Genetic mapping of the c1 locus by GBS-based BSA-seq revealed Pseudo-Response Regulator 2 as a candidate gene controlling pepper fruit color.

KEY MESSAGE: The Pseudo-Response Regulator 2 gene was identified in the c1 locus, representing a genetic factor regulating fruit color in pepper using GBS-based BSA-seq. The loci c1, c2, and y have been widely reported as genetic determinants of various ripe fruit colors in pepper. However, c1, which may impact reduced pigmentation in red, orange, and yellow fruits, is not well understood. Two cultivars showing peach or orange fruit in Capsicum chinense 'Habanero' were found to have c2 mutation and were hypothesized to segregate c1 locus in the F2 population. Habanero peach (HP) showed a reduced level of chlorophylls, carotenoids and total soluble solids in immature and ripe fruits. A microscopic examination of the fruit pericarps revealed smaller plastids and less stacked thylakoid grana in HP. The expression of many genes related to chlorophyll and carotenoid biosynthetic pathways were reduced in HP. To identify the genomic region of the c1 locus, bulked segregant analysis combined with genotyping-by-sequencing was employed on an F2 population derived from a cross between Habanero orange and HP. One SNP at chromosome 1 was strongly associated with the peach fruit color. Pepper Pseudo-Response Regulator 2 (PRR2) was located close to the SNP and cosegregated with the peach fruit color. A 41 bp deletion at the third exon-intron junction region of CcPRR2 in HP resulted in a premature termination codon. A nonsense mutation of CaPRR2 was found in C. annuum 'IT158782' which had white ripe fruit coupled with null mutations of capsanthin-capsorubin synthase (y) and phytoene synthase 1 (c2). These results will be useful for the genetic improvement in fruit color and nutritional quality in pepper.

Inferring the Genetic Determinants of Fruit Colors in Tomato by Carotenoid Profiling.

Carotenoids are essential for plant and animal nutrition, and are important factors in the variation of pigmentation in fruits, leaves, and flowers. Tomato is a model crop for studying the biology and biotechnology of fleshy fruits, particularly for understanding carotenoid biosynthesis. In commercial tomato cultivars and germplasms, visual phenotyping of the colors of ripe fruits can be done easily. However, subsequent analysis of metabolic profiling is necessary for hypothesizing genetic factors prior to performing time-consuming genetic analysis. We used high performance liquid chromatography (HPLC), employing a C30 reverse-phase column, to efficiently resolve nine carotenoids and isomers of several carotenoids in yellow, orange, and red colored ripe tomatoes. High content of lycopene was detected in red tomatoes. The orange tomatoes contained three dominant carotenoids, namely δ-carotene, ß-carotene, and prolycopene. The yellow tomatoes showed low levels of carotenoids compared to red or orange tomatoes. Based on the HPLC profiles, genes responsible for overproducing δ-carotene and prolycopene were described as lycopene ε-cyclase and carotenoid isomerase, respectively. Subsequent genetic analysis using DNA markers for segregating population and germplasms were conducted to confirm the hypothesis. This study establishes the usefulness of metabolic profiling for inferring the genetic determinants of fruit color.