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 -1and 2 expressed in chromoplast and chloroplast containing tissues, respectively. Protein modelling, phylogenetic analysis and transcription factor analysis was 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. Within the promoter region of the DXS gene present in the high colour intensity genotype sequence variation was determined in the glyceraldehyde 3-phosphate binding motif (GAPF) of the promoter region. These data can be exploited to develop tools and resources for the breeding of high colour intensity chilli pepper fruit. Key policy highlights Using the molecular findings disclosed in this article the potential exists to develop molecular markers for the breeding varieties of chilli peppers with improved aesthetic consumer preference and nutritional attributes. ### Competing Interest Statement The authors have declared no competing interest.