1The Energy and Resources Institute, India Habitat Centre, Lodhi Road, New Delhi110 003
2National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab140 306
3Chilli and Vegetable Research UnitDr. Panjabrao Deshmukh Krishi Vidyapeeth, Akola, Maharashtra 444 104
4TERI School of Advanced Studies, Plot No. 10 Institutional Area, Vasant Kunj, New Delhi110 070
*Corresponding author's e-mail: rupesh0deshmukh@gmail.com
**Present address: University of Science & Technology, Techno City, Kiling Road, Baridua, 9th Mile, Ri-Bhoi, Meghalaya793 101
Online published on 16 August, 2021.
In the present study, a total of 27 chloroplast specific SSRs (CpSSR) have been identified in the chloroplast genome of Capsicum annum L. The frequency of the SSRs was about one in 5.7 kb of the chloroplast genome. Out of 27 SSRs, 26 were mono-nucleotide repeats of A/T and one was a trinucleotide repeat (TTA). Further a set of seven markers were validated by genotyping 48 capsicum accessions comprising of cultivars from five different species and landraces of unknown identity. The seven SSR markers generated a total of 27 alleles among 48 samples used in this study. The size of the amplicons varied from 161 bp (CaCpM22 & 26) to 339 bp (CaCpM06). The polymorphic information content (PIC) value for the set of the primers used ranged from 0.11 to 0.48 with an average of 0.33. The number of alleles for markers ranged from three to six with an average of 3.28 alleles per marker. The phylogenetic analysis of the chilly accessions showed that the Bhut jolokia land race is clustered along with the C. frutescence indicating the it's probable parentage. The chloroplast genome based SSR markers identified in the present study can be further used for the marker-assisted genomic studies.
Bhut Jolokia, Capsicum, Chilly, Chloroplast, SSR
