Wu Jun, Wang Defu, Liu Yufeng, Wang Long, Qiao Xin, Zhang Shaoling
College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
BMC Genomics. 2014 Nov 3;15(1):953. doi: 10.1186/1471-2164-15-953.
MicroRNAs (miRNAs) are a class of small, endogenous RNAs that take part in regulating genes through mediating gene expressions at the post-transcriptional level in plants. Previous studies have reported miRNA identification in various plants ranging from model plants to perennial fruit trees. However, the role of miRNAs in pear (Pyrus bretschneideri) fruit development is not clear. Here, we investigated the miRNA profiles of pear fruits from different time stages during development with Illumina HiSeq 2000 platform and bioinformatics analysis. Quantitative real-time PCR was used to validate the expression levels of miRNAs.
Both conserved and species-specific miRNAs in pear have been identified in this study. Total reads, ranging from 19,030,925 to 25,576,773, were obtained from six small RNA libraries constructed for different stages of fruit development after flowering. Comparative profiling showed that an average of 90 miRNAs was expressed with significant differences between various developmental stages. KEGG pathway analysis on 2,216 target genes of 188 known miRNAs and 1,127 target genes of 184 novel miRNAs showed that miRNAs are widely involved in the regulation of fruit development. Among these, a total of eleven miRNAs putatively participate in the pathway of lignin biosynthesis, nine miRNAs were identified to take part in sugar and acid metabolism, and MiR160 was identified to regulate auxin response factor.
Comparative analysis of miRNAomes during pear fruit development is presented, and miRNAs were proved to be widely involved in the regulation of fruit development and formation of fruit quality, for example through lignin synthesis, sugar and acid metabolism, and hormone signaling. Combined with computational analysis and experimental confirmation, the research contributes valuable information for further functional research of microRNA in fruit development for pear and other species.
微小RNA（miRNA）是一类小的内源性RNA，在植物中通过在转录后水平介导基因表达来参与基因调控。先前的研究报道了从模式植物到多年生果树等各种植物中的miRNA鉴定。然而，miRNA在梨（Pyrus bretschneideri）果实发育中的作用尚不清楚。在此，我们利用Illumina HiSeq 2000平台和生物信息学分析研究了梨果实发育不同阶段的miRNA谱。采用定量实时PCR验证miRNA的表达水平。
本研究鉴定了梨中保守和物种特异性的miRNA。从为开花后果实发育的不同阶段构建的六个小RNA文库中获得了总数在19,030,925至25,576,773之间的读数。比较分析表明，平均有90个miRNA在不同发育阶段表达存在显著差异。对188个已知miRNA的2,216个靶基因和184个新miRNA的1,127个靶基因进行KEGG通路分析表明，miRNA广泛参与果实发育的调控。其中，共有11个miRNA可能参与木质素生物合成途径，9个miRNA被鉴定参与糖和酸代谢，并且鉴定出MiR160调节生长素反应因子。
本文呈现了梨果实发育过程中miRNA组的比较分析，并且证明miRNA广泛参与果实发育调控和果实品质形成，例如通过木质素合成、糖和酸代谢以及激素信号传导。结合计算分析和实验验证，该研究为进一步研究梨和其他物种果实发育中微小RNA的功能提供了有价值的信息。
