Evaluation of the genetic structure present in natural populations of four subspecies of black cherry (Prunus serotina Ehrh.) from North America using SSR markers

Guzmán, Félix Alberto; Segura, S.; Aradhya, Mallikarjuna K.; Potter, Daniel

doi:10.1016/j.scienta.2018.01.013

Cited by 17 publications

(11 citation statements)

References 28 publications

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“…Although the only other study to examine IBD in North American Prunus serotina s.l. (Guzman, Segura, Aradhya, & Potter, ) reported a considerably higher value ( R 2 = 0.45), this study differed from ours in critical respects. Besides featuring an inter‐population sampling strategy, their 18 populations spanned the four Prunus serotina s.l.…”

Section: Discussioncontrasting

confidence: 87%

A rangewide herbarium‐derived dataset indicates high levels of gene flow in black cherry (Prunus serotina)

Konrade

Shaw

Beck

2019

Ecology and Evolution

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Isolation by Distance (IBD) is a genetic pattern in which populations geographically closer to one another are more genetically similar to each other than populations which are farther apart. Black cherry (Prunus serotina Ehrh.) (Rosaceae) is a forest tree species widespread in eastern North America, and found sporadically in the southwestern United States, Mexico, and Guatemala. IBD has been studied in relatively few North American plant taxa, and no study has rigorously sampled across the range of such a widespread species. In this study, IBD and overall genetic structure were assessed in eastern black cherry (P. serotina Ehrh. var. serotina), the widespread variety of eastern North America. Eastern North America. Prunus serotina Ehrh. var. serotina (Rosaceae). Dense sampling across the entire range of eastern black cherry was made possible by genotyping 15 microsatellite loci in 439 herbarium samples from all portions of the range. Mantel tests and STRUCTURE analyses were performed to evaluate the hypothesis of IBD and genetic structure. Mantel tests demonstrated significant but weak IBD, while STRUCTURE analyses revealed no clear geographic pattern of genetic groups. The modest geographic/genetic structure across the eastern black cherry range suggests widespread gene flow in this taxon. This is consistent with P. serotina's status as a disturbance‐associated species. Further studies should similarly evaluate IBD in species characteristic of low‐disturbance forests.

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Section: Discussioncontrasting

confidence: 87%

A rangewide herbarium‐derived dataset indicates high levels of gene flow in black cherry (Prunus serotina)

Konrade

Shaw

Beck

2019

Ecology and Evolution

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“…Despite current advances in genome sequencing, microsatellite markers or simple sequence repeats (SSR) that have been converted into a DNA marker are still successfully used worldwide for routine genotyping in many crops, and for protection of ancient autochthonous olive trees in Italy (Rotondi et al 2018), evaluation of genetic redundancy in ex situ apple collections in Norway (Gasi et al 2016), evaluation of genetic structure in subspecies of black cherry from North America (Guzmán et al 2018), estimation of natural outcrossing rate and genetic diversity in Lima bean landraces from Brazil (Penha et al 2017), and in the analysis of the genetic diversity of rice cultivars in India (Dhama et al 2018). This molecular technique is also ideal for designing conservation strategies for genetic resources, and for forming and validating core collections (Porta et al 2018;de Vicente et al 2006).…”

Section: Introductionmentioning

confidence: 99%

Microsatellites to enhance characterization, conservation and breeding value of Capsicum germplasm

Guzmán¹,

Moore

Vicente

et al. 2019

Genet Resour Crop Evol

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Capsicum species are of great economic, medicinal, culinary and cultural value worldwide, however their genetic potential is still underutilized. In this study, a set of 21 microsatellite markers showed utility for distinguishing a diverse group of 42 Capsicum genotypes representing 11 species. The level of polymorphism among these genotypes was evaluated by calculating the polymorphic information content (PIC) and discriminating power (D) for each locus. A total of 208 alleles were detected at the 21 loci evaluated. Markers detecting the highest number of alleles also exhibited the highest number of rare alleles. PIC values and D estimations showed a significant positive correlation (r = 0.98; P \ 0.0000). PIC values ranged between 0.500 (marker NG20) and 0.899 (marker NG17), giving an average of 0.775. Genetic relationships among genotypes were evaluated using UPGMA clustering, Principal Coordinate Analysis (PCoA) and Bayesian model-based clustering, allowing genotypes to be discriminated into groups according to their degree of genetic similarity corresponding to distinct taxa. Based on these analyses, the 21 microsatellite included in this study now define a standard tool for efficient assessment of molecular variability of Capsicum germplasm collections conserved worldwide.

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“…Representation in plane, in a smaller number of dimensions, proves to be helpful for the identification of related genotypic groups (Cruz et al, 2011). Several studies used principal coordinates to demonstrate the divergence between genotypes using molecular data (Aitken et al, 2018;El-Esawi et al, 2018;Guzmán, Segura, Aradhya, & Potter, 2018;Taglioti et al, 2018;Wu et al, 2018;Ferreira et al, 2016;Zaher et al, 2011;Van Inghelandt, Melchinger, Lebreton, & Stich, 2010). Other studies were based on principal component analyses (Muller et al, 2018;Valcárcel, Peiró, Pérez-de-Castro, & Díez, 2018;Osawaru, Ogwu, & Dania-Ogbe, 2013;Santi et al, 2012;Jombart, Devillard, & Balloux, 2010).…”

Section: Introductionmentioning

confidence: 99%

Comparison of projection of distance techniques for genetic diversity studies

et al. 2019

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The objective of this study was to compare different graphical dispersion analysis techniques in two- or three-dimensional planes. In this study, the data from different published works were used in order to determine the best methodology for analyzing the genetic diversity of different species. In this study, efficiency is measured by the amount of original distance absorbed by the projection of distances technique, which in the case of major components is equal to the amount of total variation originally available and retained by the principal components used for dispersion purposes. The projection of dissimilarity measurement technique, principal component analysis (PCA), and principal coordinate analysis (PCoA) were used. Considering the analysis by means of three orthogonal axes, the graphical dispersion efficiency was 82.22 for PCA, 87.22 for PCoA, and 85.25 for the projection of distances technique. For the 2D analysis, considering the two main axes, the mean dispersion efficiency was 69.90 for the PCA, 75.06 for the projection technique, and 78.16 for PCoA. Considering the studies carried out with experimental data of six different species, it is concluded that the principal coordinate analysis is superior.

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Evaluation of the genetic structure present in natural populations of four subspecies of black cherry (Prunus serotina Ehrh.) from North America using SSR markers

Cited by 17 publications

References 28 publications

A rangewide herbarium‐derived dataset indicates high levels of gene flow in black cherry (Prunus serotina)

A rangewide herbarium‐derived dataset indicates high levels of gene flow in black cherry (Prunus serotina)

Microsatellites to enhance characterization, conservation and breeding value of Capsicum germplasm

Comparison of projection of distance techniques for genetic diversity studies

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