Transcriptome analysis of grapevine shoots exposed to chilling temperature for four weeks

Abstract

Low temperature is an important factor that can limit the growth of grapevine (Vitis spp.). In this study, we analyzed the transcriptome of grapevine shoots exposed to cold temperatures to identify genes expressed specifically at low temperature, determine their function based on GO-term analysis, and compare their differential expression. We analyzed two varieties that differed in cold tolerance, the more-tolerant ‘Campbell Early’ and the less-tolerant ‘Kyoho’ grapevine varieties. This was accomplished through annotation of data from sequencing short reads on the Solexa platform. We assembled more than 120 million high-quality trimmed reads using Velvet followed by Oases. Functional categorization of up-regulated transcripts revealed the conservation of genes involved in various biological processes including cellular processes, primary metabolic processes, and biological regulation. The major up-regulated genes in ‘Campbell Early’ included loci encoding response regulator 20, expansin-like B1, a leucine-rich repeat (LRR) family protein, and galactinol synthase 2. The major down-regulated genes in ‘Campbell Early’ included loci encoding fasciclinlike arabinogalactan 9, a GDSL-like lipase/acylhydrolase superfamily protein, early nodulin-like protein 14, and trichome birefringence-like 38. The differential expression observed by sequence analysis was confirmed by real-time PCR. Genes encoding a non-specific serine/threonine protein kinase, peroxidase, and ubiquitin-protein ligase showed reduced expression in response to low temperature in both grapevine varieties. Transcriptome analysis of shoots exposed to chilling could lead to new insights into the molecular basis of tolerance to low-temperature in grapevine.