CaMYB12-like underlies a major QTL for flavonoid content in pepper (Capsicum annuum) fruit.

The regulation of flavonoid biosynthesis is only partially explored in pepper (Capsicum annuum L.). The genetic basis underlying flavonoid variation in pepper fruit was studied. Variation of flavonoids in fruit of a segregating F2 population was studied using LC-MS followed by quantitative trait locus (QTL) analysis. Near-isogenic lines (NILs), BC1 S1 populations, virus-induced gene silenced (VIGS) and transgenic overexpression were used to confirm the QTL and the underlying candidate gene. A major QTL for flavonoid content was found in chromosome 5, and a CaMYB12-like transcription factor gene was identified as candidate gene. Near-isogenic lines (NILs) contrasting for CaMYB12-like confirmed its association with the flavonoid content variation. Virus-induced gene silencing (VIGS) of CaMYB12-like led to a significant decrease in the expression of several flavonoid pathway genes and a drastic decrease in flavonoid levels in silenced fruits. Expression of CaMYB12-like in the tomato slmyb12 mutant led to enhanced levels of several flavonoids in the fruit skin. Introgression of the CaMYB12-like allele into two cultivated varieties also increased flavonoid content in their fruits. A combination of metabolomic, genetic and gene functional analyses led to discovery of CaMYB12-like as a major regulator of flavonoid variation in pepper fruit and demonstrated its potential to breed for high-flavonoid content in cultivated pepper.

Genetic and biochemical analysis reveals linked QTLs determining natural variation for fruit post-harvest water loss in pepper (Capsicum).

KEY MESSAGE: Molecular markers linked to QTLs controlling post-harvest fruit water loss in pepper may be utilized to accelerate breeding for improved shelf life and inhibit over-ripening before harvest. Bell pepper (Capsicum annuum L.) is an important vegetable crop world-wide. However, marketing is limited by the relatively short shelf life of the fruit due to water loss and decay that occur during prolonged storage. Towards breeding pepper with reduced fruit post-harvest water loss (PWL), we studied the genetic, physiological and biochemical basis for natural variation of PWL. We performed quantitative trait locus (QTL) mapping of fruit PWL in multiple generations of an interspecific cross of pepper, which resulted in the identification of two linked QTLs on chromosome 10 that control the trait. We further developed near-isogenic lines (NILs) for characterization of the QTL effects. Transcriptome analysis of the NILs allowed the identification of candidate genes associated with fruit PWL-associated traits such as cuticle biosynthesis, cell wall metabolism and fruit ripening. Significant differences in PWL between the NILs in the immature fruit stage, differentially expressed cuticle-associated genes and differences in the content of specific chemical constituents of the fruit cuticle, indicated a likely influence of cuticle composition on the trait. Reduced PWL in the NILs was associated with delayed over-ripening before harvest, low total soluble solids before storage, and reduced fruit softening after storage. Our study enabled a better understanding of the genetic and biological processes controlling natural variation in fruit PWL in pepper. Furthermore, the genetic materials and molecular markers developed in this study may be utilized to breed peppers with improved shelf life and inhibited over-ripening before harvest.