Identification of Large Deletion of <i>Ccs</i> Responsible for Non-Red Fruit Color in Pepper (<i>Capsicum annuum</i>) and Development of DNA Marker to Distinguish the Deletion

Abstract

Chili pepper (Capsicum spp.) fruit color is an important agronomical trait. It has been known that a large deletion in the 5' upstream region of the Ccs gene generates non-red fruit color in pepper, but the accurate size and position of the deletion and whether all the non-red cultivars had the same large deletion or not were unclarified. In this study, to identify the Ccs upstream large deletion, we carried out diagnostic PCR using six forward primers at 300 - 900 bp intervals in the 5' untranslated region of Ccs with a fixed reverse primer for a yellow fruit pepper “Sonia Gold”. Then it was revealed that 4430 bp from -3234 bp position in upstream region to 1196 bp position in exon was deleted in Ccs of “Sonia Gold”. The allele having this deletion was named ccs-del. Probably this allele is substantially the same as ccs-p1 having 4879 bp deletion reported previously. Based on the sequence determined, we developed a PCR marker to distinguish ccs-del. Genotyping of 16 cultivars of C. annuum showed that 14 had ccs-del and the remaining two had another mutant allele ccs-3. This result indicates that ccs-del is the most common allele and widely shared in non-red fruit cultivars in C. annuum. Genotyping of 16 cultivars of C. chinense clarified that one cultivar each possessed ccs-del and ccs-3. These results indicate that major alleles responsible for non-red fruit color in C. annuum were shared across species throughout interspecific introgression.