Assessment of Molecular Diversity and Phylogenetic Analysis Among Chilli Genotypes Using Start Codon Targeted (SCoT) Markers

Abstract

Assessment of genetic diversity is pivotal to identify genotypes for the crop improvement programme in chilli. Therefore, the presentstudy was carried out to identify and characterise genetic variation among 45 chilli genotypes using Start Codon TargetedPolymorphism (SCoT) markers. Out of 18 primers, ten markers revealed significant polymorphism among the chilli accessions studied,with amplification ranging from 280 bp to 2.0 kb. A total of 81 alleles were obtained, ranging from 5 to 10 alleles, with an average of 8.1alleles per primer. Out of 81 alleles, sixty-two (76.54%) were found polymorphic in nature. The genetic similarity among the analysedgenotypes ranged from 24.2 to 100%. The UPGMA dendrogram was constructed to establish the genetic relationship among the chilligenotypes using Jaccard's coefficient. Cluster analyses grouped 45 genotypes into two major groups, which was also supported byprincipal coordinate analysis (PCoA). Analysis of molecular variance (AMOVA) showed a significant estimated value at a degree of 999permutations. The percentage of variability was higher among populations (55%) than within populations (45%). The mean Nei'sgene diversity (h) was 0.2233 and the mean Shannon's Information Index (i) was 0.3470, with the highest of both given by the SCoT-7marker. The SCoT marker-based distinguishable genetic variation in the chilli genotypes may serve as a potential aid in chilliimprovement programme. It demonstrates the utility of SCoT markers for estimating molecular diversity and genotype identificationin chilli. This study also suggests the potential of SCoT markers in further association studies in chilli.