Study of Phytoene Synthase 1 (PSY1) and Capsanthin-Capsorubin Synthase (CCS) Gene Profile in Chili Peppers (Capsicum frutescens L.) Cakra Hijau, G1/M8 Line, and HV-149

Color variation of chili (Capsicum frutescens L.) is controlled by, among others, PSY1 and CCS genes. This study aims to determine the polymorphisms of PSY1 and CCS genes from three genotypes of chili pepper, Cakra Hijau, G1/M8 line, and HV-149 which have fruit color variations at each stage of ripening. cDNA from PSY1 and CCS genes of the three chili genotypes were constructed from mRNA by reverse transcription process. Amplification PSY1 and CCS gene using Polymerase Chain Reaction (PCR) technique with a pair of primers specific for PSY1 and CCS genes. The resulting sequences were analyzed to determine the presence of Single Nucleotide Polymorphism (SNP). The molecular structure was analyzed using BioEdit, Clustal-X2, BLAST NCBI and GeneBank database. Comparing the partial PSY1 gene from 3 chili genotypes with the PSY1 gene from C. annuum (XM_016714936.2) showed 2 point mutations in each genotype. These mutations showed that different composition in amino acid sequence. The partial sequence of the CCS gene of the three chili genotypes compared with the CCS gene of C. annuum (X77289.1) showed a cytosine deletion (1265) in the CCS sequence only on the HV-149 genotype. This deletion caused an amino acid change (from threonine to isoleucine) and an early stop codon in the HV-149 genotype. The presence of several polymorphisms in the PSY1 and CCS genes may cause variations in the color formation of chilies.