Data from: Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants

Maize is well known for its exceptional structural diversity, including copy number variants (CNVs) and presence/absence variants (PAVs), and there is growing evidence for the role of structural variation in maize adaptation. While PAVs have been described in this important crop species, the extent of presence/absence variation and the relative position of inbred-specific regions remain to be elucidated. De novo genome sequencing of the F2 maize inbred line which played a key role in European breeding programs over the past 50 years revealed thousands of novel genomic regions, making up 88Mb of DNA, that are present in the F2 but not in B73. Comparison of B73 and F2 PAV localization revealed contrasted chromosomal distributions between the two inbreds and specific evolutionary dynamics of PAVs as compared to SNPs. Detailed sequence and functional annotation of F2 PAV sequences revealed hundreds of new genes with transcriptional support, but also a large fraction of repetitive sequences. Detailed analysis of sequence breakpoint highlights the role of double strand break repair, but also transposon insertion in PAV generation. Typing of the B73 and F2 PAVs in maize temperate inbreds revealed that some PAVs are found only in European Flint material, thus pinpointing structural features that may be at the origin of adaptive traits involved in the success of this material. Linkage disequilibrium (LD) analysis revealed that LD is strong within PAVs, as expected by the absence of recombination in crosses where PAV is missing in one of the parents.玉米以其极高的结构多样性著称，涵盖拷贝数变异（copy number variants, CNVs）与存在/缺失变异（presence/absence variants, PAVs），且越来越多的证据表明结构变异在玉米适应性演化中发挥重要作用。尽管已在这一重要作物中鉴定出PAVs，但目前关于存在/缺失变异的覆盖范围，以及自交系特异性区域的相对位置仍有待阐明。对过去50年欧洲育种项目中发挥关键作用的玉米F2自交系进行从头基因组测序，发现了数千个全新的基因组区域，总长度达88 Mb的DNA序列，这些区域仅存在于F2自交系中，而不存在于参考基因组B73内。对比B73与F2的PAV定位结果发现，两个自交系间的染色体分布存在显著差异，且PAVs相较于单核苷酸多态性（single nucleotide polymorphisms, SNPs）具有独特的进化动态。对F2的PAV序列进行详细的序列与功能注释，发现了数百个具有转录支持证据的新基因，同时也包含大量重复序列。对序列断点的详细分析揭示了双链断裂修复（double strand break repair）在PAV产生过程中的作用，同时也证实了转座子插入参与了PAV的形成。对温带玉米自交系中的B73与F2型PAVs进行分型分析发现，部分PAVs仅存在于欧洲硬粒玉米（European Flint）材料中，这一结果精准定位了可能与该材料适应性性状起源相关的结构特征。连锁不平衡（linkage disequilibrium, LD）分析显示，PAV区域内的连锁不平衡程度较高，这与当亲本之一缺失PAV时杂交后代无重组发生的预期结果相符。