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

Mehtap Yildiz,Pablo Cavagnaro,Davut Keleş,Faheem Shahzad Baloch,Duygu Argün,Muhammad Azhar Nadeem,Metin Koçak,Karina Barboza

doi:10.3906/tar-1902-10

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.

Highlights

Peppers (Capsicum spp.) are grown worldwide for various purposes, including fresh and cooked vegetable consumption, spices, ornaments, and medicine, and because of its high content of phytonutrients (Bosland et al, 2012)
20 inter-primer binding site (iPBS) primers yielding intense and polymorphic bands were selected for further analysis of the Turkish pepper germplasm collection
Of the 172 scorable bands, 158 (~92%) were polymorphic in the germplasm collection, whereas 83%, 69%, and 80% of the bands were polymorphic within the C. annuum, C. chinense, and C. frutescens subsets, respectively

Summary

Introduction

Peppers (Capsicum spp.) are grown worldwide for various purposes, including fresh and cooked vegetable consumption, spices, ornaments, and medicine (e.g., the compound capsaicin, present at high concentrations in hot peppers, has analgesic, antidiabetic, and anticancer effects), and because of its high content of phytonutrients (e.g., provitamin A, carotenoids, and vitamin C) (Bosland et al, 2012). There are 27 recognized Capsicum species, 5 of which were domesticated through distinct events at different primary diversification centers of America (Pickersgill, 2007; Olmstead et al, 2008; Nicolai et al, 2013). These 5 species are C. annuum, C. frutescens, C. chinense, C. pubescens, Among the 5 domesticated Capsicum species, C. annuum is the most widely distributed and economically. YILDIZ et al / Turk J Agric For important It is a diploid and self-pollinating species with a chromosome number of 2n = 24 (Gyulai et al, 2000). C. annuum was domesticated from wild bird pepper or chiltepin (C. annuum var. glabriusculum) in Mexico (Perry et al, 2007; Kraft et al, 2014)

Objectives

Methods

Results

Conclusion