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Transcriptome characterization and differential expression analysis of cold-responsive genes in young spikes of common wheat

Paper ID Volume ID Publish Year Pages File Format Full-Text
23077 43415 2014 10 PDF Available
Title
Transcriptome characterization and differential expression analysis of cold-responsive genes in young spikes of common wheat
Abstract

•Studied spring frost tolerance by cold treatment during wheat reproductive stage.•RNA-seq of mixture samples of cold-treated and control wheat young spikes.•DGE analysis of two biological samples of cold treatments (0 h and 48 h).•Investigating the transcriptional changes by combination of RNA-Seq and DGE.

With the frequent occurrence of climatic anomalies, spring frost has become a significant limiting factor on wheat production, especially during the reproductive growth stage. A high-throughput sequencing technology was applied and a total of 54 million clean reads that corresponded to 7.44 Gb of total nucleotides were generated. These reads were then de novo assembled into 120,715 unigenes with an average length of 627 bp. Functional annotations were then obtained by aligning all unigenes with public protein databases. In total, 9657 potential EST-SSRs were identified, and 6310 primer pairs for 1329 SSRs were obtained. Meanwhile, a comparison of four tag-based digital gene expression libraries, which was built from the control and cold-treated young spikes were performed. Overall, 526 up-regulated and 489 down-regulated genes were identified, and GO and KEGG pathway analyses of those genes were further conducted. Based on these results, a series of candidate genes involved in cold response pathways were identified, and 12 of them were confirmed by qRT-PCR. The combination of RNA-Seq and digital gene expression analysis in this study provides a powerful approach for investigating the transcriptional changes and obtained a large number of unigenes annotated to public databases.

Keywords
Triticum aestivum L.; Reproductive stage; Transcriptome; Digital gene expression profile; Frost responsive gene
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Transcriptome characterization and differential expression analysis of cold-responsive genes in young spikes of common wheat
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Publisher
Database: Elsevier - ScienceDirect
Journal: Journal of Biotechnology - Volume 189, 10 November 2014, Pages 48–57
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us