Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32611, USA.
Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
Genetics. 2022 Jul 30;221(4). doi: 10.1093/genetics/iyac080.
We examine the impact of sustained elevated ozone concentration on the leaf transcriptome of 5 diverse maize inbred genotypes, which vary in physiological sensitivity to ozone (B73, Mo17, Hp301, C123, and NC338), using long reads to assemble transcripts and short reads to quantify expression of these transcripts. More than 99% of the long reads, 99% of the assembled transcripts, and 97% of the short reads map to both B73 and Mo17 reference genomes. Approximately 95% of the genes with assembled transcripts belong to known B73-Mo17 syntenic loci and 94% of genes with assembled transcripts are present in all temperate lines in the nested association mapping pan-genome. While there is limited evidence for alternative splicing in response to ozone stress, there is a difference in the magnitude of differential expression among the 5 genotypes. The transcriptional response to sustained ozone stress in the ozone resistant B73 genotype (151 genes) was modest, while more than 3,300 genes were significantly differentially expressed in the more sensitive NC338 genotype. There is the potential for tandem duplication in 30% of genes with assembled transcripts, but there is no obvious association between potential tandem duplication and differential expression. Genes with a common response across the 5 genotypes (83 genes) were associated with photosynthesis, in particular photosystem I. The functional annotation of genes not differentially expressed in B73 but responsive in the other 4 genotypes (789) identifies reactive oxygen species. This suggests that B73 has a different response to long-term ozone exposure than the other 4 genotypes. The relative magnitude of the genotypic response to ozone, and the enrichment analyses are consistent regardless of whether aligning short reads to: long read assembled transcripts; the B73 reference; the Mo17 reference. We find that prolonged ozone exposure directly impacts the photosynthetic machinery of the leaf.
我们研究了持续升高的臭氧浓度对 5 种不同玉米自交系叶片转录组的影响，这些自交系在生理上对臭氧的敏感程度不同（B73、Mo17、Hp301、C123 和 NC338），我们使用长读长来组装转录本，并用短读长来定量表达这些转录本。超过 99%的长读长、99%的组装转录本和 97%的短读长都可以映射到 B73 和 Mo17 参考基因组。大约 95%具有组装转录本的基因属于已知的 B73-Mo17 同源基因座，并且 94%具有组装转录本的基因存在于嵌套关联作图泛基因组中的所有温带系中。虽然在应对臭氧胁迫时，替代性剪接的证据有限，但在 5 种基因型中，差异表达的幅度存在差异。在抗臭氧的 B73 基因型中（151 个基因），对持续臭氧胁迫的转录反应适中，而在更敏感的 NC338 基因型中，有超过 3300 个基因的表达显著不同。在具有组装转录本的基因中，有 30%的基因可能存在串联重复，但潜在的串联重复与差异表达之间没有明显的关联。在 5 种基因型中具有共同反应的基因（83 个基因）与光合作用有关，特别是光系统 I。在 B73 中没有差异表达但在其他 4 种基因型中具有响应的基因的功能注释确定了活性氧物种。这表明 B73 对长期臭氧暴露的反应与其他 4 种基因型不同。无论是否将短读长比对到长读组装转录本、B73 参考基因组或 Mo17 参考基因组，基因型对臭氧的反应幅度和富集分析都是一致的。我们发现，长时间的臭氧暴露直接影响叶片的光合作用机制。
