Characterization of microsatellite markers in <i>Fagus sylvatica</i> L. and <i>Fagus orientalis</i> Lipsky

Pastorelli, Roberta; Smulders, M.J.M.; Westende, W.P.C. van 't; Vosman, Ben; Giannini, Raffaello; Vettori, Cristina; Vendramin, G. G.

doi:10.1046/j.1471-8286.2003.00355.x

Cited by 85 publications

(73 citation statements)

References 10 publications

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“…European beech (F. sylvatica) is an economically important, widespread and widely studied tree species (Magri et al 2006) for which few microsatellite markers are available (Pastorelli et al 2003).…”

Section: Methodsmentioning

confidence: 99%

“…DNA analysis was done using size SSR markers in Haye: FS1-46, FCM5, FS1-25, FS1-03, FS3-04, SFC-0161 and 4 SSR markers in Ventoux and Sainte Baume: FS1-46, FCM5, FS1-25, FS1-15. Details of their PCR amplification are reported in Tanaka et al (1999); Pastorelli et al (2003); Asuka et al (2004). PCR products were separated on an automated 96-capillary MegaBACE TM 1000 sequencer (GE Healthcare).…”

Section: Methodsmentioning

confidence: 99%

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Population estimators or progeny tests: what is the best method to assess null allele frequencies at SSR loci?

Oddou‐Muratorio

Vendramin²,

Buiteveld

et al. 2008

Conserv Genet

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Nuclear SSRs are notorious for having relatively high frequencies of null alleles, i.e. alleles that fail to amplify and are thus recessive and undetected in heterozygotes. In this paper, we compare two kinds of approaches for estimating null allele frequencies at seven nuclear microsatellite markers in three French Fagus sylvatica populations: (1) maximum likelihood methods that compare observed and expected homozygote frequencies in the population under the assumption of Hardy-Weinberg equilibrium and (2) direct null allele frequency estimates from progeny where parent genotypes are known. We show that null allele frequencies are high in F. sylvatica (7.0% on average with the population method, 5.1% with the progeny method), and that estimates are consistent between the two approaches, especially when the number of sampled maternal half-sib progeny arrays is large. With null allele frequencies ranging between 5% and 8% on average across loci, population genetic parameters such as genetic differentiation (F ST ) may be mostly unbiased. However, using markers with such average prevalence of null alleles (up to 15% for some loci) can be seriously misleading in fine scale population studies and parentage analysis.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Population estimators or progeny tests: what is the best method to assess null allele frequencies at SSR loci?

Oddou‐Muratorio

Vendramin²,

Buiteveld

et al. 2008

Conserv Genet

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“…Four highly polymorphic microsatellites (FS1-15, FS4-46, FS3-04 and mfc5 for samples from Austrian stands, and FS1-15, FS4-46, FS1-25 and mfc5 for Pollen flow in beech A Piotti et al samples from French stands) developed in beech by Pastorelli et al (2003) and Tanaka et al (1999) were used to genotype all individuals. These microsatellites were selected because they showed Mendelian inheritance, a high level of polymorphism (Pastorelli et al, 2003) and because they were unlinked (Scalfi et al, 2004).…”

Section: Study Sites Sample Collection and Microsatellite Analysismentioning

confidence: 99%

“…These microsatellites were selected because they showed Mendelian inheritance, a high level of polymorphism (Pastorelli et al, 2003) and because they were unlinked (Scalfi et al, 2004). PCR amplifications were performed following the conditions reported in Pastorelli et al (2003) and fragment size detection was conducted as described by Buiteveld et al (2007).…”

Section: Study Sites Sample Collection and Microsatellite Analysismentioning

confidence: 99%

Comparison of pollen gene flow among four European beech (Fagus sylvatica L.) populations characterized by different management regimes

et al. 2011

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The study of the dispersal capability of a species can provide essential information for the management and conservation of its genetic variability. Comparison of gene flow rates among populations characterized by different management and evolutionary histories allows one to decipher the role of factors such as isolation and tree density on gene movements. We used two paternity analysis approaches and different strategies to handle the possible presence of genotyping errors to obtain robust estimates of pollen flow in four European beech (Fagus sylvatica L.) populations from Austria and France. In each country one of the two plots is located in an unmanaged forest; the other plots are managed with a shelterwood system and inside a colonization area (in Austria and France, respectively). The two paternity analysis approaches provided almost identical estimates of gene flow. In general, we found high pollen immigration (B75% of pollen from outside), with the exception of the plot from a highly isolated forest remnant (B50%). In the two unmanaged plots, the average within-population pollen dispersal distances (from 80 to 184 m) were higher than previously estimated for beech. From the comparison between the Austrian managed and unmanaged plots, that are only 500 m apart, we found no evidence that either gene flow or reproductive success distributions were significantly altered by forest management. The investigated phenotypic traits (crown area, height, diameter and flowering phenology) were not significantly related with male reproductive success. Shelterwood seems to have an effect on the distribution of within-population pollen dispersal distances. In the managed plot, pollen dispersal distances were shorter, possibly because adult tree density is three-fold (163 versus 57 trees per hectare) with respect to the unmanaged one.

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“…However, the sequences of the currently most commonly used genetic markers in beech (Fagus sylvatica L.) are not directly observed and are usually unknown. Only particular aspects of the variation are investigated within PCR-amplified DNA fragments such as the number of tandem repeats in microsatellite motives (e.g., Pastorelli et al 2003) or the absence or presence of restriction sites in amplified fragment length polymorphisms (AFLPs; e.g., Gailing and von Wühlisch 2004). The amplified genomic regions are usually either unknown such as in anonymous AFLPs or are located in non-coding regions of the DNA (most microsatellites).…”

Section: Introductionmentioning

confidence: 99%

DNA sequence variation and development of SNP markers in beech (Fagus sylvatica L.)

Seifert¹,

Vornam²,

Finkeldey³

2012

Eur J Forest Res

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European beech (Fagus sylvatica L.) is one of the most important deciduous tree species in Central Europe. The potential of beech to adapt to climate change, higher temperatures, and less precipitation in the summer months is still unknown. Most studies in beech used microsatellite, AFLP (amplified fragment length polymorphism), or isozyme markers, which have only a restricted potential to analyze adaptation. Only few studies investigated genes probably involved in the adaptation to drought stress and bud phenology in beech. In this study, SNP (single nucleotide polymorphisms) markers were developed in order to analyze adaptation and their technical advantages compared to microsatellites and AFLPs were discussed. Partial sequences of ten candidate genes probably involved in drought stress and/or bud phenology were identified at the genomic level, and SNPs and indels (insertions/deletions) in coding and non-coding regions were analyzed. Plant material was sampled along a precipitation gradient in Germany. In total, 8,145 bp were sequenced and analyzed, 4,038 bp were located in exon and 4,107 bp in intron regions. 63 SNPs and 11 indels were detected, which are differently distributed over the studied gene regions. The nucleotide diversity ranged from 0 to 6.62 (p 9 10 -3 ) and is comparable to other tree species, whereas the mean nucleotide diversity (2.64) for F. sylvatica is comparatively low. These results will help to investigate the genetic basis of drought stress and bud burst and to conduct association mapping in natural populations. Furthermore, the detected SNPs can also be used for population genetic studies.

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Characterization of microsatellite markers in Fagus sylvatica L. and Fagus orientalis Lipsky

Cited by 85 publications

References 10 publications

Population estimators or progeny tests: what is the best method to assess null allele frequencies at SSR loci?

Population estimators or progeny tests: what is the best method to assess null allele frequencies at SSR loci?

Comparison of pollen gene flow among four European beech (Fagus sylvatica L.) populations characterized by different management regimes

DNA sequence variation and development of SNP markers in beech (Fagus sylvatica L.)

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