Transcript profiling during salt stress of young cotton (Gossypium hirsutum) seedlings via Solexa sequencing

Abstract

Genome-wide gene expression profiling was conducted by Solexa sequencing in order to gain insight into the transcriptome dynamics that are associated with salt stress of cotton seedlings. A total of 145,794 and 138,518 clean tags were generated from the control and salinity libraries, respectively. Of these, 75,500 (51.8%) and 72,077 (52.0%) tags were matched to the reference genes. The most differentially regulated tags with a log2ratio [2 or [-2 (P \ 0.001) were analyzed further, representing 125 up-and 171 down-regulated genes except for unknown transcripts, which were classified into ten functional categories. The most enriched categories were those of metabolism, signaling pathway, environmental response and transcription. Many genes or biological pathways were found to be commonly shared between salt and other abiotic stresses in plants such as genes participating in environmental response, ABA signaling JA signaling, etc. Furthermore, the expression patterns of 12 genes were assessed by quantitative real-time PCR, and the results obtained showed general agreement with the Solexa data. Further analysis indicated the important roles of selected genes in salt tolerance by comparison with the mRNA levels in salt-tolerant cotton cultivar ZM3 with that in salt-sensitive cultivar LM6. Overall, we reveal the complex changes at the transcriptional level during salt stress of cotton seedlings and provide useful starting points for more in-depth analyses of cotton's salt tolerance.

Transcriptome Sequencing and De Novo Analysis of a Cytoplasmic Male Sterile Line and Its Near-Isogenic Restorer Line in Chili Pepper (Capsicum annuum L.)

“…RT-PCR results basically confirmed the reliability of our transcriptome analysis. However, the two techniques essentially use different algorithms, which may explain the above-mentioned some inconsistent results [49]–[51].…”

De Novo Transcriptome Characterization, Gene Expression Profiling and Ionic Responses of Nitraria sibirica Pall. under Salt Stress

“…confirmed that carbohydrate metabolic processes, hydrolase activity and catalytic activity items contained some of the identified salt-responsive transcripts. Studies with the transcriptome of Gossypium hirsutum seedlings under salt stress also reported that most enriched categories referred to metabolism and signalling pathways, among others [67]. From the KEGG enrichment analysis, pathways involved in amino sugar and nucleotide sugar metabolism; plant hormone signal transduction; alanine, aspartate and glutamate metabolism; and alpha-linolenic acid metabolism, among others, were up-regulated, whereas those involved in starch and sucrose metabolism and phenylpropanoid biosynthesis, among others, were down-regulated under salt stress.…”

Effect of salt stress on genes encoding translation-associated proteins inArabidopsis thaliana

“…(Col-0) seeds were surface sterilized and placed on Murashige and Skoog (MS) semisolid agar plates (with 1% sucrose, 1.5% agar, pH 6.8) 40 in a growth chamber at 16 h light (150 μE m -2 s -1 , 20°C, 60% relative humidity)/8 h dark (16°C, 75% relative humidity) cycle. Uniformly developed 16-d-old seedlings from plates were transferred into liquid medium, 41 and kept on a rotary shaker (100 rpm, continuous light) for 20 h at 22°C. Thereafter, NaCl (150 mM final concentration) was added to the medium.…”