Combined analysis of mRNA and miRNA identifies dehydration and salinity responsive key molecular players in citrus roots

Abstract

Citrus is one of the most economically important fruit crops around world. Drought and salinity stresses adversely affected its productivity and fruit quality. However, the genetic regulatory networks and signaling pathways involved in drought and salinity remain to be elucidated. With RNA-seq and sRNA-seq, an integrative analysis of miRNA and mRNA expression profiling and their regulatory networks were conducted using citrus roots subjected to dehydration and salt treatment. Differentially expressed (DE) mRNA and miRNA profiles were obtained according to fold change analysis and the relationships between miRNAs and target mRNAs were found to be coherent and incoherent in the regulatory networks. GO enrichment analysis revealed that some crucial biological processes related to signal transduction (e.g. ‘MAPK cascade’), hormone-mediated signaling pathways (e.g. abscisic acid- activated signaling pathway’), reactive oxygen species (ROS) metabolic process (e.g. ‘hydrogen peroxide catabolic process’) and transcription factors (e.g., ‘MYB, ZFP and bZIP’) were involved in dehydration and/or salt treatment. The molecular players in response to dehydration and salt treatment were partially overlapping. Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) analysis further confirmed the results from RNA-seq and sRNA-seq analysis. This study provides new insights into the molecular mechanisms how citrus roots respond to dehydration and salt treatment.

Screening and Evaluation of Saline–Alkaline Tolerant Germplasm of Rice (Oryza sativa L.) in Soda Saline–Alkali Soil

“…with salt tolerance, abiotic stresses in rice, and other crops. Manu Kumar et al elaborated on the relationship of OsSta2 with salt tolerance and abiotic stress in rice [52][53][54][55][56][57][58]. Salt tolerant varieties can be produced using marker-assisted selection or genetic engineering by introducing salt-tolerance genes [43].…”

Integrated mRNA and miRNA expression profiling analyses of Pinus massoniana roots and shoots in response to phosphate deficiency

“…The results showed that the morphological changes were consistent with previous observations, and a large number of DEGs and DE miRNAs were identified. Some reports have demonstrated that the miRNA-mRNA regulatory network responds to abiotic stress (Xie et al, 2017). In this work, we attempted to construct a low-Pi-induced miRNA-mRNA regulatory network according to the DEG and DE miRNA datasets.…”

Identification of Appropriate Reference Genes for Normalizing miRNA Expression in Citrus Infected by Xanthomonas citri subsp. citri

“…A large body of evidence has shown that miRNA-mediated posttranscriptional regulation plays a fundamental role in plant responses to stressful factors, including pathogen infection, salt, drought, heat, cold, nutrient deficiency and metal toxicity [81][82][83][84][85][86]. A great deal of effort has been focused on the identification and functional analysis of plant miRNAs in response to the infection of pathogens, such as viruses [87][88][89], bacteria [16,[90][91][92] and fungi [13,93,94], which have provided valuable information as to the role miRNAs play in plant-pathogen interactions [95,96].…”