Genome-Wide Identification and Capsaicinoid Biosynthesis-Related Expression Analysis of the R2R3-MYB Gene Family in Capsicum annuum L.

Abstract

Capsaicinoids are naturally specialized metabolites in pepper and are the main reason that Capsicum fruits have a pungent smell. During the synthesis of capsaicin, MYB transcription factors play key regulatory roles. In particular, <i>R2R3-MYB</i> subfamily genes are the most important members of the MYB family and are critical candidate factors in capsaicinoid biosynthesis. The 108 <i>R2R3-MYB</i> genes in pepper were identified in this study and all are shown to have two highly conserved MYB binding domains. Phylogenetic and structural analyses clustered <i>CaR2R3-MYB</i> genes into seven groups. Interspecies collinearity analysis found that the <i>R2R3-MYB</i> family contains 16 duplicated gene pairs and the highest gene density is on chromosome 00 and 03. The expression levels of <i>CaR2R3-MYB</i> differentially expressed genes (DEGs) and capsaicinoid-biosynthetic genes (CBGs) in fruit development stages were obtained <i>via</i> RNA-seq and quantitative polymerase chain reaction (qRT-PCR). Co-expression analyses reveal that highly expressed <i>CaR2R3-MYB</i> genes are co-expressed with CBGs during early stages of pericarp and placenta development processes. It is speculated that six candidate <i>CaR2R3-MYB</i> genes are involved in regulating the synthesis of capsaicin and dihydrocapsaicin. This study is the first systematic analysis of the <i>CaR2R3-MYB</i> gene family and provided references for studying their molecular functions. At the same time, these results also laid the foundation for further research on the capsaicin characteristics of <i>CaR2R3-MYB</i> genes in pepper.