Genome-wide analysis of long noncoding RNAs affecting floral bud dormancy in pears in response to cold stress

Author:

Li Liang1,Liu Jinhang1,Liang Qin1,Zhang Yanhui2,Kang Kaiquan3,Wang Wenting1,Feng Yu1,Wu Shaohua1,Yang Chao1,Li Yongyu1

Affiliation:

1. College of Horticulture, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Cangshan District, Fuzhou 350002, China

2. Economic Crop Station, Agricultural and Rural Bureau of Yongtai County, 32 Tashan Road, Yongtai Country, Fuzhou 350700, China

3. Lianjiang State-Owned Forest Farm in Fujian Province, 31 Xifeng Road, Lianjiang Country, Fuzhou 350500, China

Abstract

Abstract 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.

Funder

National Natural Science Foundation of China

Doctoral Program of Higher Education of China

Publisher

Oxford University Press (OUP)

Subject

Plant Science,Physiology

Reference93 articles.

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