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Strawberry is often subjected to cold stress in temperate regions when insulation measures are not strictly applied in protected cultivation. Cold stress adversely influences plant growth and development by triggering a massive change to the transcriptome. To provide the potential strategies in improving strawberry cold tolerance and give a glimpse into the understanding of the complex cold signaling pathways in plants, this study identified attractive candidate genes and revealed diverse regulatory networks that responded to cold stress in strawberry (Fragaria×ananassa) by a transcriptomic analysis. Totally, there were 2397 differentially expressed genes (DEGs) under cold stress treatment (T1) vs. normal treatment (CK). Of these, 1180 DEGs were upregulated, while 1217 DEGs were downregulated. Functional enrichment analysis showed that DEGs were significantly (adjusted P value < 0.05) overrepresented in six pathways including plant hormone signal transduction, flavonoid biosynthesis, mitogen-activated protein kinase (MAPK) signaling, starch and sucrose metabolism, circadian rhythm, and alpha-linolenic acid metabolism. The cold signaling initiated expression of downstream cold-responsive (COR) genes with cis-acting element ABRE or CRT/DRE in the ABA-independent or ABA-dependent pathway to impel plant defense against the stress. Strikingly, GIGANTEA (gene id 101308922), two-component response regulator-like PRR95 (gene id 101295449), and ethylene-responsive transcription factor ERF105-like (gene id 101295082) were dramatically induced under low-temperature treatment, indicating that they played an important role in response to cold stress in strawberry.
Pubmed ID: 31467865
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Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software Python package that provides infrastructure to process data from high-throughput sequencing assays. While the main purpose of HTSeq is to allow you to write your own analysis scripts, customized to your needs, there are also a couple of stand-alone scripts for common tasks that can be used without any Python knowledge.
View all literature mentionsR package to identify differentially expressed genes from RNA-Seq data.
View all literature mentionsA commercial organization which provides assay technologies to isolate DNA, RNA, and proteins from any biological sample. Assay technologies are then used to make specific target biomolecules, such as the DNA of a specific virus, visible for subsequent analysis.
View all literature mentionsIntegrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies.
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