Li Liang, Liu Jinhang, Liang Qin, Zhang Yanhui, Kang Kaiquan, Wang Wenting, Feng Yu, Wu Shaohua, Yang Chao, Li Yongyu
College of Horticulture, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, China.
Economic Crop Station, Agricultural and Rural Bureau of Yongtai County, 32 Tashan Road, Yongtai Country, Fuzhou 350700, China.
Tree Physiol. 2021 May 14;41(5):771-790. doi: 10.1093/treephys/tpaa147.
The versatile role of long noncoding RNAs (lncRNAs) in plant growth and development has been established, but a systematic identification and analysis of lncRNAs in the pear has not been reported. Bud dormancy is a crucial and complicated protective mechanism for plants in winter. The roles of lncRNAs in the dormancy process remain largely unclear. In this study, we induced pear floral buds to enter into different dormant statuses by simulating four different chilling accumulation conditions. Then, a time series of RNA-seq analysis was performed and we identified 7594 lncRNAs in Pyrus pyrifolia (Burm. F.) Nakai that have not been identified. The sequence and expression of the lncRNAs were confirmed by PCR analysis. In total, 6253 lncRNAs were predicted to target protein-coding genes including 692 cis-regulated pairs (596 lncRNAs) and 13,158 trans-regulated pairs (6181 lncRNAs). Gene Ontology analysis revealed that most of lncRNAs' target genes were involved in catalytic activity, metabolic processes and cellular processes. In the trend analysis, 124 long-term cold response lncRNAs and 80 short-term cold response lncRNAs were predicted. Regarding the lncRNA-miRNA regulatory networks, 59 lncRNAs were identified as potential precursors for miRNA members of 20 families, 586 lncRNAs were targets of 261 pear miRNAs and 53 lncRNAs were endogenous target mimics for 26 miRNAs. In addition, three cold response lncRNAs, two miRNAs and their target genes were selected for expression confirmed. The trend of their expression was consistent with the predicted relationships among them and suggested possible roles of lncRNAs in ABA metabolic pathway. Our findings not only suggest the potential roles of lncRNAs in regulating the dormancy of pear floral buds but also provide new insights into the lncRNA-miRNA-mRNA regulatory network in plants.
长链非编码RNA（lncRNAs）在植物生长发育中的多功能作用已得到证实，但尚未见对梨中lncRNAs进行系统鉴定和分析的报道。芽休眠是植物冬季至关重要且复杂的保护机制。lncRNAs在休眠过程中的作用仍不清楚。本研究通过模拟四种不同的低温积累条件，诱导梨花芽进入不同的休眠状态。然后，进行了一系列的RNA测序分析，我们在白梨（Pyrus pyrifolia (Burm. F.) Nakai）中鉴定出7594个未被鉴定的lncRNAs。通过PCR分析证实了lncRNAs的序列和表达。总共预测有6253个lncRNAs靶向蛋白质编码基因，包括692个顺式调控对（596个lncRNAs）和13158个反式调控对（6181个lncRNAs）。基因本体分析表明，大多数lncRNAs的靶基因参与催化活性、代谢过程和细胞过程。在趋势分析中，预测了124个长期冷响应lncRNAs和80个短期冷响应lncRNAs。关于lncRNA-miRNA调控网络，59个lncRNAs被鉴定为20个家族miRNA成员的潜在前体，586个lncRNAs是261个梨miRNA的靶标，53个lncRNAs是26个miRNA的内源性靶标模拟物。此外，选择了三个冷响应lncRNAs、两个miRNA及其靶基因进行表达验证。它们的表达趋势与预测的它们之间的关系一致，并暗示了lncRNAs在脱落酸代谢途径中的可能作用。我们的研究结果不仅表明lncRNAs在调节梨花芽休眠中的潜在作用，而且为植物中lncRNA-miRNA-mRNA调控网络提供了新的见解。
