Data from: Insights into the maize pan-genome and pan-transcriptome

Genomes at the species level are dynamic, with genes present in every individual (core) and genes in a subset of individuals (dispensable) that collectively constitute the pan-genome. Using transcriptome sequencing of seedling RNA from 503 maize (Zea mays) inbred lines to characterize the maize pan-genome, we identified 8681 representative transcript assemblies (RTAs) with 16.4% expressed in all lines and 82.7% expressed in subsets of the lines. Interestingly, with linkage disequilibrium mapping, 76.7% of the RTAs with at least one single nucleotide polymorphism (SNP) could be mapped to a single genetic position, distributed primarily throughout the nonpericentromeric portion of the genome. Stepwise iterative clustering of RTAs suggests, within the context of the genotypes used in this study, that the maize genome is restricted and further sampling of seedling RNA within this germplasm base will result in minimal discovery. Genome-wide association studies based on SNPs and transcript abundance in the pan-genome revealed loci associated with the timing of the juvenile-to-adult vegetative and vegetative-to-reproductive developmental transitions, two traits important for fitness and adaptation. This study revealed the dynamic nature of the maize pan-genome and demonstrated that a substantial portion of variation may lie outside the single reference genome for a species.

物种水平的基因组处于动态变化状态，包含所有个体均携带的核心基因，以及仅存在于部分个体中的附属基因，二者共同构成泛基因组（pan-genome）。本研究对503个玉米（Zea mays）自交系的幼苗RNA开展转录组测序以解析玉米泛基因组，共鉴定得到8681个代表性转录本组装体（representative transcript assemblies, RTAs），其中16.4%在所有自交系中均表达，82.7%仅在部分自交系中表达。值得注意的是，通过连锁不平衡作图，76.7%携带至少一个单核苷酸多态性（single nucleotide polymorphism, SNP）的RTAs可被定位至单个遗传位点，且这些位点主要分布于基因组的非着丝粒周围区域。对RTAs开展的逐步迭代聚类分析显示，就本研究使用的基因型材料而言，玉米基因组的可变范围有限，在此种质资源基础上进一步对幼苗RNA进行采样，新发现的转录本数量将极为有限。基于泛基因组内的SNP与转录本丰度开展的全基因组关联研究，揭示了与幼龄到成年营养生长、营养生长向生殖发育转变的时序相关的遗传位点——这两个性状对于作物适合度与适应性均具有重要意义。本研究阐明了玉米泛基因组的动态特性，并证实物种的单个参考基因组之外，还存在大量的遗传变异。