Abstract
BackgroundSalt stress is one of the most representative abiotic stresses that severely affect plant growth and development. MicroRNAs (miRNAs) are well known for their significant involvement in plant responses to abiotic stresses. Although miRNAs implicated in salt stress response have been widely reported in numerous plant species, their regulatory roles in the adaptive response to salt stress in radish (Raphanus sativus L.), an important root vegetable crop worldwide, remain largely unknown.ResultsSolexa sequencing of two sRNA libraries from NaCl-free (CK) and NaCl-treated (Na200) radish roots were performed for systematical identification of salt-responsive miRNAs and their expression profiling in radish. Totally, 136 known miRNAs (representing 43 miRNA families) and 68 potential novel miRNAs (belonging to 51 miRNA families) were identified. Of these miRNAs, 49 known and 22 novel miRNAs were differentially expressed under salt stress. Target prediction and annotation indicated that these miRNAs exerted a role by regulating specific stress-responsive genes, such as squamosa promoter binding-like proteins (SPLs), auxin response factors (ARFs), nuclear transcription factor Y (NF-Y) and superoxide dismutase [Cu-Zn] (CSD1). Further functional analysis suggested that these target genes were mainly implicated in signal perception and transduction, regulation of ion homeostasis, basic metabolic processes, secondary stress responses, as well as modulation of attenuated plant growth and development under salt stress. Additionally, the expression patterns of ten miRNAs and five corresponding target genes were validated by reverse-transcription quantitative PCR (RT-qPCR).ConclusionsWith the sRNA sequencing, salt-responsive miRNAs and their target genes in radish were comprehensively identified. The results provide novel insight into complex miRNA-mediated regulatory network of salt stress response in radish, and facilitate further dissection of molecular mechanism underlying plant adaptive response to salt stress in root vegetable crops.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1416-5) contains supplementary material, which is available to authorized users.
Highlights
Salt stress is one of the most representative abiotic stresses that severely affect plant growth and development
Overview of transcriptome and small RNA (sRNA) sequencing in radish To establish an overall reference sequence database, a cDNA library constructed from radish roots was sequenced, totally 57.03 M raw reads were generated and 130,953 contigs were obtained [NCBI Sequence Read Archive (SRA) with the GenBank accession No.SRS706782]
On account of the fact that prolonged salt stress could usually lead to some secondary stresses such as oxidative stress and nutrition disorder [55], the results indicated that these miRNA-regulated target genes might play significant roles in plant adaptive response to salt stress, as an indispensable part of regulatory network responsive to salt stress in radish (Figure 8)
Summary
Salt stress is one of the most representative abiotic stresses that severely affect plant growth and development. MicroRNAs (miRNAs) are well known for their significant involvement in plant responses to abiotic stresses. MicroRNAs (miRNAs) are a series of endogenous small non-coding RNA molecules, which negatively regulate gene expression at transcriptional and post-transcriptional levels by modulating both mRNA degradation and translational suppression based on sequence complementarity with their target(s) [4]. Aside from the roles in modulating a wide range of essential biochemical, molecular and physiological processes, many studies reported that miRNAs were involved in plant responses to a variety of abiotic stresses such as salt [7,8], drought [9,10], heat [11,12], cold [7,13] and oxidative stress [14]
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