Pervasive gene content variation and copy number variation in both maize and its undomesticated progenitor. Pervasive gene content variation and copy number variation in both maize and its undomesticated progenitor

Different individuals of the same species are generally thought to have very similar genomes. However, there is growing evidence that structural variation in the form of copy number variation (CNV) and presence-absence variation (PAV) can lead to variation in the genome content of individuals within a species. In order to investigate the potential contribution of CNV and PAV to genomic diversity in maize we used array comparative genomic hybridization (CGH) to compare gene content and copy number variation among 25 diverse maize inbreds 14 genotypes of the wild ancestor of maize, teosinte. The microarray included multiple probes for each of the ~32,500 stringently filtered genes identified in the B73 reference genome. We identified 479 genes exhibiting higher copy number in some genotypes (UpCNV) and 3,410 genes that have either fewer copies or are missing in the genome of at least one genotype relative to B73 (DownCNV/PAV). Many of these DownCNV/PAV are examples of genes that are present in B73 but missing from the genome of several other genotypes. Over 70% of the CNV/PAV examples are identified in multiple genotypes and the majority of events are observed in both maize and teosinte suggesting that these reflect relatively old variants that are not associated with domestication or maize improvement. Many of the genes affected by CNV/PAV are either maize-specific or members of genes families suggesting that the gene loss can be tolerated through buffering by redundant functions encoded elsewhere in the genome. Many plant genomes are relatively large and contain the remnant of whole genome duplications which may provide the ability to tolerate high levels of structural variation. While this structural variation may not result in major qualitative variation due to genetic buffering, it may significantly contribute to quantitative variation. Overall design: 1-2 replications of 25 maize inbred and 14 teosinte genotypes were hybridized to an array designed from the ~32,400 genes in the maize B73 reference genome.

同一物种的不同个体通常被认为拥有高度相似的基因组。然而，越来越多的证据表明，以拷贝数变异（copy number variation, CNV）和有无变异（presence-absence variation, PAV）为表现形式的结构变异，可导致同一物种内不同个体间基因组内容产生差异。为探究拷贝数变异与有无变异对玉米基因组多样性的潜在贡献，本研究采用阵列比较基因组杂交（array comparative genomic hybridization, CGH）技术，对25个多样化玉米自交系以及14份玉米野生祖先大刍草（teosinte）的基因内容与拷贝数变异进行了比较分析。该芯片针对B73参考基因组中经严格筛选得到的约32500个基因，每个基因设置了多个探针。本研究共鉴定出479个在部分基因型中拷贝数更高的基因（UpCNV），以及3410个相较于B73，在至少一个基因型中拷贝数更低或完全缺失的基因（DownCNV/PAV）。其中大量DownCNV/PAV基因存在于B73基因组中，但在其他多个基因型的基因组中发生了缺失。超过70%的CNV/PAV事件可在多个基因型中被鉴定到，且多数变异事件同时在玉米与大刍草中被观测到，这表明这些变异属于相对古老的变异类型，与驯化过程或玉米品种改良并无关联。受CNV/PAV影响的诸多基因要么为玉米特异性基因，要么属于某一基因家族，这暗示基因缺失可通过基因组其他位置编码的冗余功能进行缓冲，从而得以耐受。许多植物基因组规模相对庞大，且保留有全基因组复制的残余序列，这或许为其耐受高水平的结构变异提供了基础。尽管这类结构变异可能因遗传缓冲效应而不会引发显著的质量性状变异，但却可能对数量性状变异产生重要贡献。实验整体设计：针对玉米B73参考基因组中约32400个基因制备芯片，对25份玉米自交系与14份大刍草基因型样本分别开展1-2次重复杂交实验。