Comparative transcriptional analysis reveled genes related to short winter-dormancy regulation in Camellia sinensis

The perennial tea plant ( Camellia sinensis ) is a beverage crop consumed worldwide. Its annual production is significantly affected by the length of winter dormancy (WD) in temperate regions. By intensive phenotype-based selection, we bred a new short WD tea cultivar, named ‘Emei Wenchun’ (EW), which has a dormancy period that is approximately half the length of that of the regular cultivars. To understand the genetic basis of short WD trait of EW, we performed full-length transcript sequencing using the PacBio single-molecule real-time (SMRT) platform and analyzed the transcript expression levels in the buds by Illumina RNA-SEq. We obtained a total of 101,720 full-length non-chimeric sequences from 9.79 Gb of SMRT clean data, resulting in 30,720 non-redundancy full-length transcripts. These transcripts were mapped to 12,819 gene loci, including 2135 novel loci, and revealed 7980 alternative splicing events. In addition, 695 long non-coding RNAs (lncRNAs) and 1,183 fusion transcripts were predicted. By integrating with the RNA-Seq data, we compared the expression levels of the transcripts in dormant and growing buds of EW and a normal WD cultivar (‘Chuan Cha 2’). A total of 15,009 differentially expressed transcripts (DETs) were identified. GO and KEGG enrichment analyses of the DETs revealed critical terms and pathways for the regulation of WD. The key candidate transcripts that were likely to be involved in the WD regulation, including MASDs , NF-YCs , AP2-ERFs , and plant hormone-related genes, were discussed. Results from our analyses provide valuable information to understand the genetic basis of the regulation of WD in Camellia sinensis .