Translation initiation codon (ATG) or SCoT markers-based polymorphism study within and across various Capsicum accessions: insight from their amplification, cross-transferability and genetic diversity

Abstract

Being an economical and nutritional crop, Capsicum appeases people's peppery taste and is found to bewidely distributed all over the world having vast diversity. In the present study, genetic polymorphism, cross transferability (CT) and genetic diversity were examined among the 54 different accessions of Capsicum species including 49 of Capsicum annuum, three of C. baccatum and two of C. frutescens, using a set of 36 start codon targeted (SCoT) primers. Of the total, 35 SCoT markers showed successful amplification profile among chilli germplasms and an average primer polymorphism was reported as 81.52% which ranged from 50% (SCoT-6) to 100% (SCoT-11). A total of 365 amplicons were obtained with an average of 10.43 bands per primer and the length of the bands ranged from 150 bp to 1.2 kb. Further, polymorphic information content value of SCoT markers ranged from 0.42 (for SCoT-25) to 0.86 (SCoT-27) with an average of 0.78. The average value of CT of SCoT markers was 44.08% ranged from 14.25% to 57.26% among different chilli accessions. A dendrogram was constructed and established genetic relationship among 54 capsicum species, with the help of translation initiation codon polymorphisms or SCoT primer amplification. This study suggests the effectiveness of SCoT marker system for characterizing and assessing genetic diversity of Capsicum germplasm, which can be used for evolutionary studies and to identify agronomically important traits.