Comparative transcriptome analysis reveals differential transcription in heat-susceptible and heat-tolerant pepper (Capsicum annum L.) cultivars under heat stress

Heat stress is an important agricultural problem around the world. In pepper (Capsicum annum L.), heat stress seriously affects pollination and yield. However, to date, the molecular basis of heat stress has not been extensively studied. Using the HiSeq™ 2000 sequencing platform, the seedling transcriptome of heat-susceptible C.annuum ‘S590’(CaS) and heat-tolerant ‘R597’ (CaR) under the heat stress was examined. Over five million clean reads were generated from each library, each corresponding to a coverage of >250,000 nt. About 73% of the reads were mapped to the pepper genome, and 3,799 and 4,010 differentially expressed genes (DEGs) were identified in ‘R597’ (CaR) and ‘S590’(CaS), respectively. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses determined that the identified DEGs were involved in heat shock protein, heat shock transcription factors, hormone, as well as calcium and kinase signaling. Further validation identified 35 genes that were involved in stress response, and that most of the heat shock proteins were upregulated in two genotypes, and highly expressed in susceptible S590 than in tolerant cultivar R597; the transcription factors and hormone signaling genes showed higher levels of expression in the heat-tolerant cultivar R597 than that observed in the heat-susceptible S590. These findings facilitate in better understanding of the molecular mechanism underlying heat stress in different pepper genotypes.