Genome-wide analysis of salt-responsive and novel microRNAs in Populus euphratica by deep sequencing

Abstract

BackgroundPopulus euphratica is a representative model woody plant species for studying resistance to abiotic stresses such as drought and salt. Salt stress is one of the most common environmental factors that affect plant growth and development. MicroRNAs (miRNAs) are small, noncoding RNAs that have important regulatory functions in plant growth, development, and response to abiotic stress.ResultsTo investigate the miRNAs involved in the salt-stress response, we constructed four small cDNA libraries from P. euphratica plantlets treated with or without salt (300 mM NaCl, 3 days) in either the root or leaf. Using high-throughput sequencing to identify miRNAs, we found 164 conserved miRNAs belonging to 44 families. Of these, 136 novel miRNAs were from the leaf, and 128 novel miRNAs were from the root. In response to salt stress, 95 miRNAs belonging to 46 conserved miRNAs families changed significantly, with 56 miRNAs upregulated and 39 miRNAs downregulated in the leaf. A comparison of the leaf and root tissues revealed 155 miRNAs belonging to 63 families with significantly altered expression, including 84 upregulated and 71 downregulated miRNAs. Furthermore, 479 target genes in the root and 541 targets of novel miRNAs in the leaf were predicted, and functional information was annotated using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases.ConclusionsThis study provides a novel visual field for understanding the regulatory roles of miRNAs in response to salt stress in Populus.

Thiourea priming enhances salt tolerance through co-ordinated regulation of microRNAs and hormones in Brassica juncea

“…The observed size distributions of adapter cleaned reads showed classes from 21–23 nt with majority of 23 nt, followed by 21nt, and 22nt (Supplementary Figure 1) which was similar to previously reported size distribution in plants4748. The conserved miRNAs were identified by mapping cleaned reads to miRBase.…”

Elucidating the molecular mechanisms mediating plant salt‐stress responses

“…The siRNAs are generated from double‐stranded RNA precursors, and are grouped into trans ‐acting siRNAs (ta‐siRNAs), heterochromatic siRNAs (hc‐siRNAs), natural antisense transcript‐derived siRNAs (nat‐siRNAs), and long siRNAs (lsiRNAs) (Barrera‐Figueroa et al ., ). Studies indicate that siRNAs and miRNAs have roles in salt‐stress responses (Borsani et al ., ; Shen et al ., ; Carnavale Bottino et al ., ; Si et al ., ; Tian et al ., ; Feng et al ., ; Jian et al ., ; Srivastava et al ., ). In mangroves, ta‐siRNAs may be involved in regulating chromatin structural stability and/or gene expression, and balancing the conflicting demands between plant growth and stress resistance under high‐salt conditions (Wen et al ., ).…”

The genetic architecture of shoot–root covariation during seedling emergence of a desert tree, Populus euphratica

“…In this article, we report the results of the genetic architecture of the developmental dynamics of shoot–root relationships in Euphrates Poplar ( Populus euphratica Oliv.). As the only woody plant species that can grow in the harsh desert, P. euphratica has many desirable properties for ecophysiological studies of growth allocation, such as high tolerance to extreme temperature, salinity, drought and wind, and considerable variability in such tolerance (Ferreira et al ., ; Si et al ., ). Our study was based on a full‐sib family of 370 genotyped members derived from two different trees sampled from a natural stand in northwestern China.…”