A new set of mono‐ and dinucleotide chloroplast microsatellites in Fagaceae

Sebastiani, Federico; Carnevale, Silvana; Vendramin, G. G.

doi:10.1111/j.1471-8286.2004.00635.x

Cited by 55 publications

(40 citation statements)

References 16 publications

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“…We selected 35 cpSSR loci that had been used in population genetic studies of forest trees, especially in oaks (see Table S1 in Appendix 1), including 8 markers developed for dicotyledonous angiosperms (Weising & Gardner 1999), 16 made specifically for oaks (Deguilloux et al 2003) and 11 created for Fagaceae (Sebastiani et al 2004). The loci were divided into four marker sets, each consisting of 6-11 loci, and subjected to PCR-multiplex protocols (Table S1 in Appendix 1).…”

Section: Chloroplast Microsatellitesmentioning

confidence: 99%

“…Several universal cpSSR loci have been identified for angiosperm taxa (Weising & Gardner 1999). In addition, a number of loci have been designed specifically for oaks (Deguilloux et al 2003) or in general for Fagaceae (Sebastiani et al 2004). Since then, several phylogeographic studies have been done in oaks employing cpSSR markers (Grivet et al 2006, Magri et al 2007, Pakkad et al 2008, Tovar-Sanchez et al 2008.…”

Section: Introductionmentioning

confidence: 99%

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Chloroplast microsatellites as a tool for phylogeographic studies: the case of white oaks in Poland

Chmielewski¹,

Meyza²,

Chybicki³

et al. 2015

iForest

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Assessing the distribution of chloroplast DNA (cpDNA) haplotype variation is useful for studying the phylogeography of angiosperms. In the last two decades the cpDNA phylogeography of white oaks in Europe has been extensively studied, mostly based on the PCR-RFLP technique. However, PCR-RFLPs have low mutation rates and are primarily useful for reconstructing patterns at large geographical scales and lack resolution at fine spatial scales. Here we evaluate the usefulness of chloroplast microsatellites (cpSSR) as an alternative to PCRRFLPs in Polish oak populations which have been underrepresented in previous studies. Eighty-five cpSSR haplotypes were detected using 14 cpSSR loci and a broad collection of 6680 trees sampled throughout Poland. Haplotype diversity was significantly lower in Q. petraea (He = 0.798) than in Q. robur (He = 0.820). Only 17 haplotypes (H01-H17) were found in 13 or more individuals, comprising together 97.9% of the sample. Most frequent cpSSR haplotypes were related to PCR-RFLP haplotypes, establishing the cross-references between the two marker systems. There was significant concordance between the matrices of genetic distances obtained by PCR-RFLP haplotypes and cpSSR haplotypes. Phylogenetic relationships among cpSSR haplotypes supported the existence of the three predominant maternal lineages of oaks in Poland: Iberian (7.8%), Apennine (20.6%) and Balkan (65.5%). The results are discussed with regards to the usefulness of cpSSR markers for phylogeographic studies.

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Section: Chloroplast Microsatellitesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Chloroplast microsatellites as a tool for phylogeographic studies: the case of white oaks in Poland

Chmielewski¹,

Meyza²,

Chybicki³

et al. 2015

iForest

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“…As cpDNA evolves clonally, there are similarities whatever the marker system used although the spatial resolution might differ. Some authors have used chloroplast microsatellites (GAILING et al, 2007a, b) developed by DEGUILLOUX et al (2003a) or universal markers (SEBASTIANI et al, 2004;WEISING and GARDNER, 1999) to adress the origin of a planted stand or to genetically characterize a specific region ( Table 1). Haplotypes derived from the cpSSRs and PCR-RFLP are strongly related, and cpSSRs show many rare alleles which could be used at a local scale for traceability purposes (CHMIELEWSKI et al, 2015).…”

Section: Molecular Markers Availablementioning

confidence: 99%

Tracing the origin and species identity of Quercus robur and Quercus petraea in Europe: a review

Blanc-Jolivet

Liesebach

2015

Silvae Genetica

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Traceability of forest material has received recently increasing interest and European regulations already apply on forest reproductive material and timber. DNA fingerprinting methods allow identification of species and control of geographic origin, providing that genetic reference data is available. In this review, we focus on the two economically important European oak species, Quercus robur and Q. petraea. We describe the available molecular markers and data, and discuss their applicability for traceability systems of forest reproductive material at a European scale. We also provide insights on the use of DNA fingerprinting on timber material.

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“…Co. Ltd. (China) according to primer characteristics reported in other species (Vendramin et al, 1996;Weising and Gardner, 1999;Cheng et al, 2003;Chung and Staub, 2003;Sebastiani et al, 2004;Hu et al, 2009).…”

Section: Optimization Of the Cpssr-pcr System And Primer Screeningmentioning

confidence: 99%

Optimization of chloroplast microsatellite PCR conditions and primer screening for endangered Rheum officinale, Rheum palmatum, and Rheum tanguticum

et al. 2014

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ABSTRACT. Chloroplast microsatellite primers were developed in order to provide more population genetic information of endangered Rheum officinale, R. palmatum, and R. tanguticum for conservation. The dried roots and rhizomes of these plants are important in traditional Chinese medicine. The results showed that the optimum concentrations of Mg 2+, Taq DNA polymerase, dNTPs, template DNA, and primers in a 25-μL reaction system were 2.0 mM, 1.0 U, 0.10 mM, 20 ng, and 0.8 μM, respectively. Fourteen of 53 primer combinations were chosen for their high clarity and repetition in three species, and their annealing temperatures ranged from 56 to 58°C. These primers and the optimized polymerase chain reaction system may provide a tool for understanding the demography and genetic variation of these endangered plants.

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A new set of mono‐ and dinucleotide chloroplast microsatellites in Fagaceae

Cited by 55 publications

References 16 publications

Chloroplast microsatellites as a tool for phylogeographic studies: the case of white oaks in Poland

Chloroplast microsatellites as a tool for phylogeographic studies: the case of white oaks in Poland

Tracing the origin and species identity of Quercus robur and Quercus petraea in Europe: a review

Optimization of chloroplast microsatellite PCR conditions and primer screening for endangered Rheum officinale, Rheum palmatum, and Rheum tanguticum

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