Identification of novel SNPs in Pun1 locus for pungency in Capsicum species

Abstract

Abstract Background Capsaicin and its analogues known as capsaicinoids are the principal sources of pungency in Capsicum spp, detectable by mammalian taste receptors. In this study, a characterization of chilli germplasm was done based on capsaicin concentration. The goal of this study was to figure out what causes Capsicum spp. to lose their pungency. Methods and Results The experimental material involved forty-nine genotypes of chilli collected from different states of India representing different agro-ecological regions and were evaluated for several quantitative and biochemical traits. Wide variation in capsaicin content was observed among the genotypes. Bhut Jolokia (Capsicum chinense) showed highest capsaicin content (10500.75 µg/g). In order to understand the variation in pungency content, molecular analysis of Pun1 gene was done for discovering SNP in the selected genotypes.The five genotypes namely Bhut Jolokia, Kashmiri-Long-1, Byadgi Dabbi, Byadgi Kaddi and Nishat-1with high, medium and no pungency content were selected for the molecular analysis of Pun1 gene. Single primer pair was employed for amplification of Pun1gene in Capsicum chinense and Capsicum annuum (with amplicon size of 650bp). However, in the non-pungent variety (Nishat-1), the 650bp DNA fragment was not amplified due to 2.5kb deletion spanning the putative promoter and first exon of AT3. DNA amplification was followed by sequencing. Sequence alignment between Pun1 gene sequences of genotypes Bhut Jolokia (Capsicum chinense) and Kashmiri-Long − 1 (Capsicum annuum) with high capsaicin content and medium capsaicin content, respectively, revealed variations at 13 places and alignment of amino acid sequences deduced from nucleotide sequences revealed 5variations in amino-acid sequences. Furthermore, protein structure prediction in C. chinense and C. annuum identified certain structural changes. Conclusion The observed variation in protein structure might be responsible for high capsaicin production in one genotype as compared to the other and hence the protein conformation determines its interaction with the substrate.