Identification and characterization of microRNAs related to salt stress in broccoli, using high-throughput sequencing and bioinformatics analysis

BMC Plant Biology

Research Article

Hongyu Deng¹  Xiaojun Luo¹  Kaitai Yao¹  Yunhong Tian²  Yihan Qiu³  Shen Qian³  Zuoping Huang³  Dan Sun³  Ying Liu³  Tao Zhou³  Bing Hou³  Yunming Tian⁴ 

[1] Cancer Research Institute, Southern Medical University, Guangzhou, Guangdong Province, People’s Republic of China;Cancer Research Institute, Southern Medical University, Guangzhou, Guangdong Province, People’s Republic of China;Department of Oncology, Armed Police Hospital of Guangdong Province, Guangzhou, Guangdong Province, People’s Republic of China;Department of Oncology, Armed Police Hospital of Guangdong Province, Guangzhou, Guangdong Province, People’s Republic of China;State Key Laboratory of Oncology of Southern China, Guangzhou, Guangdong Province, People’s Republic of China;Department of Radiation Oncology, Cancer Center of Sun Yat-Sen University, Guangzhou, Guangdong Province, People’s Republic of China;

关键词: Broccoli;    Salt stress;    High-throughput sequencing;    microRNA;   

DOI  :  10.1186/s12870-014-0226-2

 received in 2014-01-25, accepted in 2014-08-12,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundMicroRNAs (miRNAs) are a new class of endogenous regulators of a broad range of physiological processes, which act by regulating gene expression post-transcriptionally. The brassica vegetable, broccoli (Brassica oleracea var. italica), is very popular with a wide range of consumers, but environmental stresses such as salinity are a problem worldwide in restricting its growth and yield. Little is known about the role of miRNAs in the response of broccoli to salt stress. In this study, broccoli subjected to salt stress and broccoli grown under control conditions were analyzed by high-throughput sequencing. Differential miRNA expression was confirmed by real-time reverse transcription polymerase chain reaction (RT-PCR). The prediction of miRNA targets was undertaken using the Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO) database and Gene Ontology (GO)-enrichment analyses.ResultsTwo libraries of small (or short) RNAs (sRNAs) were constructed and sequenced by high-throughput Solexa sequencing. A total of 24,511,963 and 21,034,728 clean reads, representing 9,861,236 (40.23%) and 8,574,665 (40.76%) unique reads, were obtained for control and salt-stressed broccoli, respectively. Furthermore, 42 putative known and 39 putative candidate miRNAs that were differentially expressed between control and salt-stressed broccoli were revealed by their read counts and confirmed by the use of stem-loop real-time RT-PCR. Amongst these, the putative conserved miRNAs, miR393 and miR855, and two putative candidate miRNAs, miR3 and miR34, were the most strongly down-regulated when broccoli was salt-stressed, whereas the putative conserved miRNA, miR396a, and the putative candidate miRNA, miR37, were the most up-regulated. Finally, analysis of the predicted gene targets of miRNAs using the GO and KO databases indicated that a range of metabolic and other cellular functions known to be associated with salt stress were up-regulated in broccoli treated with salt.ConclusionA comprehensive study of broccoli miRNA in relation to salt stress has been performed. We report significant data on the miRNA profile of broccoli that will underpin further studies on stress responses in broccoli and related species. The differential regulation of miRNAs between control and salt-stressed broccoli indicates that miRNAs play an integral role in the regulation of responses to salt stress.

【 授权许可】

Unknown   
© Tian et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.