title: Transcriptome characterization and differential expression analysis of cold-responsive genes in young spikes of common wheat.
abstract: 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.
authors.affiliation: Crop Research Institute, Shandong Academy of Agricultural Sciences, China; Key Laboratory of Wheat Biology & Genetic Improvement On North Yellow & Huai River Valley, Ministry of Agriculture, China; National Engineering Laboratory For Wheat & Maize, Jinan 250100, Shandong, China.
authors.forename: Shujuan
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Crop Research Institute, Shandong Academy of Agricultural Sciences, China; Key Laboratory of Wheat Biology & Genetic Improvement On North Yellow & Huai River Valley, Ministry of Agriculture, China; National Engineering Laboratory For Wheat & Maize, Jinan 250100, Shandong, China.
authors.forename: Guoqi
authors.initials: G
authors.lastname: Song
authors.affiliation: Crop Research Institute, Shandong Academy of Agricultural Sciences, China; Key Laboratory of Wheat Biology & Genetic Improvement On North Yellow & Huai River Valley, Ministry of Agriculture, China; National Engineering Laboratory For Wheat & Maize, Jinan 250100, Shandong, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Gao
authors.affiliation: Crop Research Institute, Shandong Academy of Agricultural Sciences, China; Key Laboratory of Wheat Biology & Genetic Improvement On North Yellow & Huai River Valley, Ministry of Agriculture, China; National Engineering Laboratory For Wheat & Maize, Jinan 250100, Shandong, China.
authors.forename: Yulian
authors.initials: Y
authors.lastname: Li
authors.affiliation: Crop Research Institute, Shandong Academy of Agricultural Sciences, China; Key Laboratory of Wheat Biology & Genetic Improvement On North Yellow & Huai River Valley, Ministry of Agriculture, China; National Engineering Laboratory For Wheat & Maize, Jinan 250100, Shandong, China.
authors.forename: Dong
authors.initials: D
authors.lastname: Guo
authors.affiliation: Crop Research Institute, Shandong Academy of Agricultural Sciences, China; Key Laboratory of Wheat Biology & Genetic Improvement On North Yellow & Huai River Valley, Ministry of Agriculture, China; National Engineering Laboratory For Wheat & Maize, Jinan 250100, Shandong, China.
authors.forename: Qingqi
authors.initials: Q
authors.lastname: Fan
authors.affiliation: Crop Research Institute, Shandong Academy of Agricultural Sciences, China; Key Laboratory of Wheat Biology & Genetic Improvement On North Yellow & Huai River Valley, Ministry of Agriculture, China; National Engineering Laboratory For Wheat & Maize, Jinan 250100, Shandong, China.
authors.forename: Xinxia
authors.initials: X
authors.lastname: Sui
authors.affiliation: Crop Research Institute, Shandong Academy of Agricultural Sciences, China; Key Laboratory of Wheat Biology & Genetic Improvement On North Yellow & Huai River Valley, Ministry of Agriculture, China; National Engineering Laboratory For Wheat & Maize, Jinan 250100, Shandong, China.
authors.forename: Xiusheng
authors.initials: X
authors.lastname: Chu
authors.affiliation: Crop Research Institute, Shandong Academy of Agricultural Sciences, China; Key Laboratory of Wheat Biology & Genetic Improvement On North Yellow & Huai River Valley, Ministry of Agriculture, China; National Engineering Laboratory For Wheat & Maize, Jinan 250100, Shandong, China.
authors.forename: Chengyan
authors.initials: C
authors.lastname: Huang
authors.affiliation: Crop Research Institute, Shandong Academy of Agricultural Sciences, China; Key Laboratory of Wheat Biology & Genetic Improvement On North Yellow & Huai River Valley, Ministry of Agriculture, China; National Engineering Laboratory For Wheat & Maize, Jinan 250100, Shandong, China.
authors.forename: Jianjun
authors.initials: J
authors.lastname: Liu
authors.affiliation: Crop Research Institute, Shandong Academy of Agricultural Sciences, China; Key Laboratory of Wheat Biology & Genetic Improvement On North Yellow & Huai River Valley, Ministry of Agriculture, China; National Engineering Laboratory For Wheat & Maize, Jinan 250100, Shandong, China. Electronic address: lgy111@126.com.
authors.forename: Genying
authors.initials: G
authors.lastname: Li
mesh_terms: D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*; D014908:Triticum / Q000235:genetics*
keywords: Digital gene expression profile; Frost responsive gene; Reproductive stage; Transcriptome; Triticum aestivum L.