Comprehensive analysis of differentially expressed genes and transcriptional regulation induced by salt stress in two contrasting cotton genotypes

Abstract

BackgroundCotton (Gossypium spp.) is one of the major fibre crops of the world. Although it is classified as salt tolerant crop, cotton growth and productivity are adversely affected by high salinity, especially at germination and seedling stages. Identification of genes and miRNAs responsible for salt tolerance in upland cotton (Gossypium hirsutum L.) would help reveal the molecular mechanisms of salt tolerance. We performed physiological experiments and transcriptome sequencing (mRNA-seq and small RNA-seq) of cotton leaves under salt stress using Illumina sequencing technology.ResultsWe investigated two distinct salt stress phases—dehydration (4 h) and ionic stress (osmotic restoration; 24 h)—that were identified by physiological changes of 14-day-old seedlings of two cotton genotypes, one salt tolerant and the other salt sensitive, during a 72-h NaCl exposure. A comparative transcriptomics was used to monitor gene and miRNA differential expression at two time points (4 and 24 h) in leaves of the two cotton genotypes under salinity conditions. The expression patterns of differentially co-expressed unigenes were divided into six groups using short time-servies expression miner software. During a 24-h salt exposure, 819 transcription factor unigenes were differentially expressed in both genotypes, with 129 unigenes specifically expressed in the salt-tolerant genotype. Under salt stress, 108 conserved miRNAs from known families were differentially expressed at two time points in the salt-tolerant genotype. We further analyzed the predicted target genes of these miRNAs along with the transcriptome for each time point. Important expressed genes encoding membrane receptors, transporters, and pathways involved in biosynthesis and signal transduction of calcium-dependent protein kinase, mitogen-activated protein kinase, and hormones (abscisic acid and ethylene) were up-regulated. We also analyzed the salt stress response of some key miRNAs and their target genes and found that the expressions of five of nine target genes exhibited significant inverse correlations with their corresponding miRNAs. On the basis of these results, we constructed molecular regulatory pathways and a potential regulatory network for these salt-responsive miRNAs.ConclusionsOur comprehensive transcriptome analysis has provided new insights into salt-stress response of upland cotton. The results should contribute to the development of genetically modified cotton with salt tolerance.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-760) contains supplementary material, which is available to authorized users.

Transcriptome analysis reveals that distinct metabolic pathways operate in salt-tolerant and salt-sensitive upland cotton varieties subjected to salinity stress

“…However, only a few salt stress-inducible genes have been documented in cotton, such as GhNHX1 [25], GhDREB [26], GhERF2-GhERF6 [27][28][29], GhNAC1-GhNAC13 [30,31], GhMT3a [32], GhMPK2 [33], GhMKK5 [34], GhZFP1 [35], GhCIPK6 [36], GhWRKY17 [37], GhWRKY39-1 [38], and GbRLK [39]. With the success of the cotton whole-genome sequencing [40,41], and the widespread use of microarrays and next-generation sequencing, some salt-related regulatory factors and genes have been identified in cotton at genome-wide level [6,[42][43][44]. For example, some members of transcription factor families such as WRKY, NAC, MYB, and C2H2 have been reported to play an important role in salt tolerance of cotton [6,[42][43][44].…”

“…Generally, mechanisms underlying salinity tolerance in plants involve maintaining homeostasis (including ionic and osmotic homeostasis), detoxification, and growth regulation [9], and these mechanisms have been reported at the molecular level, cellular level, and whole plant level [10]. Previous studies identified a possible mechanism involved in the salt-stress response in cotton [6,[11][12][13][14] and Arabidopsis [15][16][17]. When exposed to salt stress, plants maintain ionic homeostasis (i.e., a low concentration of Na + and a high concentration of K + ) in the cytosol [18].…”

“…Although upland cotton is a moderately salt-tolerant crop, with a salinity threshold of 7.7 dS m −1 [7], the yield is drastically reduced with increased salinity. The tolerance to salinity varies considerably among cotton varieties, and identifying the molecular mechanisms associated with increased salt tolerance may pave the way for developing lines with improved salt tolerance [6,8].…”

“…Understanding the molecular mechanisms underlying the plant's response to salinity stress will facilitate efforts to develop crop plants with enhanced resistance to high salinity [2][3][4][5][6]. Upland cotton (Gossypium hirsutum L.) is an important natural fiber and oil crop and provides edible protein for livestock feed.…”

The identification and characteristics of salinity-related microRNAs in gills of Portunus trituberculatus

“…So far, miRNAs have been identified in a few aquatic crustacean species, and these were involved in regulation of oocyte meiosis , adaptive immunity Ou et al 2012;Zeng et al 2015), and drug response (ValenzuelaMiranda et al 2015). Previous reports have shown that some plant miRNAs respond to salinity stress and that some miRNA targets are salt stress-related genes (Xie et al 2014;Peng et al 2014;Frazier et al 2011). This suggests that miRNAs play important roles in plant salt stress responses.…”