Abstract
The cotton diploid species, Gossypium arboreum, shows important properties of stress tolerance and good genetic stability. In this study, through mRNA-seq, we de novo assembled the unigenes of multiple samples with 3h H2O, NaCl, or PEG treatments in leaf, stem and root tissues and successfully obtained 123,579 transcripts of G. arboreum, 89,128 of which were with hits through BLAST against known cotton ESTs and draft genome of G. raimondii. About 36,961 transcripts (including 1,958 possible transcription factor members) were identified with differential expression under water stresses. Principal component analysis of differential expression levels in multiple samples suggested tissue selective signalling responding to water stresses. Venn diagram analysis showed the specificity and intersection of transcripts’ response to NaCl and PEG treatments in different tissues. Self-organized mapping and hierarchical cluster analysis of the data also revealed strong tissue selectivity of transcripts under salt and osmotic stresses. In addition, the enriched gene ontology (GO) terms for the selected tissue groups were differed, including some unique enriched GO terms such as photosynthesis and tetrapyrrole binding only in leaf tissues, while the stem-specific genes showed unique GO terms related to plant-type cell wall biogenesis, and root-specific genes showed unique GO terms such as monooxygenase activity. Furthermore, there were multiple hormone cross-talks in response to osmotic and salt stress. In summary, our multidimensional mRNA sequencing revealed tissue selective signalling and hormone crosstalk in response to salt and osmotic stresses in G. arboreum. To our knowledge, this is the first such report of spatial resolution of transcriptome analysis in G. arboreum. Our study will potentially advance understanding of possible transcriptional networks associated with water stress in cotton and other crop species.
Highlights
Cotton is an essential crop for producing fiber used in textiles and is a major oil source
The seedling plants were treated by 17% polyethylene glycol (PEG) and 150 mM NaCl for 3 hours, and three tissues including root, stem, and leaf, were respectively harvested for mRNA-seq analysis
As to PP2Cs and ABFs, majority of their members in cotton and Arabidopsis were up-regulated by salt and osmotic stresses. These results indicated that the transcripts in cotton shared similar abscisic acid (ABA) signalling pathway as those in Arabidopsis responding to water stresses, while there was slight difference in the members of SNF1related protein kinase 2 (SnRK2), the cotton homologous were down-regulated by NaCl in root tissue but the Arabidopsis genes were not responded to salt stress in root tissue
Summary
Cotton is an essential crop for producing fiber used in textiles and is a major oil source. Cotton yield is dramatically reduced under drought and high salinity conditions [1,2,3,4,5,6]. Water stress (mainly including both salt and drought stresses) is a major environmental stress that many plants have to cope with during their whole life cycle [7,8,9,10,11,12]. High salinity disturbs cytoplasmic K+/Na+ homeostasis and can result in ion toxicity and osmotic stress, as well as altering growth regulation, etc [8,9,10,18,19]
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