Genetic diversity analysis in the Turkish pepper germplasm using iPBS (inter-primer binding site) retrotransposon-based markers

YILDIZ, M.; KOÇAK, M.; NADEEM, M. A.; CAVAGNARO, P. F.; BARBOZA, K.; BALOCH, F. S. ; ALTıNOZ, D.; KELEş, D.

TURKISH JOURNAL OF AGRICULTURE AND FORESTRY SCIENCES

TUBITAK SCIENTIFIC & TECHNICAL RESEARCH COUNCIL TURKEY

Año: 2019

1300-011X

Capsicum is one of the most diverse genera and includes economically important crop species, such as bell pepper (C. annuum) and chilli pepper (C. annuum, C. chinense, C. frutescens), cultivated and consumed worldwide. In Turkey, a broad and phenotypically diverse pepper germplasm collection has been traditionally used and maintained by local growers throughout the country, and gene banks for these species have been created. In the present study, we characterized genetic diversity and population structure in a collection 94 pepper accessions using iPBS (inter-primer binding site) retrotransposon-based markers. A total of 20 iPBS primers were used to generate 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 the taxa analyzed were clearly differentiated by the iPBS markers. The marker?s polymorphism information content (PIC) 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 the C. annuum accessions from the other pepper species, with a few sub-clusters observed among the latter, including groups with accessions of both C. frutescens and C. chinense. At inter-species level, the three clustering methods clearly discriminated C. annuum from C. frutescens and C. chinense. No clear association was found between iPBS-based clustering and the accessions geographical origin or their fruit characteristics. 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.