Diversity Analysis and Association Mapping of Fruit Colors in Capsicum annuum

C. annuum peppers were domesticated around 7,000 years ago and contain various compounds of nutritional value such as Vitamin C and Vitamin A precursors known as carotenoids. Carotenoids are the pigments responsible for color in plants, algae and bacteria. Color perception is explained by color spaces; commonly used color spaces in plant studies are CIELAB and the Munsell color system. The individual contributions of the color components (L*, a*, b*, hue and chroma) of these color spaces contribute to the overall color variation seen in peppers and were analyzed in this study. Multiple color diversity analysis tests showed that there are three main clusters found in C. annuum that was not based on geographical location and that lighter peppers clustered together for color component L*. The percentages of total variation contributed by color components L*, a*, b*, hue and chroma are as follows: 10.5%, 14.9%, 10.4%, 37.1% and 10.10%, respectively. A total of 30 linked markers were found using the association mapping approach for the 5 color components. HpmsE026 was found to be a significant marker for color component a* and may play a role in the carotenoid biosynthetic pathway. Marker HpmsE090 associated with hue was found to be linked to the intergenic space between homeodomain leucine zipper protein HD-Zip and Peptidyl-prolyl cis-trans isomerase which are involved in fruit senescence and maturity. Understanding the variation in the contribution of each color component as well as the markers linked to these components, will provide insight into pepper color variation.