Exploring the genetic makeup and population structure among Capsicum accessions for crop improvement and breeding curriculum insights

Background Capsicum or chilli is an important crop in India which exhibits immense structural and genetic variations reflecting their intra- and inter-specific relationships. The aim of this study was to establish relationships amongst 54 Capsicum accessions through analysis of genetic and population structure using ISSR markers. Results Out of 19, successful DNA amplifications were shown by 7 ISSR primers and a total of 80 bands were identified ranging between 8 and 14 with an average of 11.43 bands/primer. A significant degree of polymorphic information content (PIC), discriminating power (DP), resolving power (RP), effective multiplex ratio (EMR), and marker index (MI) were identified as 0.39, 0.70, 6.40, 5.88, and 2.30, respectively, using ISSR markers in chillies. The cross-transferability ranged from 8.0 to 72.15% with an average of 52.63% among chillies. Amongst genetic information, grand mean values were 0.264, 0.180, 0.376, 0.296, and 0.180, which correspond to Shannon’s information index ( I ), expected heterozygosity ( He ), Nei ’ s gene diversity, total diversity among species ( Ht ), diversity within species ( Hs ), respectively. Further, the coefficients of gene differentiation ( Gst ) and gene flow ( Nm ) were 0.393 and 0.773, representing higher genetic variation among the population which was confirmed by analysis of molecular variance (AMOVA). Conclusion ISSR markers represented a potent system for the estimation of relationships or variation studies and generated information useful for planning crop management and improvement strategies in chilli breeding.