Integration of mRNA and miRNA Analysis Reveals the Molecular Mechanism of Cotton Response to Salt Stress

Abstract

To identify the regulatory network of known and novel microRNAs (miRNAs) and their targets responding to salt stress, a combined analysis of mRNA libraries, small RNA libraries, and degradome libraries were performed. In this study, we used unique molecular identifiers (UMIs), which are more sensitive, accurate, and reproducible than traditional methods of sequencing, to quantify the number of molecules and correct for amplification bias. We identified a total of 312 cotton miRNAs using seedlings at 0, 1, 3, and 6 h after NaCl treatment, including 80 known ghr-miRNAs and 232 novel miRNAs and found 155 miRNAs that displayed significant differential expression under salt stress. Among them, fifty-nine differentially expressed miRNAs were simultaneously induced in two or three tissues, while 66, 11, and 19 were specifically expressed in the roots, leaves, and stems, respectively. It is indicated there were different populations of miRNAs against salt stress in roots, leaves and stems. 399 candidate targets of salt-induced miRNAs showed significant differential expression before and after salt treatment, and 72 targets of 25 miRNAs were verified by degradome sequencing data. Furthermore, the regulatory relationship of miRNA-target gene was validated experimentally via 5′RLM-RACE, proving our data reliability. Gene ontology and KEGG pathway analysis found that salt-responsive miRNA targets among the differentially expressed genes were significantly enriched, and mainly involved in response to the stimulus process and the plant hormone signal transduction pathway. Furthermore, the expression levels of newly identified miRNA mir1 and known miRNAs miR390 and miR393 gradually decreased when subjected to continuous salt stress, while overexpression of these miRNAs both increased sensitivity to salt stress. Those newly identified miRNAs and mRNA pairs were conducive to genetic engineering and better understanding the mechanisms responding to salt stress in cotton.

Integrated Full-Length Transcriptome and MicroRNA Sequencing Approaches Provide Insights Into Salt Tolerance in Mangrove (Sonneratia apetala Buch.-Ham.)

“…Majority of the sRNA reads were unannotated, which possibly attributed to the scarcity of genome information on this species, and implied that numerous sRNAs still remain to be identified in S. apetala. The annotation performed here was in line with previous reports of other plants such as cotton (Zhan et al, 2021) and Ipomoea batatas L. (Yang et al, 2020). Analysis of the length distribution of these sRNA indicated that most were 21-nt and 24-nt (Figure 1), which has also been observed in other mangrove species, including Bruguiera gymnorrhiza and Kandelia (Wen et al, 2016).…”

Understanding the physiological and molecular mechanism of salinity stress tolerance in plants

“…Osa-mR939 overexpression enhances tillers and early flowering, but reduces the tolerance to salinity and drought stress in Oryza sativa. miRNA396c overexpression enhances NaCl stress tolerance through the mediation of water retention, chlorophylls accumulation, cell membrane Na + /H + , antioxidant enzymes and transcription factors, but reduces the tolerance to alkali and salt stress in Arabidopsis and Oryza sativa (Zhan et al, 2021).…”

Transcriptome and Metabolome Analyses of Salt Stress Response in Cotton (Gossypium hirsutum) Seed Pretreated with NaCl

“…Salinity stress is among the most prominent stresses (abiotic) usually faced by cotton (Gossypium hirsutum) crops around the globe. Salinization hinders the sustainable productivity and development of plants by negatively influencing the metabolic and biological pathways [1]. The increasing amount of NaCl, MgCl 2 , and CaCl 2 as a consequence of many activities, such as wastewater treatment, freshwater channel alterations, or deicing of roads with salt applications is deteriorating the natural environment [2,3].…”

“…Upland cotton is classified as moderately tolerant to salt and can withstand a saline medium without being significantly harmed, which is comparable to other major cash crops [1,2,15]. Moreover, the cultivars of G. hirsutum vary considerably regarding their tolerance toward salinity.…”

“…The sensitivity of the crop to the salinity condition is highly specific to the growth stage and salt type. Understanding the response of the cotton crop to salt, its tolerance mechanism, and comprehensive knowledge related to management practices may be helpful [1,17]. Recently, many advanced studies, such as whole-genome sequencing, on different cotton species (diploid and tetraploid) facilitated us with the reference genome(s) of cotton for a better understanding of genes and transcription factors in relation to their functions under stress conditions in terms of controlling several biological and metabolic pathways [2,6,14,[16][17][18][19][20].…”