A Further Analysis of the Relationship between Yellow Ripe-Fruit Color and the Capsanthin-Capsorubin Synthase Gene in Pepper (<i>Capsicum</i> sp.) Indicated a New Mutant Variant in <i>C. annuum</i> and a Tandem Repeat Structure in Promoter Region

<div><p>Mature pepper (<i>Capsicum</i> sp.) fruits come in a variety of colors, including red, orange, yellow, brown, and white. To better understand the genetic and regulatory relationships between the yellow fruit phenotype and the capsanthin-capsorubin synthase gene (<i>Ccs</i>), we examined 156 <i>Capsicum</i> varieties, most of which were collected from Northwest Chinese landraces. A new <i>ccs</i> variant was identified in the yellow fruit cultivar CK7. Cluster analysis revealed that CK7, which belongs to the <i>C. annuum</i> species, has low genetic similarity to other yellow <i>C. annuum</i> varieties. In the coding sequence of this <i>ccs</i> allele, we detected a premature stop codon derived from a C to G change, as well as a downstream frame-shift caused by a 1-bp nucleotide deletion. In addition, the expression of the gene was detected in mature CK7 fruit. Furthermore, the promoter sequences of <i>Ccs</i> from some pepper varieties were examined, and we detected a 176-bp tandem repeat sequence in the promoter region. In all <i>C. annuum</i> varieties examined in this study, the repeat number was three, compared with four in two <i>C. chinense</i> accessions. The sequence similarity ranged from 84.8% to 97.7% among the four types of repeats, and some putative <i>cis</i>-elements were also found in every repeat. This suggests that the transcriptional regulation of <i>Ccs</i> expression is complex. Based on the analysis of the novel <i>C. annuum</i> mutation reported here, along with the studies of three mutation types in yellow <i>C. annuum</i> and <i>C. chinense</i> accessions, we suggest that the mechanism leading to the production of yellow color fruit may be not as complex as that leading to orange fruit production.</p>