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. 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.

中文翻译：

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商业玉米育种计划中与关键创始人系相关的单倍型结构。

高密度单倍型分析揭示了 1976 年至 1992 年注册的前 PVP 与关键玉米创始人之间存在显着的单倍型共享，并揭示了公司和杂种优势群体在单倍型共享模式上的异同。几十年来，私营种子行业开发的专有近交系一直是推动成功的北美玉米杂交种遗传增益的主要来源。工业种质的大部分历史可以追溯到关键的创始人系，其中一些对于突出杂种优势群体的发展至关重要。以前的研究总结了具有过期植物品种保护 (ex-PVP) 的商业自交系之间基于谱系的关系、遗传多样性和种群结构。然而，对于历史创始人和前 PVP 之间的单倍型共享程度知之甚少。更好地了解创始人和前 PVP 之间的关系，可以深入了解行业种质中的单倍型和杂种优势群结构。我们对 212 个玉米自交系进行了 1130 万个 SNP 的高密度单倍型分析，其中包括 157 个 1976-1992 年注册的前 PVP 和 55 个与 PVP 相关的公共品系。在这些品系中，有 12 个在文献回顾中确定的关键创始人：207、A632、B14、B37、B73、LH123HT、LH82、Mo17、Oh43、OH7、PHG39 和 Wf9。我们的结果显示，平均而言，前 PVP 基因组的 81.6% 与这 12 个创始人系中的至少 1 个共享，当仅限于 B73、Mo17 和 207 时，超过一半共享。杂种优势群体和主要美国之间的可量化相似性和对比种子工业公司也被观察到。