The stiff-stalk heterotic group in Maize (Zea mays L.) is an important source of inbreds used in U.S. commercial hybrid production. Founder inbreds B14, B37, B73, and, to a lesser extent, B84, are found in the pedigrees of a majority of commercial seed parent inbred lines. We created high-quality genome assemblies of B84 and four expired Plant Variety Protection (ex-PVP) lines LH145 representing B14, NKH8431 of mixed descent, PHB47 representing B37, and PHJ40, which is a Pioneer Hi-Bred International (PHI) early stiff-stalk type. Sequence was generated using long-read sequencing achieving highly contiguous assemblies of 2.13–2.18 Gbp with N50 scaffold lengths >200 Mbp. Inbred-specific gene annotations were generated using a core five-tissue gene expression atlas, whereas transposable element (TE) annotation was conducted using de novo and homology-directed methodologies. Compared with the reference inbred B73, synteny analyses revealed extensive collinearity across the five stiff-stalk genomes, although unique components of the maize pangenome were detected. Comparison of this set of stiff-stalk inbreds with the original Iowa Stiff Stalk Synthetic breeding population revealed that these inbreds represent only a proportion of variation in the original stiff-stalk pool and there are highly conserved haplotypes in released public and ex-Plant Variety Protection inbreds. Despite the reduction in variation from the original stiff-stalk population, substantial genetic and genomic variation was identified supporting the potential for continued breeding success in this pool. The assemblies described here represent stiff-stalk inbreds that have historical and commercial relevance and provide further insight into the emerging maize pangenome.

中文翻译：

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玉米硬茎杂种质资源库中的基因组变异

玉米硬茎杂种优势群L.) 是美国商业杂交生产中使用的自交系的重要来源。创始人自交系 B14、B37、B73 以及在较小程度上的 B84 存在于大多数商业种子亲本自交系的谱系中。我们创建了 B84 和四个过期植物品种保护 (ex-PVP) 系 LH145 代表 B14、NKH8431 混合血统、PHB47 代表 B37 和 PHJ40 的高质量基因组组装，PHJ40 是 Pioneer Hi-Bred International (PHI) 早期僵硬-茎类型。使用长读长测序生成序列，实现 2.13-2.18 Gbp 的高度连续组装，N50 支架长度 > 200 Mbp。使用核心五组织基因表达图谱生成近交特异性基因注释，而使用从头和同源定向方法进行转座因子（TE）注释。与参考近交系 B73 相比，同线性分析揭示了五个硬茎基因组的广泛共线性，尽管检测到玉米泛基因组的独特成分。将这组硬茎自交系与原始爱荷华硬茎合成育种群体的比较表明，这些近交系仅代表原始硬茎库中的一部分变异，并且在已发布的公共和植物前品种保护中存在高度保守的单倍型近交系。尽管原始硬茎种群的变异减少了，但确定了大量的遗传和基因组变异，支持在该池中继续育种成功的潜力。