Inter- and intraspecific differentiation of Capsicum annuum and Capsicum pubescens using ISSR and SSR markers

Ibarra-Torres, Patricia; Valadez-Moctezuma, Ernestina; Pérez-Grajales, Mario; Rodríguez-Campos, Jacobo; Jaramillo-Flores, M. E.

doi:10.1016/j.scienta.2014.10.054

Cited by 24 publications

(20 citation statements)

References 30 publications

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“…All of these selected 14 primer pairs resulted in a higher level of polymorphism with an average of 85.6% in Turkish pepper germplasms. The number of polymorphic bands obtained in this study is higher than those previously performed by Ibarra-Torres et al (2015) and Aktas et al (2009). Ibarra-Torres et al (2015) found 24 and 36 polymorphic SSRs and ISSRs for addressing inter-and intraspecific diversity in C. pubescens and C. annuum, respectively.…”

Section: Resultscontrasting

confidence: 78%

Exploring the genetic variations and population structure of Turkish pepper (Capsicum annuum L.) genotypes based on peroxidase gene markers

et al. 2018

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is thought as one of the most diverse and significant genera due to its varied uses in different parts of the world. In this study, we worked with a total of 71 pepper genotypes from different locations of Turkey to investigate the level of their diversity using the peroxidase gene polymorphism (POGP) markers to reveal their population structure. For this purpose, 14 peroxidase primer pairs were used. They produced 139 bands (mean = 9.9 bands/primer), of which ~ 85.6% were polymorphic in the all germplasm collection. Polymorphism information content (PIC) ranged between 0.48 and 0.97 with an average of 0.75. Range and mean values for gene diversity () were 0.09-0.22 and 0.17, respectively. Shannon's information index () per POGP marker ranged from 0.18 to 0.35 with a mean of 0.29. Using three clustering methods (unweighted pair-group method with arithmetic means, principal coordinate analysis, and STRUCTURE) revealed a clear separation of all the accessions from and accessions in our study. Clusters did not establish an association between the accessions and their geographical origin. This is the first study exploring the population structure through the genetic diversity of Turkish peppers from different regions of the country based on the peroxidase gene markers.

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Section: Resultscontrasting

confidence: 78%

Exploring the genetic variations and population structure of Turkish pepper (Capsicum annuum L.) genotypes based on peroxidase gene markers

et al. 2018

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“…In the present study, 20 iPBS markers generated 172 clear, unambiguous bands, of which 158 (92%) were polymorphic, indicating a high level of polymorphism in the pepper germplasm evaluated. In comparisons with other studies of pepper, the number of polymorphic bands obtained in this study was higher than that found by Ibarra-Torres et al (2015) using ISSR and SSR markers to address inter-and intraspecific diversity in C. pubescens and C. annuum (24 and 36 polymorphic SSRs and ISSRs, respectively), by Aktas et al (2009) using amplified fragment length polymorphisms (AFLPs) to assess the genetic diversity of Turkish C. annuum accessions (56 polymorphic AFLPs), and by Akyavuz et al (2018) using peroxidase gene polymorphism markers for the genetic diversity of Turkish peppers (120 polymorphic bands). Conversely, Krishnamurthy et al (2015) used the AFLPs of a collection of 59 C. annuum and C. baccatum accessions, reporting higher numbers of total (414) and polymorphic bands (389) when compared to the present study, although the level of polymorphism in their study (94%) was comparable to ours (92%).…”

Section: Ipbs Markers For Diversity Analysis In Peppercontrasting

confidence: 73%

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

Yıldız¹,

Koçak²,

Nadeem³

et al. 2020

Turk J Agric For

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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.

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“…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

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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.

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Inter- and intraspecific differentiation of Capsicum annuum and Capsicum pubescens using ISSR and SSR markers

Cited by 24 publications

References 30 publications

Exploring the genetic variations and population structure of Turkish pepper (Capsicum annuum L.) genotypes based on peroxidase gene markers

Exploring the genetic variations and population structure of Turkish pepper (Capsicum annuum L.) genotypes based on peroxidase gene markers

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

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

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