identified through literature review. We summarize haplotype structure and diversity among these 212 inbreds as well as haplotype sharing between the ex-PVPs and the 12 key founders. We find that more than 75% of the haplotypes present in these ex-PVPs are shared with at least one of the 12 key founders and the trends in haplotype sharing with founders by company are similar to previous pedigree-based studies. We summarize genome-wide and region-specific haplotype differences among companies and heterotic groups. To facilitate exploration of the haplotype data, a visualization tool was developed using the Shiny framework in R. We summarize this visualization framework using a subset of the 212 inbreds to demonstrate visualization of genome-wide haplotypes. Together, the results from this study demonstrate how haplotype sharing analysis can be utilized to characterize germplasm diversity and provide additional insight into the breeding history of commercial maize.