Genotyping a large collection of pepper (Capsicum spp.) with SSR loci brings new evidence for the wild origin of cultivated C. annuum and the structuring of genetic diversity by human selection of cultivar types

Nicolaı̈, Maryse; Cantet, Melissa; Lefebvre, Véronique; Sage-Palloix, Anne-Marie; Palloix, Alain

doi:10.1007/s10722-013-0006-0

Cited by 110 publications

(151 citation statements)

References 47 publications

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“…Pacheco-Olvera et al (2012) reported expected heterozygosity in C. annuum of 0.47 for wild populations and 0.42 for native Mexican chili populations. Moreover, Nicolaï et al (2013) found heterozygosity of 0.59 in native C. annuum populations and 0.78 in C. annuum var. glabriusculum.…”

Section: Population Genetic Diversitymentioning

confidence: 96%

Characterization of genetic diversity of native 'Ancho' chilipopulations of Mexico using microsatellite markers

Toledo-Aguilar

López-Sánchez

Santacruz-Várela

et al. 2016

Chilean J. Agric. Res.

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Section: Population Genetic Diversitymentioning

confidence: 96%

Characterization of genetic diversity of native 'Ancho' chilipopulations of Mexico using microsatellite markers

Toledo-Aguilar

López-Sánchez

Santacruz-Várela

et al. 2016

Chilean J. Agric. Res.

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“…Additional phenotypic information was not enough available to help building the core collections despite it can help to optimize further screening and analyses of agronomical traits (Nicolaï et al 2013). In grapevine, Emanuelli et al (2013) compared a phenotypic and a genetic core collection.…”

Section: Definition Of Inra Diploid Core Collections For Association mentioning

confidence: 99%

Genetic Diversity, Population Structure, Parentage Analysis, and Construction of Core Collections in the French Apple Germplasm Based on SSR Markers

et al. 2016

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In-depth characterization of apple genetic resources is a prerequisite for genetic improvement and for germplasm management. In this study, we fingerprinted a very large French collection of 2163 accessions with 24 SSR markers in order to evaluate its genetic diversity, population structure, and genetic relationships, to link these features with cultivar selection date or usage (old or modern, dessert or cider cultivars), and to construct core collections. Most markers were highly discriminating and powerful for varietal identification, with a probability of identity P (ID) over the 21 retained SSR loci close to 10 −28. Pairwise comparisons revealed 34 % redundancy and 18.5 % putative triploids. The results showed that the germplasm is highly diverse with an expected heterozygosity H e of 0.82 and observed heterozygosity H o of 0.83. A Bayesian model-based clustering approach revealed a weak but significant structure in three subgroups (F ST = 0.014-0.048) corresponding, albeit approximately, to the three subpopulations defined beforehand (Old Dessert, Old Cider, and Modern Cultivars). Parentage analyses established already known and yet unknown relationships, notably between old cultivars, with the frequent occurrence of cultivars such as BKing of Pippin^and BCalville Rouge d'Hiver^as founders. Finally, core collections based on allelic diversity were constructed. A large dessert core collection of 278 cultivars contained 90 % of the total dessert allelic diversity, whereas a dessert subcore collection of 48 cultivars contained 71 % of diversity. For cider apples, a 48-cultivar core collection contained 83 % of the total cider allelic diversity.

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“…Among these, Single Sequence Repeat (SSR) or microsatellite markers, which target tandem repeats of ditri-or tetra-nucleotide DNA motifs, are both highly polymorphic within populations and randomly distributed throughout the genome in both transcribed and nontranscribed sequences (Saghai-Maroof et al, 1994;Manzelli et al, 2007). SSR markers have been successfully used to evaluate genetic diversity in several crop species such as wheat (Fufa et al, 2005), Pennisetum purpureum (Azevedo et al, 2012), Capsicum (Nicolai et al, 2013), Sorghum (Cuevas et al, 2014), barley (Shakhatreh et al, 2015), Vigna subterranea (Molosiwa et al, 2015), maize (Salami et al, 2016) and some underutilized species such as buckwheat and wild melon (Roy et al, 2012;Zhang and Zao, 2013). For pearl millet characterization, several SSR markers were developed (Mariac et al, 2006;Stich et al, 2010;Nepolean et al, 2012) and used to evaluate its genetic diversity at the regional scale in west Africa.…”

Section: Introductionmentioning

confidence: 99%

Assessment of genetic diversity among cultivated Pearl millet (Pennisetum glaucum, Poaceae) accessions from Benin, West Africa

Adéoti¹,

Djèdatin²,

Ewedje³

et al. 2017

Afr. J. Biotechnol.

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Simple sequence repeat (SSR) molecular markers were used for genetic diversity analysis and population structure of the cultivated Pearl millet in Benin, West Africa. In order to assess the level of genetic diversity, 14 polymorphic SSR markers were used to screen 114 accessions from different agroecological zones in Benin. SSR markers were found to reveal a total of 57 alleles with an average of 4.071 allele per locus. Genetic diversity index varied from 0.099 to 0.633 with an average of 0.405. The average observed heterozygosity was found to reach 0.425. The analysis of molecular variance showed no real differentiation between regions. Only 5% of genetic variation was observed between samples collected from north-eastern and north-western region. A high level of variation (95%) was observed among accessions. Moreover, both principal component analysis (PCA) and the dendrogram obtained from the genetic distance among accessions revealed the absence of any specific structuration of accessions from each region under study. Our results confirmed diversity among cultivated Pearl millet in Benin and such diversity is not clustering according to geographical patterns.

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Genotyping a large collection of pepper (Capsicum spp.) with SSR loci brings new evidence for the wild origin of cultivated C. annuum and the structuring of genetic diversity by human selection of cultivar types

Cited by 110 publications

References 47 publications

Characterization of genetic diversity of native 'Ancho' chilipopulations of Mexico using microsatellite markers

Characterization of genetic diversity of native 'Ancho' chilipopulations of Mexico using microsatellite markers

Genetic Diversity, Population Structure, Parentage Analysis, and Construction of Core Collections in the French Apple Germplasm Based on SSR Markers

Assessment of genetic diversity among cultivated Pearl millet (Pennisetum glaucum, Poaceae) accessions from Benin, West Africa

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