International Journal Bioautomation (Dec 2015)

Comparative Transcriptome Analysis of Hot Pepper (Capsicum annuum L.) Leaf Heterosis by RNA-seq

  • Tao Li,
  • Heng-ming Wang,
  • Zhi-liang Li,
  • Xiao-wang Xu

Journal volume & issue
Vol. 19, no. 4
pp. 447 – 458


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Heterosis has been mostly used in hot pepper breeding and production, but the molecular basis of heterosis has not been extensively studied. In this study, comparative transcriptomes analysis of parental lines (D6, D7) and F1 hybrids (D6×D7 and D7×D6) was performed. A total of 0.6 billion raw reads, and 0.44 billion high-quality reads were obtained after the filtering process. Statistical analysis of genes with presence/deletion variations showed that, there were 1068 (6.20%) and 780 (4.56%) genes in the "single parent express consistent type" in the direct (D6×D7) and reciprocal (D7×D6) F1 hybrids, respectively. More genes fit into the non-additive expression type in two F1 hybrids compared to the parents, and less than 8% of the genes belong to the additive expression type. 66.08% in direct and 62.96% in reciprocal F1 hybrids belong to the epistatic dominance expression pattern. There were more differentially expressed genes (DEGs) between the two parental lines (351) than between the two hybrids (17). The results of gene ontology (GO) analysis showed that there were obvious differences in electron transmission and photorespiration between two F1 hybrids. GO terms for regulating plant hypersensitive responses, and MAPK pathways were only enriched in the direct hybrid (D6×D7).