Genetic diversity and population structure analysis – a prerequisite for constructing a mini core collection of Balkan Capsicum annuum germplasm

Abstract

Pepper (Capsicum annuum L.) is one of the most important vegetable crops worldwide. The Balkans, including Bulgaria, are considered as the secondary centre of pepper diversity especially for C. annuum, where local forms with diverse phenotypes and qualities have formed due to the specific agro-climatic conditions and breeding traditions. Evaluation of the genetic diversity and structure of a pepper collection is an important tool for further development of new varieties and the maintenance of sustainable agriculture. In this study, a set of 179 C. annuum accessions collected from different locations in the Balkan Peninsula was genotyped with 21 simple sequence repeat (SSR; microsatellite) markers. In total, 146 alleles were amplified among which the majority were with low frequencies (<5%). The mean He, Ho and PIC for the 21 SSR loci in the whole set were 0.531, 0.249 and 0.483, respectively. Model-based structure analysis divided the collection into 3 main clusters (K = 3) that grouped accessions with distinct fruit traits like shape, size, pungency. Further genetic structure analysis at increasing Ks suggested the presence of sub-clustering within the three main clusters. A Balkan C. annuum mini core collection was constructed based on the allelic diversity and the inferred genetic structure. As far as the mini core collection captured substantial part of the allele richness, genetic and phenotypic diversity of the analysed 176 non-redundant accessions, while maintaining good representativeness, we believe it will be of high interest to pepper breeders and germplasm conservation specialists.

Morphological and molecular diversity in mid-late and late maturity genotypes of cauliflower

“…Model-based population structure analysis (STRUCTURE) depicts homogeneous mixture and provides understanding about the introgression in the present population within gene pool, thereby elucidate grouping better than dendrogram. The differentiations at K = 2 revealed almost consistency in pedigree of genotypes with introgression in few genotypes and this mix is quite obvious as breeding genotypes is a continuous process through recombination and outcrossing events [ 55 ]. Such introgression will continue to rise in the genetic resources [ 56 ].…”

Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family

“…Their findings unveiled the presence of two distinct genetic groups, which aligned with differences in fruit type and geographical distribution, highlighting the impact of both natural and human-driven factors on the genetic structure of pepper germplasm. In a study by Christov et al. (2021) , attention was shifted to Balkan pepper accessions.…”

“…Their findings unveiled the presence of two distinct genetic groups, which aligned with differences in fruit type and geographical distribution, highlighting the impact of both natural and human-driven factors on the genetic structure of pepper germplasm. In a study by Christov et al (2021), attention was shifted to Balkan pepper accessions. By genotyping 179 C. annuum accessions from different locations in the Balkan Peninsula, the authors identified three main clusters based on fruit traits such as shape, size, and pungency.…”