Genetic diversity analysis in the Turkish pepper germplasm using iPBS retrotransposon- based markers

Abstract

Capsicum is one of the most important and diverse plant taxa, widely used as a spice and vegetable worldwide, including Turkey. Germplasm characterization is an essential step for crop breeding. In the present study, we characterized the genetic diversity and population structure of a collection of 94 pepper accessions using inter-primer binding site (iPBS) retrotransposon-based markers. A total of 20 iPBS primers were used that generated 172 bands (mean = 8.6 bands/primer), of which ~92% were polymorphic in the entire germplasm collection, whereas 83%, 69%, and 80% of the bands were polymorphic within the C. annuum, C. chinense, and C. frutescens subsets, respectively. All of the taxa analyzed were clearly differentiated by the iPBS markers. The polymorphism information content of the markers ranged between 0.15 and 0.99, with an average of 0.66. Cluster analyses by different methods (UPGMA, STRUCTURE, and principal coordinate analysis) revealed a clear separation of all of the C. annuum accessions from the other pepper species, with a few subclusters observed among the latter, including groups with accessions of both C. frutescens and C. chinense. At the interspecies level, the 3 clustering methods clearly discriminated C. annuum from C. frutescens and C. chinense. No clear association was found between the iPBS-based clustering and geographical origin or fruit characteristics of the accessions. This is the first report characterizing the genetic diversity and population structure in the Turkish pepper germplasm using iPBS markers. It is expected that these data will serve as a foundation for the development of new and improved pepper varieties.

Exploring the Genetic Diversity and Population Structure of Turkish Laurel Germplasm by the iPBS-Retrotransposon Marker System

“…The maximum number of effective alleles is always desirable because they show the existence of greater genetic variations. Mean effective number of alleles (1.36) found in this study were higher than the reported by previous studies in various crops using iPBS-retrotransposons markers [25,50]. Mean gene diversity (0.22) resulted in this study was found higher than the reported by earlier studies [25,48,50] and thus explains the presence of higher diversity in studied germplasm.…”

“…Mean effective number of alleles (1.36) found in this study were higher than the reported by previous studies in various crops using iPBS-retrotransposons markers [25,50]. Mean gene diversity (0.22) resulted in this study was found higher than the reported by earlier studies [25,48,50] and thus explains the presence of higher diversity in studied germplasm. Shannon's information index is an important criterion to understand the variation as it distinguishes the genetic diversity in a population combining abundance and evenness [51].…”

“…Shannon's information index is an important criterion to understand the variation as it distinguishes the genetic diversity in a population combining abundance and evenness [51]. Mean Shannon's information index (0.35) was found greater than the reported by earlier studies using the same molecular marker [25,50]. Genetic distance was calculated among the 94 Turkish laurel genotypes and mean genetic distance was 0.228.…”

“…Previous studies have proven iPBS-retrotransposon a highly reproducible, robust and trustable marker system [22,23,40,41]. Our earlier studies in wild emmer [8], pea [24], tobacco [25], common bean [48], pepper [50] and safflower [51] also found this marker system highly robust, and trustable, which can be used for the investigation of genetic diversity in any crop. Similarly, Mehmood et al [41] also found this marker system highly reproducible, robust and trustable.…”

DNA fingerprinting and genetic diversity analysis of world quinoa germplasm using iPBS-retrotransposon marker system

“…This might be possible due to differences in studied germplasm. Shannon's information index is an important benchmark to assess variations in studied germplasm as it differentiates the genetic diversity in a population combining abundance and evenness (Yildiz et al, 2019). Mean Shannon's information index was 0.16, which was found lower than reported by earlier studies using different molecular markers for quinoa (Saad-Allah and Youssef, 2018;Hossein-Pour et al, 2019).…”