Abstract
BackgroundSalinity is a major abiotic stress that limits upland cotton growth and reduces fibre production worldwide. To reveal genetic regulation via transcript and protein levels after salt stress, we comprehensively analysed the global changes in mRNA, miRNA, and protein profiles in response to salt stress in two contrasting salt-tolerant cotton genotypes.ResultsIn the current study, proteomic and mRNA-seq data were combined to reveal that some genes are differentially expressed at both the proteomic and mRNA levels. However, we observed no significant change in mRNA corresponding to most of the strongly differentially abundant proteins. This finding may have resulted from global changes in alternative splicing events and miRNA levels under salt stress conditions. Evidence was provided indicating that several salt stress-responsive proteins can alter miRNAs and modulate alternative splicing events in upland cotton. The results of the stringent screening of the mRNA-seq and proteomic data between the salt-tolerant and salt-sensitive genotypes identified 63 and 85 candidate genes/proteins related to salt tolerance after 4 and 24 h of salt stress, respectively, between the tolerant and sensitive genotype. Finally, we predicted an interaction network comprising 158 genes/proteins and then discovered that two main clusters in the network were composed of ATP synthase (CotAD_74681) and cytochrome oxidase (CotAD_46197) in mitochondria. The results revealed that mitochondria, as important organelles involved in energy metabolism, play an essential role in the synthesis of resistance proteins during the process of salt exposure.ConclusionWe provided a plausible schematic for the systematic salt tolerance model; this schematic reveals multiple levels of gene regulation in response to salt stress in cotton and provides a list of salt tolerance-related genes/proteins. The information here will facilitate candidate gene discovery and molecular marker development for salt tolerance breeding in cotton.
Highlights
Salinity is a major abiotic stress that limits upland cotton growth and reduces fibre production worldwide
Identification of differentially expressed (DE) salt tolerance-related genes/proteins To further analyse the specificity of the DE salt tolerance-related genes/proteins between both genotypes at the two time points, we developed the following stringent screening parameters: (i) “Differentially expressed gene (DEG)&protein ns” and “diff.same” types commonly up- or down-regulated between Nan Dan Ba Di Da Hua (NH) and Earlistaple 7 (E7) (i.e., DEGs with |log2E4/E0| |log2N4/N0| ≥ 0.5); (ii) “DEGs&protein ns”, with opposite responses to salt (i.e., “DEGs&protein ns” with log2E4/E0 ≥ 1 and log2N4/N0 ≤ − 1 or vice versa); (iii) “DEGs&protein ns” and “diff.same” types upor down-regulated only in the salt-tolerant genotype (E7); (iv) “Differentially abundant protein (DAP)&gene ns” commonly up- or down-regulated between NH and E7 (i.e., DAPs with | Quantitation (E4/E0)| > |Quantitation (N4/N0)|); and (v) “DAPs&gene ns” types up- or down-regulated only in the salt-tolerant genotype (E7)
We comprehensively analysed the global changes in mRNA, miRNA, and protein profiles in response to salt stress in two contrasting salt-tolerant cotton genotypes
Summary
Salinity is a major abiotic stress that limits upland cotton growth and reduces fibre production worldwide. To reveal genetic regulation via transcript and protein levels after salt stress, we comprehensively analysed the global changes in mRNA, miRNA, and protein profiles in response to salt stress in two contrasting salt-tolerant cotton genotypes. Abiotic stresses such as salinity are severely threatening crop productivity and reducing the quality of plants worldwide [1]. Apart from these studies, other studies involving rice [19], wheat [20, 21], tomato [22], cotton [23,24,25], and soybean [26] have been conducted to understand the differences in gene/protein expression between salt-sensitive and salt-tolerant genotypes
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