We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.

我们报告了 26 个近交系的从头基因组组装、转录组、注释和甲基化组，这些近交系是玉米嵌套关联作图群体的创始人。这些不同基因组中的泛基因数量超过 103,000 个，其中大约三分之一存在于所有基因型中。结果表明，玉米的古老四倍体特征直到今天仍在通过分馏而退化。重复阵列的出色连续性和着丝粒的完整注释揭示了主要细胞学标志的额外变异。我们证明，将结构变异与单核苷酸多态性相结合可以提高定量作图研究的能力。我们还记录了 DNA 甲基化水平的变异，并证明非甲基化区域富含导致表型变异的顺式调控元件。