New Insights into Capsicum spp Relatedness and the Diversification Process of Capsicum annuum in Spain

Abstract

The successful exploitation of germplasm banks, harbouring plant genetic resources indispensable for plant breeding, will depend on our ability to characterize their genetic diversity. The Vegetable Germplasm Bank of Zaragoza (BGHZ) (Spain) holds an important Capsicum annuum collection, where most of the Spanish pepper variability is represented, as well as several accessions of other domesticated and non-domesticated Capsicum spp from all over the five continents. In the present work, a total of 51 C. annuum landraces (mainly from Spain) and 51 accessions from nine Capsicum species maintained at the BGHZ were evaluated using 39 microsatellite (SSR) markers spanning the whole genome. The 39 polymorphic markers allowed the detection of 381 alleles, with an average of 9.8 alleles per locus. A sizeable proportion of alleles (41.2%) were recorded as specific alleles and the majority of these were present at very low frequencies (rare alleles). Multivariate and model-based analyses partitioned the collection in seven clusters comprising the ten different Capsicum spp analysed: C. annuum, C. chinense, C. frutescens, C. pubescens, C. bacatum, C. chacoense and C. eximium. The data clearly showed the close relationships between C. chinense and C. frutescens. C. cardenasii and C. eximium were indistinguishable as a single, morphologically variable species. Moreover, C. chacoense was placed between C. baccatum and C. pubescens complexes. The C. annuum group was structured into three main clusters, mostly according to the pepper fruit shape, size and potential pungency. Results suggest that the diversification of C. annuum in Spain may occur from a rather limited gene pool, still represented by few landraces with ancestral traits. This ancient population would suffer from local selection at the distinct geographical regions of Spain, giving way to pungent and elongated fruited peppers in the South and Center, while sweet blocky and triangular types in Northern Spain.

Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing

“…have been estimated by different approaches, including the use of biochemical, morphological and molecular markers [11–15]. Molecular markers permit in-depth characterization of germplasm [16] and improve the efficiency and precision of conventional plant breeding schemes through marked-assisted selection.…”

“…Molecular markers permit in-depth characterization of germplasm [16] and improve the efficiency and precision of conventional plant breeding schemes through marked-assisted selection. Amplified Fragment Length Polymorphism (AFLP), Simple Sequence Repeat (SSR) and Single Nucleotide Polymorphism (SNP) markers proved useful in detecting genetic diversity and determining genetic relationships in pepper germplasm [13–15]. However, although AFLP and SSR markers were widely used due to their highly polymorphic nature [14, 15], this was partly related to a high genotyping error rate limiting their application for genetic studies.…”

“…Amplified Fragment Length Polymorphism (AFLP), Simple Sequence Repeat (SSR) and Single Nucleotide Polymorphism (SNP) markers proved useful in detecting genetic diversity and determining genetic relationships in pepper germplasm [13–15]. However, although AFLP and SSR markers were widely used due to their highly polymorphic nature [14, 15], this was partly related to a high genotyping error rate limiting their application for genetic studies. Indeed, AFLP and SSR gel-based genotyping is very laborious and can be affected by human errors.…”

“…Although several SNP-based marker studies have been performed so far [27–30], no GBS work is reported in Solanaceae with the exception of potato [31]. Indeed, the genetic structure and diversity present in Capsicum germplasm was only investigated using a large set of SSR markers [14, 15]. The recent whole genome sequencing of Capsicum [32, 33] provides a unique opportunity to estimate chromosome wide molecular diversity and precisely infer pepper population structure, enhancing the information derived from GBS data.…”

Genome-Wide Divergence and Linkage Disequilibrium Analyses for Capsicum baccatum Revealed by Genome-Anchored Single Nucleotide Polymorphisms

“…Several studies mainly explored genetic distances and phylogenetic analysis in C. annuum (Lefebvre et al, 1993; Prince et al, 1995; Paran et al, 1998; Livingstone et al, 1999; Rodriguez et al, 1999; Patricia Toquica et al, 2003; Kim and Kim, 2005; Lefebvre, 2005; Portis et al, 2007; Aguilar-Meléndez et al, 2009a; Mimura et al, 2012; Hill et al, 2013; Nicolaï et al, 2013; González-Pérez et al, 2014). We have only a few reports of the genetic diversity and population structure of C. baccatum var.…”