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.
Highlights
Around the world, drought and salinity as two major concerns for agriculture negatively affect plant growth and development, which lead to a decline in yield and quality[1]
After mapping clean reads to the clementina genome, approximately 83.26% (DR)–83.91% (SA) reads were successfully aligned, with 72.87–73.81% of reads mapped to CDS regions, and 3.19–3.73% of reads mapped to introns or intergenic regions, while 1.87–2.12% of reads had multiple alignments
There were 2574 mRNAs and 76 miRNAs that were differentially expressed in citrus root under salt and/or dehydration treatments
Summary
Drought and salinity as two major concerns for agriculture negatively affect plant growth and development, which lead to a decline in yield and quality[1]. A large number of efforts have been performed to elucidate the molecular mechanisms underlying plant adaptation to drought and salinity stress, and it has been well established that gene expression regulation at transcriptional and post-transcriptional is an important strategy for plants to combat these two stresses[4]. Experimental data show that drought and salinity can negatively affect citrus numerous biological and metabolic pathways, including photosynthesis, carbon fixation, ROS as well as respiration[22,23], just as reflected at molecular level that a very large number of genes have been involved. We have identified a large number of genes, transcription factors and miRNAs to be involved in the regulation of salt and dehydration response. The results of this study provided a deep insight into the molecular mechanisms how citrus roots fight salt and dehydration stress, which will contribute to improve tolerance of citrus to these two stresses in future
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