Genomic Strategies to Mine Alleles That Control Capsaicin, Dihydrocapsaicin and Related Compounds

The genus Capsicum consists of approximately 30 species and out of which only five species are domesticated. These are grouped into three complexes namely Capsicum annuum complex, Capsicum baccatum complex and Capsicum pubescens complex.  HPLC quantification of capsaicin and dihydrocapsaicin is currently in progress to assess the natural variation among the group annuum. We designed primers for Caffeoyl COA methyltransferase and Vanillin Aminotransferease that are in the pathways of capsaicin  and used to amplify the genomic DNAs and cDNA from the fruits at various developmental stages in various accessions. The cloned products were analyzed for the allelic variation.  Current study is to identify functional alleles in precursor genes for capsaicin and related compounds and use them for the association mapping among 100 heirloom collections of annuum.  FISH analysis for noting the copy number variation of these genes in the Capsicum genome is in progress. Results pertaining to various objectives as mentioned above will be discussed.