Morphological and molecular characterization of two distinct chilli cultivars from North Eastern India with special reference to pungency related genes

King chilli and Dalle Khursani are the two hottest chilli (Capsicum sp.) cultivars widely grown in NE region of India but a well-organized study pertaining to King chilli and Dalle Khursani is unavailable. We have characterized twenty-two accessions of King chilli and Dalle Khursani, collected from different states of NE region with respect to 27 morphological parameters and using 30 SSR markers. The allelic status of three key pungency related genes viz, putative aminotransferase (pAmt or Pun1), acyl-CoA synthetase (Acs1) and β-ketoacyl-ACP synthase (Kas1) was also determined. Maximum morphological variation was observed for fruit traits and traits like plant growth habit, plant height, etc., which can be used to distinguish between the two cultivars. SSR markers HpmsE062 and HpmsE063 were able to distinguish between the three different cultivars (including a nonpungent bell pepper), while HpmsE116 and HpmsE139 distinguish King chilli from Dalle Khursani. Ward clustering method grouped all the eleven Dalle Khursani accessions together with non-pungent C. annuum accession in one cluster. Sequencing across Acs1 revealed total of eight SNPs and three InDels. Seven SNPs including three within exonic regions were conserved between bell pepper, Dalle Khursani and the reference pungent C. annuum accession. A 2 bp InDel at position 50-51 bp and a 3 bp InDel at position 6313-6315 bp were found to be uniquely conserved haplotypes in both Dalle Khursani and King Chilli. A total of 16 SNPs were found within the sequenced region of Pun1 gene, of which eight SNPs lie within the coding region. Three novel exonic SNPs were found in Dalle Khursani. All eight SNPs found in the intronic region for Pun1 were conserved across Dalle Khursani and the two pungent reference sequences of C. annuum. Our SSR and SNP data suggests that Dalle Khursani is genetically closer to pungent C. annuum. This work provides insights into the genotype of two hottest chillies and paves way for their utilization in chilli improvement programme.