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Mature pepper ( Capsicum  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 ( Ccs ), we examined 156  Capsicum  varieties, most of which were collected from Northwest Chinese landraces. A new  ccs  variant was identified in the yellow fruit cultivar CK7. Cluster analysis revealed that CK7, which belongs to the  C. annuum  species, has low genetic similarity to other yellow  C. annuum  varieties. In the coding sequence of this  ccs  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  Ccs  from some pepper varieties were examined, and we detected a 176-bp tandem repeat sequence in the promoter region. In all  C. annuum  varieties examined in this study, the repeat number was three, compared with four in two  C. chinense  accessions. The sequence similarity ranged from 84.8% to 97.7% among the four types of repeats, and some putative  cis -elements were also found in every repeat. This suggests that the transcriptional regulation of  Ccs  expression is complex. Based on the analysis of the novel  C. annuum  mutation reported here, along with the studies of three mutation types in yellow  C. annuum  and  C. chinense  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.

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