The characterisation of phytoene synthase-1 and 2, and 1-D-deoxy-xylulose 5-phosphate synthase genes from red chilli pepper (Capsicum annuum)

The red colouration of ripe chilli pepper fruit is due to the presence of the carotenoid capsanthin. 1-D-deoxy-xylulose 5-phosphate synthase (DXS) and phytoene synthase(s) (PSY) are influential biosynthetic steps in the carotenoid pathway. A panel of chilli accessions for varying fruit colour intensity revealed the correlation of carotenoid content with PSY and DXS transcript levels. The PSY and DXS genes were sequenced from high and low carotenoid genotypes to deduce potential allelic variation. PSY-1 and -2 showed tissue-specific expression, with PSY-1 and -2 expressed in chromoplast and chloroplast containing tissues, respectively. Protein modelling, phylogenetic analysis and transcription factor analysis were conducted to understand how the allelic variation identified could affect carotenoid biosynthesis and regulation, and subsequently colour intensity phenotype. A candidate mutation located in the transit peptide of the PSY-1 protein sequence was identified in the low colour intensity genotype. Sequence variation within the promoter region of the DXS gene present in the high colour intensity genotype was determined in the glyceraldehyde 3-phosphate binding motif (GAPF). These data can be exploited to develop tools and resources for the breeding of high colour intensity chilli pepper fruit.