Identification of Rapeseed MicroRNAs Involved in Early Stage Seed Germination under Salt and Drought Stresses

Abstract

Drought and salinity are severe and wide-ranging abiotic stresses that substantially affect crop germination, development and productivity, and seed germination is the first critical step in plant growth and development. To comprehensively investigate small-RNA targets and improve our understanding of miRNA-mediated post-transcriptional regulation networks during Brassica napus seed imbibition under drought and salt stresses, we constructed three small-RNA libraries from B. napus variety ZS11 embryos exposed to salt (200 mM NaCl, denoted “S”), drought (200 g L−1 PEG-6000, denoted “D”), and distilled water (denoted “CK”) during imbibition and sequenced them using an Illumina Genome Analyzer. A total of 11,528,557, 12,080,081, and 12,315,608 raw reads were obtained from the CK, D, and S libraries, respectively. Further analysis identified 85 known miRNAs belonging to 31 miRNA families and 882 novel miRNAs among the three libraries. Comparison of the D and CK libraries revealed significant down-regulation of six miRNA families, miR156, miR169, miR860, miR399, miR171, and miR395, whereas only miR172 was significantly up-regulated. In contrast, comparison of the S library with the CK library showed significant down-regulation of only two miRNA families: miRNA393 and miRNA399. Putative targets for 336, 376, and 340 novel miRNAs were successfully predicted in the CK, D, and S libraries, respectively, and 271 miRNA families and 20 target gene families [including disease resistance protein (DIRP), drought-responsive family protein (DRRP), early responsive to dehydration stress protein (ERD), stress-responsive alpha-beta barrel domain protein (SRAP), and salt tolerance homolog2 (STH2)] were confirmed as being core miRNAs and genes involved in the seed imbibition response to salt and drought stresses. The sequencing results were partially validated by quantitative RT-PCR for both conserved and novel miRNAs as well as the predicted target genes. Our data suggest that diverse and complex miRNAs are involved in seed imbibition, indicating that miRNAs are involved in plant hormone regulation, and may play important roles during seed germination under salt- or drought-stress conditions.

Identification and Target Prediction of MicroRNAs in Ulmus pumila L. Seedling Roots under Salt Stress by High-Throughput Sequencing

“…The phosphoinositide phosphatase gene was predicted to be a target of upu-miR399, a result that has been verified in other plants [60,61]. The MIR399 family showed a down-regulated tendency in MSL compared with CK, consistent with previous research on Brassica napus L. in which miR399 expression was inhibited under salt stress [62]. Finally, the expressions of upu-miR398d and upu-miR399d were validated by qRT-PCR.…”

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 ., ).…”

Dynamic roles of microRNAs in nutrient acquisition and plant adaptation under nutrient stress: A review

“…MiRNAs are diverse regulatory molecules of small size and are considered chief controllers for the growth and development of various plants. Several miRNAs have been found to take part in diverse functions and fundamentally involved in numerous physiological events, such as stem cell proliferation, leaf and floral development, flowering initiation, tissue and organ buildup, as well as regulation of positive responses to various biotic and abiotic stresses (Willmann and Poethig, 2005;Sunkar et al, 2007;Zhou et al, 2012;Guo et al, 2013;Song et al, 2013;Wang B et al, 2014;Gao et al, 2016;Jian et al, 2016). Since miRNAs are involved in the regulation of essentially all cellular metabolic pathways, transformation of their biogenesis is of supreme importance for the maintenance of cellular homeostasis.…”