Genetic diversity and assessment of markers linked to resistance and pungency genes in Capsicum germplasm

Dato, Francesco Di; Parisi, Mario; Cardi, Teodoro; Tripodi, Pasquale

doi:10.1007/s10681-014-1345-4

Cited by 31 publications

(24 citation statements)

References 56 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Such erroneous classifications have been reported in other works (González-Pérez et al, 2014), and they bring to light the usefulness of genotyping the genetic resources maintained in the germplasm banks, as a guarantee of their appropriate conservation. However, SSRs still provide valuable information in exploratory works of genetic diversity, and they remain as the markers of choice in several Capsicum studies (Di Dato et al, 2015;Ibarra-Torres et al, 2015;Naegele et al, 2015). In total, 93.7% of them showed PIC values higher than 0.5, which confirmed that those SSR markers were highly informative.…”

Section: Discussionmentioning

confidence: 73%

Deciphering Genetic Diversity in the Origins of Pepper (Capsicum spp.) and Comparison with Worldwide Variability

Silvar

García‐González

2016

Crop Science

View full text Add to dashboard Cite

Several attempts in recent decades have been devoted to investigating the genetic and phenotypic diversity harbored by the genus Capsicum. Particular efforts have been directed to old varieties or landraces. However, the genus is still under‐researched, and further investigations that accurately define the relationships among species and identify those geographic regions with greater variability are required. In the present work, 107 Capsicum landraces from Ecuador, Peru, and Bolivia were evaluated with a set of 16 microsatellite markers. In total, 187 alleles were detected in the Andean collection, and 49.7% of those were recorded as unique alleles. Indices of genetic diversity were high and very similar in the three evaluated countries, although the domesticated Capsicum species carrying the highest diversity varied among them: C. frutescens (L.) in Ecuador, C. chinense (Jacq.) in Peru, and C. annuum (L.) in Bolivia. Comparison of Andean accessions with others coming from diverse origins revealed intraspecific genetic differentiation in C. annuum, C. chinense, C. frutescens, C. baccatum (L.), and C. pubescens (Ruiz et Pav.), following a geographic pattern. Similarly, assessment of the genetic diversity currently maintained in Ecuadorian Capsicum species brought to light a dramatic decrease in the genetic variability of cultivated peppers when compared with those harbored by old landraces. Analysis of genetic relationships among Capsicum species was in agreement with previous taxonomic classifications: C. annuum, C. chinense, and C. frutescens were clustered as independent and highly related species; C. cardenasii (Heiser et Smith) and C. eximium (Hunz.) were indistinguishable as a single species; and C. chacoense (Hunz.) was placed between C. pubescens and C. annuum complexes.

show abstract

Section: Discussionmentioning

confidence: 73%

Deciphering Genetic Diversity in the Origins of Pepper (Capsicum spp.) and Comparison with Worldwide Variability

Silvar

García‐González

2016

Crop Science

View full text Add to dashboard Cite

show abstract

“…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.…”

Section: Introductionmentioning

confidence: 99%

“…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.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2016

View full text Add to dashboard Cite

BackgroundKnowledge on population structure and genetic diversity in vegetable crops is essential for association mapping studies and genomic selection. Genotyping by sequencing (GBS) represents an innovative method for large scale SNP detection and genotyping of genetic resources. Herein we used the GBS approach for the genome-wide identification of SNPs in a collection of Capsicum spp. accessions and for the assessment of the level of genetic diversity in a subset of 222 cultivated pepper (Capsicum annum) genotypes.ResultsGBS analysis generated a total of 7,568,894 master tags, of which 43.4% uniquely aligned to the reference genome CM334. A total of 108,591 SNP markers were identified, of which 105,184 were in C. annuum accessions. In order to explore the genetic diversity of C. annuum and to select a minimal core set representing most of the total genetic variation with minimum redundancy, a subset of 222 C. annuum accessions were analysed using 32,950 high quality SNPs. Based on Bayesian and Hierarchical clustering it was possible to divide the collection into three clusters. Cluster I had the majority of varieties and landraces mainly from Southern and Northern Italy, and from Eastern Europe, whereas clusters II and III comprised accessions of different geographical origins. Considering the genome-wide genetic variation among the accessions included in cluster I, a second round of Bayesian (K = 3) and Hierarchical (K = 2) clustering was performed. These analysis showed that genotypes were grouped not only based on geographical origin, but also on fruit-related features.ConclusionsGBS data has proven useful to assess the genetic diversity in a collection of C. annuum accessions. The high number of SNP markers, uniformly distributed on the 12 chromosomes, allowed the accessions to be distinguished according to geographical origin and fruit-related features. SNP markers and information on population structure developed in this study will undoubtedly support genome-wide association mapping studies and marker-assisted selection programs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3297-7) contains supplementary material, which is available to authorized users.

show abstract

“…Pvr1-R1, and pvr1-R2, according to Di Dato et al (2015). The amplification of CSO, PR-Bs3, 131 T200A, CAPS-p-amt 2 , SCAR-p-amt 6 was performed as described in their original reports (Caranta 132 et al, 1999, Römer et al, 2010, Rubio et al, 2008, Tanaka et al, 2010a, Jeong et al, 2015.…”

mentioning

confidence: 99%

Screening old peppers (Capsicum spp.) for disease resistance and pungency-related traits

Silvar

García‐González

2017

Scientia Horticulturae

View full text Add to dashboard Cite

18A broad panel of Capsicum spp. landraces, mostly originating in the Andean region, was assessed 19 with thirteen molecular markers linked to disease resistance and pungency-related traits. Tsw and L 4 20 were the most common loci observed within the collection, although resistant alleles associated to 21 Pvr4, Phyto.5.2, and Cmr1 were also recorded in approximately 30 % of pepper genotypes. South 22America and, namely the Andean region, revealed as a promising source of disease resistances, 23 particularly against potyviruses. Clustering analysis split the collection into forty groups, each one 24 carrying a distinctive combination of resistant alleles. Capsicum annuum and C. chinense showed 25 the greatest variability, while the other Capsicum species generated homogeneous clusters with 26 well-defined haplotypes. Capsicum chinense appeared as the most promising species for breeding 27 purposes, with various accessions showing potential resistance to more than 80 % of assessed 28 diseases. PCoA analysis did not show a connection between those resistant genotypes and particular 29 geographical regions. The pungency trait was predicted for 85.5 % of pepper accessions. Markers 30 linked to capsinoids content did not amplify or did not displayed polymorphism. 31 32 33

show abstract

Genetic diversity and assessment of markers linked to resistance and pungency genes in Capsicum germplasm

Cited by 31 publications

References 56 publications

Deciphering Genetic Diversity in the Origins of Pepper (Capsicum spp.) and Comparison with Worldwide Variability

Deciphering Genetic Diversity in the Origins of Pepper (Capsicum spp.) and Comparison with Worldwide Variability

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

Screening old peppers (Capsicum spp.) for disease resistance and pungency-related traits

Contact Info

Product

Resources

About