Development and application of a suite of non-pungency markers for the Pun1 gene in pepper (Capsicum spp.)

Pungency in peppers is due to the presence of capsaicinoid molecules, which are only produced in Capsicum species. The major gene Pun1 is required for the production of capsaicinoids. Three distinct mutant alleles of Pun1 have been found in three cultivated Capsicum species, one of which has been widely utilized by breeders. Although these mutations have been previously identified, a robust collection of molecular markers for the set of alleles is not available. This has been hindered by the existence of at least one paralogous locus that tends to amplify with Pun1. We present a suite of markers that can differentiate the four Pun1 alleles and test them on a diverse panel of pepper lines and in an F2 population segregating for pungency. These markers will be useful for pepper breeding, germplasm characterization, and seed purity testing.