Development and characterization of microsatellite markers in black poplar (Populus nigra L.)

Schoot, J. van der; Pospíšková, Markéta; Vosman, Ben; Smulders, M.J.M.

doi:10.1007/s001220051485

Cited by 171 publications

(114 citation statements)

References 12 publications

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“…Moreover, five of them are those used in the previous work of Fossati et al [15], which will allow us to compare the results obtained. The SSR loci used and corresponding linkage groups (LG) were the following: PTR2 (LG IX), PTR4 (LG III) [9] and PTR7 (LG XII) [27] developed for P. tremuloides; WPMS9 (LG VI), WPMS14 (LG V), WPMS16 (LG VII), WPMS18 (LG not found), WPMS20 (LG not found) developed for P. nigra [33,37]; PMGC14 (LG XIII) and ORPM127 (LG IV) developed for P. trichocarpa [36]. The forward primer for each locus was previously labelled with one of the three fluorochromes: 6-FAM, HEX or NED (Applied Biosystems, Foster City, Ca, USA), and a common fluorochrome label for different SSR markers was chosen for nonoverlapping allele ranges.…”

Section: Dna Extraction and Ssr Analysismentioning

confidence: 99%

“…Initial reaction volumes and amplification conditions were described by the following authors: for PTR2 and PTR4, Dayanandan et al [9]; for PTR7, Rahman et al [27]; for WPMS14, WPMS16, WPMS18 and WPMS20, Smulders et al [33]; for WPMS9, Van der Schoot et al [37]; for PMGC14, Tabbener et al [34]; and for ORPM127, Tuskan et al [36]. In all cases, we used a GeneAmp 9700 thermal cycler (Applied Biosystems) and the amplified fragments were analysed in an ABI-PRISM 310 genetic analyser (Applied Biosystems) using GeneScan ROX-500 as the internal standard.…”

Section: Dna Extraction and Ssr Analysismentioning

confidence: 99%

“…In the last decade, several authors have designed specific SSR primers for particular Populus species: for P. tremuloides, [9,27]; for P. nigra, [33,37]; and for P. trichocarpa [36], most of them available at Poplar Molecular Genetics Cooperative data base (http://www.ornl.gov/sci/ipgc/ssr_resource.htm). As many of them have shown their usefulness on different poplar species or hybrids, it is advisable to use them for the molecular description of commercial poplars, most of which are interspecific hybrids [3,15,29,40].…”

Section: Introductionmentioning

confidence: 99%

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Développement de marqueurs microsatellites pour l’identification et la certification des clones commerciaux de peuplier en Espagne

et al. 2008

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-In order to protect the legitimate interests of the poplar breeders, growers and industries, we have developed a reliable and affordable certification tool for commercial poplars in Spain. We have carried out a genetic description of the 28 commercial clones of the current Spanish National Catalogue using 10 microsatellite molecular markers (SSR). The results clearly show that in the Spanish National Catalogue there are labelling mistakes including synonymies, supported by a combined probability of identity (PI) of 1.18 × 10 −9 . We have also demonstrate that it is possible to identify all the different clones (genotypes) with only three microsatellites, that show a combined probability of identity of 2.4 × 10 −4 , and we have optimised the protocols to reduce the time and the economical costs of the analysis. This SSR-based tool could be incorporated in the current certification protocols, to avoid duplication of accessions and identification mistakes.commercial poplar clone / microsatellite / identification / Spanish national catalogue Résumé -Développement de marqueurs microsatellites pour l'identification et la certification des clones commerciaux de peuplier en Espagne. Dans le but de protéger les intérêts légitimes des cultivateurs, des sélectionneurs et des industriels de la populiculture, nous avons mis au point un outil de certification fiable et accessible pour les clones de peupliers commerciaux en Espagne. Nous avons fait une description génétique des 28 clones commerciaux de l'actuel catalogue national espagnol en utilisant 10 marqueurs moléculaires microsatellites (SSR). Les résultats obtenus indiquent clairement que ce catalogue contient des erreurs d'identification, dont des clones synonymes, soutenues par une probabilité combinée d'identité (PI) de 1.18 × 10 −9 . Nous avons également démontré qu'il est possible d'identifier tous les génotypes différents avec 3 microsatellites, qui montrent une probabilité combinée d'identité de 2.4 × 10 −4 , et nous avons optimisé les protocoles afin de réduire le temps et le coût de l'analyse. Cet outil fondé sur les SSR pourrait être intégré dans les protocoles actuels de certification afin d'éviter la duplication des matériaux et les erreurs d'identification.clone commercial de peuplier / microsatellite / identification / catalogue national espagnol

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Section: Dna Extraction and Ssr Analysismentioning

confidence: 99%

Section: Dna Extraction and Ssr Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Développement de marqueurs microsatellites pour l’identification et la certification des clones commerciaux de peuplier en Espagne

et al. 2008

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“…[20,45,51,70,83,104]) and the STS nuclear gene marker win3 [41]. Recently, a microsatellite marker (WPMS09) [96] was found useful to differentiate between genes of P. deltoides and P. nigra [37,100] (cf. Glossary).…”

Section: Detection Of Hybridizationmentioning

confidence: 99%

“…They considered the most frequent alleles as common alleles of the species whereas the rarest alleles were considered to provide an upper estimate of possible [41,92,98] hybridization with the Lombardy poplar [46]. The SSR locus WPMS09 [96] showed the lowest frequency of the two alleles shared with P. nigra cv. 'Italica' (< 0.05) [46].…”

Section: Detection Of Hybridizationmentioning

confidence: 99%

Natural hybridization between cultivated poplars and their wild relatives: evidence and consequences for native poplar populations

Broeck

Villar²,

Bockstaele

et al. 2005

Ann. For. Sci.

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-It is recognized that introgressive hybridization and gene flow from domesticated species into their wild relatives can have a profound effect on the persistence and evolution of wild populations. Here, we review published literature and recent data concerning introgressive hybridization involving numerous species of the genus Populus. First, we briefly refer to some concepts and terminology before reviewing examples of natural and anthropogenic hybridization. Second, we examine whether natural genetic barriers could limit introgressive hybridization. Threat and possible consequences of anthropogenic hybridization are discussed in order to finally suggest conservation strategies for native poplar populations.

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The use of digital image‐based morphometrics to study the phenotypic mosaic in taxa with porous genomes

Lexer

Joseph

Loo

et al. 2009

TAXON

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Rapid recent developments in DNA sequencing and genetic marker technologies call for the establishment of cost‐effective, automated phenotyping assays for evolutionary biology and systematics, so that the effects of DNA polymorphisms and epigenetic changes on the phenotype can be evaluated. We discuss the use of digital image‐based morphometrics in evolutionary biology and systematics with special emphasis on studies of taxa with porous genomes, i.e., taxa that do not conform to the traditional view of whole‐genome isolation between species. We outline the phenomenon of the 'phenotypic mosaic' in taxa with porous genomes using well‐documented examples from the literature and describe three important challenges arising for taxonomists: (1) character conflict in phylogenetic studies, (2) biased sampling of traits in morphological studies, and (3) cryptic ecological speciation. We demonstrate the use of geometric morphometrics using a combined molecular and morphometric dataset from an interspecific hybrid zone between two divergent Eurasian species of Populus, P. alba (white poplar) and P. tremula (European aspen). Elliptic Fourier analysis (EFA)‐based morphometric data were collected for 527 leaf specimens from 84 trees with known genomic composition as determined by a set of 30 nuclear DNA microsatellites. In addition, to demonstrate the ease of scoring functionally relevant phenotypes via digital image analysis, quantitative differences in leaf reflectance were examined and their structural basis determined using scanning electron microscopy (SEM). The EFA results indicate a heritable inter‐individual component for symmetric aspects and an important intra‐individual component for asymmetric aspects of variation in leaf outlines. Symmetric traits displayed a striking variety of phenotypes in hybrids compared to their parental species, consistent with the notion of the phenotypic mosaic. Linear discriminant analysis of these morphometric traits revealed (1) clear differentiation between parental species and (2) divergence between recombinant hybrids and their sympatric backcross parent P. alba, mediated primarily by two P. tremula–like and two transgressive traits. Our results demonstrate the usefulness of geometric morphometrics to interrogate multiple independent phenotypic characters and detect individual traits affected by introgression and divergence in taxa with porous genomes. Digital image‐based morphometrics holds great promise for large‐scale studies of relationships between DNA polymorphism and phenotypes in evolutionary biology.

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Development and characterization of microsatellite markers in black poplar (Populus nigra L.)

Cited by 171 publications

References 12 publications

Développement de marqueurs microsatellites pour l’identification et la certification des clones commerciaux de peuplier en Espagne

Développement de marqueurs microsatellites pour l’identification et la certification des clones commerciaux de peuplier en Espagne

Natural hybridization between cultivated poplars and their wild relatives: evidence and consequences for native poplar populations

The use of digital image‐based morphometrics to study the phenotypic mosaic in taxa with porous genomes

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