Abstract
BackgroundLeaf senescence is an important developmental programmed degeneration process that dramatically affects crop quality and yield. The regulation of senescence is highly complex. Although senescence regulatory genes have been well characterized in model species such as Arabidopsis and rice, there is little information on the control of this process in cotton. Here, the senescence process in cotton (Gossypium hirsutum L.) leaves was investigated over a time course including young leaf, mature leaf and leaf samples from different senescence stages using RNA-Seq.ResultsOf 24,846 genes detected by mapping the tags to Gossypium genomes, 3,624 genes were identified as differentially expressed during leaf senescence. There was some overlap between the genes identified here and senescence-associated genes previously identified in other species. Most of the genes related to photosynthesis, chlorophyll metabolism and carbon fixation were downregulated; whereas those for plant hormone signal transduction were upregulated. Quantitative real-time PCR was used to evaluate the results of RNA-Seq for gene expression profiles. Furthermore, 519 differentially expressed transcription factors were identified, notably WRKY, bHLH and C3H. In addition, 960 genes involved in the metabolism and regulation of eight hormones were identified, of which many genes involved in the abscisic acid, brassinosteroid, jasmonic acid, salicylic acid and ethylene pathways were upregulated, indicating that these hormone-related genes might play crucial roles in cotton leaf development and senescence. However, most auxin, cytokinin and gibberellin pathway-related genes were downregulated, suggesting that these three hormones may act as negative regulators of senescence.ConclusionsThis is the first high-resolution, multiple time-course, genome-wide comprehensive analysis of gene expression in cotton. These data are the most comprehensive dataset currently available for cotton leaf senescence, and will serve as a useful resource for unraveling the functions of many specific genes involved in cotton leaf development and senescence.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0433-5) contains supplementary material, which is available to authorized users.
Highlights
Leaf senescence is an important developmental programmed degeneration process that dramatically affects crop quality and yield
Lin et al BMC Plant Biology (2015) 15:43 senescence-associated genes (SAGs) and senescencerelated mutants in various plant species, including plants such as Arabidopsis thaliana, Oryza sativa, and Medicago truncatula [5,6,7,8,9,10]. Among these SAGs, numerous transcription factors (TFs) such as NAC, WRKY, MYB [11], kinases and receptor-like kinases [12], signal transduction-related proteins, and regulators of metabolism are involved in regulating leaf senescence, indicating that senescence is an integrated response to many signals that are governed by highly complex transcriptional regulatory networks
When mapping the digital gene expression (DGE) tags, we carefully considered the reference sequences, because the mapping percentages of tags were critical for downstream analysis G. hirsutum is a primary cultivated allotetraploid species and has a tetraploid genome (AD; 2n = 4 × = 52)], whereas, G. raimondii and G. arboreum are diploid cotton species and have D genome and A genome, respectively (D/A; 2n = 2× = 26) [61,62]
Summary
Leaf senescence is an important developmental programmed degeneration process that dramatically affects crop quality and yield. Lin et al BMC Plant Biology (2015) 15:43 senescence-associated genes (SAGs) and senescencerelated mutants in various plant species, including plants such as Arabidopsis thaliana, Oryza sativa, and Medicago truncatula [5,6,7,8,9,10]. Among these SAGs, numerous transcription factors (TFs) such as NAC, WRKY, MYB [11], kinases and receptor-like kinases [12], signal transduction-related proteins, and regulators of metabolism are involved in regulating leaf senescence, indicating that senescence is an integrated response to many signals that are governed by highly complex transcriptional regulatory networks.
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
