Wen Ming, Xie Munan, He Lian, Wang Yushuai, Shi Suhua, Tang Tian
State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China.
State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
Genome Biol Evol. 2016 Dec 31;8(11):3529-3544. doi: 10.1093/gbe/evw252.
Differences in expression levels are an important source of phenotypic variation within and between populations. MicroRNAs (miRNAs) are key players in post-transcriptional gene regulation that are important for plant development and stress responses. We surveyed expression variation of miRNAs and mRNAs of six accessions from two rice subspecies Oryza sativa L. ssp. indica and Oryza sativa L. ssp. japonica using deep sequencing. While more than half (53.7%) of the mature miRNAs exhibit differential expression between grains and seedlings of rice, only 11.0% show expression differences between subspecies, with an additional 2.2% differentiated for the development-by-subspecies interaction. Expression variation is greater for lowly conserved miRNAs than highly conserved miRNAs, whereas the latter show stronger negative correlation with their targets in expression changes between subspecies. Using a permutation test, we identified 51 miRNA-mRNA pairs that correlate negatively or positively in expression level among cultivated rice. Genes involved in various metabolic processes and stress responses are enriched in the differentially expressed genes between rice indica and japonica subspecies. Our results indicate that stabilizing selection is the major force governing miRNA expression in cultivated rice, albeit positive selection may be responsible for much of the between-subspecies expression divergence.
表达水平的差异是种群内部和种群之间表型变异的重要来源。微小RNA（miRNA）是转录后基因调控的关键参与者，对植物发育和应激反应至关重要。我们使用深度测序技术对来自两个水稻亚种（籼稻和粳稻）的六个品种的miRNA和mRNA的表达变异进行了调查。虽然超过一半（53.7%）的成熟miRNA在水稻的谷粒和幼苗之间表现出差异表达，但只有11.0%在亚种之间表现出表达差异，另有2.2%在亚种与发育的相互作用中表现出差异。低保守miRNA的表达变异比高保守miRNA更大，而后者在亚种间表达变化中与其靶标的表达呈更强的负相关。通过置换检验，我们在栽培稻中鉴定出51对miRNA-mRNA对，它们在表达水平上呈负相关或正相关。参与各种代谢过程和应激反应的基因在籼稻和粳稻亚种间差异表达的基因中富集。我们的结果表明，稳定选择是控制栽培稻中miRNA表达的主要力量，尽管正选择可能是亚种间表达差异的主要原因。
