Identification and Validation of an Allele Specific Marker Associated with Pungency in Capsicum spp.

Pungency or heat in Capsicum spp. is due to the accumulation of unique secondary compounds known as capsaicinoids in their placental tissues. Detecting presence or absence of pungency at the nursery stage is a challenging task in CMS based hybrid pepper breeding programs. In this study a DNA sequence possibly related to pungency trait with high similarity to Pun1 or At3 gene was investigated. Nucleotide alignment of the obtained sequences and corresponding fragment from the data base has revealed a 16bp deletion in C.annuum ‘Maor’. A multiplex agarose based co-dominant marker was designed to detect the identified polymorphism and named it as Cen1. This Cen1 marker is validated in a panel of 27 pepper genotypes belonging to C.annuum, C.chinensis, C.frutescens and C.baccatum for its wide utility. All these Capsicum accessions were correctly discriminated with phenotype. In addition, the ability of Cen1 marker to discriminate homozygous and heterozygous plants was demonstrated in F1 hybrids crossed from a non pungent ‘Maor’ and a pungent ‘Habanero’. The Cen1 marker was also associated with phenotypic character in the tested genotypes. Moreover the linkage association of Cen1 with At3 or Pun1 gene has also been discussed. Therefore the developed functional marker in this study will be highly useful in marker assisted selection (MAS) programmes, germplasam characterization and seed purity testing of chilli.