Unravelling the genetic diversity and phylogenetic relationships of Indian Capsicum through fluorescent banding

Hot chilli species of Capsicum are one of the most significant spice crops in India having several genetically distinct cultivars. The present study was targeted to upgrade chromosomal database of 15 cultivars belonging to C. annuum L., C. frutescens L. and C. chinense Jacq. EMA-based fluorochrome banding with GC-specific stain Chromomycin A3 (CMA) was elemental to reveal specialization in karyotypes that could not be traced out by Giemsa-stained preparations. CMA banding pattern was combined with karyomorphometric indices to statistically evaluate chromosomal relationship among the cultivars. The marker chromosome pairs 11 and 12 containing nucleolar CMA bands could be suggested as the evolutionary landmarks in ‘C. annuum complex’. We found direct correspondence between fruit morphotype variation and CMA banding pattern to demonstrate maximum genetic diversity within C. annuum, followed by C. frutescens while Bhut jolokia of C. chinense displayed genetic uniformity. UPGMA phenogram upheld distinct species separation, cultivar diversity and relationships within and among the species. Out of nine C. annuum cultivars, at least two cultivars showed some sort of genetic relationship with C. chinense, particularly the Ghee cultivar shares more proximity with C. chinense. The fluorescent karyotype database reliably symbolized uniqueness of Capsicum germplasm of India, especially from the NEH sector that grows Bhut jolokia. Our attempt is believed to complement genomic investigation in the popular and exotic chilli cultivars of India and interest breeders in search of alternative genetic resources.