Abstract
BackgroundMicroRNAs (miRNAs) play a critical role in responses to biotic and abiotic stress and have been characterized in a large number of plant species. Although flax (Linum usitatissimum L.) is one of the most important fiber and oil crops worldwide, no reports have been published describing flax miRNAs (Lus-miRNAs) induced in response to saline, alkaline, and saline-alkaline stresses.ResultsIn this work, combined small RNA and degradome deep sequencing was used to analyze flax libraries constructed after alkaline-salt stress (AS2), neutral salt stress (NSS), alkaline stress (AS), and the non-stressed control (CK). From the CK, AS, AS2, and NSS libraries, a total of 118, 119, 122, and 120 known Lus-miRNAs and 233, 213, 211, and 212 novel Lus-miRNAs were isolated, respectively. After assessment of differential expression profiles, 17 known Lus-miRNAs and 36 novel Lus-miRNAs were selected and used to predict putative target genes. Gene ontology term enrichment analysis revealed target genes that were involved in responses to stimuli, including signaling and catalytic activity. Eight Lus-miRNAs were selected for analysis using qRT-PCR to confirm the accuracy and reliability of the miRNA-seq results. The qRT-PCR results showed that changes in stress-induced expression profiles of these miRNAs mirrored expression trends observed using miRNA-seq. Degradome sequencing and transcriptome profiling showed that expression of 29 miRNA-target pairs displayed inverse expression patterns under saline, alkaline, and saline-alkaline stresses. From the target prediction analysis, the miR398a-targeted gene codes for a copper/zinc superoxide dismutase, and the miR530 has been shown to explicitly target WRKY family transcription factors, which suggesting that these two micRNAs and their targets may significant involve in the saline, alkaline, and saline-alkaline stress response in flax.ConclusionsIdentification and characterization of flax miRNAs, their target genes, functional annotations, and gene expression patterns are reported in this work. These findings will enhance our understanding of flax miRNA regulatory mechanisms under saline, alkaline, and saline-alkaline stresses and provide a foundation for future elucidation of the specific functions of these miRNAs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0808-2) contains supplementary material, which is available to authorized users.
Highlights
MicroRNAs play a critical role in responses to biotic and abiotic stress and have been characterized in a large number of plant species
Discovery of miRNAs responsive to saline, alkaline, and saline-alkaline stresses in flax To identify Linum usitatissimum (Lus)-miRNAs responsive to saline, alkaline, and saline-alkaline stresses, differentially expressed miRNAs in each sample were compared to the control
Of the novel miRNAs, 18, 20, and 12 were significantly up-regulated, while 20, 14, and 12 were significantly down-regulated in AS, alkaline-salt stress (AS2), and neutral salt stress (NSS) libraries, respectively (Fig. 2b, Additional file 3). These results suggest that these miRNAs might have coordinating functions in response to saline, alkaline, and saline-alkaline stresses in flax
Summary
MicroRNAs (miRNAs) play a critical role in responses to biotic and abiotic stress and have been characterized in a large number of plant species. Flax (Linum usitatissimum L.) is one of the most important fiber and oil crops worldwide, no reports have been published describing flax miRNAs (Lus-miRNAs) induced in response to saline, alkaline, and saline-alkaline stresses. Salt stress is one of the major environmental stresses that limit worldwide agricultural crop yields and will continue to be of concern in future years. In responses to salt stress, such as ionic and osmotic stress, crops have evolved multiple molecular networks to regulate homeostasis and maintain their growth and development. Alkaline-salt stress is generally associated with NaHCO3 or Na2CO3 presence and crops growing in alkaline soils suffer from both high pH stress and CO32-/HCO3- stress [2]. Understanding of the saline-alkaline stress response may help to improve crop tolerance to salt stress. The mechanisms of plant alkaline-salt tolerance are poorly understood
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