Éditeur(s) : HAL CCSD SpringerLink
Résumé : Trinucleotide microsatellites have proven to be the markers of choice in human genetic analysis because they are easier to genotype than dinucleotides. Their development can be more time-consuming due to their lower abundance in the genome. We isolated trinucleotide microsatellites in Norway spruce (Picea abies K.) using an enrichment procedure for the genomic-library construction. Here we report on the characterisation of 85 ATC microsatellite-containing clones, from which 39 markers were developed. Many of the clones showed the occurrence of tandem repeats of higher order than the trinucleotide ones, often resembling minisatellite repeats. The sequencing of a sample of the alleles at one of the loci revealed size homoplasy due to base substitutions within the microsatellite region. The presence of ATC motifs within repetitive sequence families was observed. We found a significant relationship between the level of polymorphism and the length of the microsatellite. The levels of variability for ATC trinucleotide markers were lower than those for dinucleotides, both when tested on all loci in a set of six individuals and on a subset of loci in four natural populations. This difference is most likely attributable to lower mutation rates for trinucleotide than for dinucleotide loci. The availability of markers with different mutation rates allows one to select the proper marker set to investigate population processes on different time scales.
Theoretical and Applied Genetics

hal-01032029
https://hal.archives-ouvertes.fr/hal-01032029
DOI : 10.1007/s00122-002-0986-1

Éditeur(s) : HAL CCSD Wiley
Résumé : Unveiling the genetic basis of local adaptation to environmental variation is a major goal in molecular ecology. In rugged landscapes characterized by environmental mosaics, living populations and communities can experience steep ecological gradients over very short geographical distances. In lowland tropical forests, interspecific divergence in edaphic specialization (for seasonally flooded bottomlands and seasonally dry terra firme soils) has been proven by ecological studies on adaptive traits. Some species are nevertheless capable of covering the entire span of the gradient; intraspecific variation for adaptation to contrasting conditions may explain the distribution of such ecological generalists. We investigated whether local divergence happens at small spatial scales in two stands of Eperua falcata (Fabaceae), a widespread tree species of the Guiana Shield. We investigated Single Nucleotide Polymorphisms (SNP) and sequence divergence as well as spatial genetic structure (SGS) at four genes putatively involved in stress response and three genes with unknown function. Significant genetic differentiation was observed among sub-populations within stands, and eight SNP loci showed patterns compatible with disruptive selection. SGS analysis showed genetic turnover along the gradients at three loci, and at least one haplotype was found to be in repulsion with one habitat. Taken together, these results suggest genetic differentiation at small spatial scale in spite of gene flow. We hypothesize that heterogeneous environments may cause molecular divergence, possibly associated to local adaptation in E. falcata.
ISSN: 1010-061X

hal-01032412
https://hal.archives-ouvertes.fr/hal-01032412
DOI : 10.1111/jeb.12069

Éditeur(s) : HAL CCSD De Gruyter
Résumé : International audience
This study aims at better understanding the respective influences of specific gravity (γ), microfibril angle (MFA), and cell-wall matrix polymers on viscoelastic vibrational properties of wood in axial direction. The wide variations of properties between normal wood (NW) and compression wood (CW) are in focus. Three young bent trees (Picea abies, Pinus sylvestris and Pinus pinaster) that recovered verticality were sampled. Several observed differences between NW and CW were highly significant in terms of anatomical, physical (γ, shrinkage, CIELab colorimetry), mechanical (compressive strength), and vibrational properties. Specific dynamic modulus of elasticity (E'/γ) decreases with increasing MFA, and Young's modulus (E') can be satisfactorily explained by γ and MFA. Apparently, the type of the cell wall polymer matrix is not influential in this regard. The damping coefficient (tanδ) does not depend solely on MFA of NW and CW. The tanδ - E'/γ relationship evidences that, at equivalent E'/γ, the tanδ of CW is approx. 34% lower than that of NW. This observation is ascribed to the more condensed nature of CW lignins, and this is discussed in the context of previous findings in other hygrothermal and time/frequency domains. It is proposed that the lignin structure and the amount and type of extractives, which are both different in various species, are partly responsible for taxonomy-related damping characteristics.
ISSN: 0018-3830

hal-00808062
https://hal.archives-ouvertes.fr/hal-00808062
https://hal.archives-ouvertes.fr/hal-00808062/document
https://hal.archives-ouvertes.fr/hal-00808062/file/Changes_viscoelastic_vibrational_Bremaud_al.pdf
DOI : 10.1515/hf-2011-0186

Éditeur(s) : Elsevier
Résumé : The composition of the glacial vegetation of southern French plains has been a matter of debate for several decades. Vegetation is considered as steppic according to French and Spanish lacustrine pollen records whereas cave deposits suggest the presence of mesothermophilous trees through the Last Glacial Maximum. In our paper, we display new palynological records from marine sediments of the Gulf of Lions. They indicate the presence of Abies, Picea and deciduous Quercus in the Gulf of Lions, certainly located in the drainage basins of the Pyreneo-Languedocian rivers. These populations that were sensitive to short climatic events during Marine Isotopic Stage 2 could have been linked to northeastern Spanish and southeastern French relicts already evidenced by phylogenetic data. These trees were absent from the Rhone drainage basin during the deglaciation and certainly also disappeared from the Pyreneo-Languedocian drainage basins from ca 17 to 15 ky cal BP. Finally, the Last Glacial Maximum does not appear as stable, cold and dry as previously thought.
Quaternary Science Reviews (0277-3791) (Elsevier), 2007-04 , Vol. 26 , N. 7-8 , P. 1037-1054

Droits : 2007 Elsevier Ltd All rights reserved.
http://archimer.ifremer.fr/doc/2007/publication-2804.pdf
DOI:10.1016/j.quascirev.2006.12.009
http://archimer.ifremer.fr/doc/00000/2804/

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : In order to analyze the large-scale structure of the genome of Norway spruce (Picea abies Karst.), a pseudo-testcross genetic linkage map was built using markers of six different types, belonging to the low (amplified fragment length polymorphisms, simple sequence repeats) or high (sequence-specific amplified polymorphisms, inter-retrotransposon amplified polymorphisms) copy-number fraction of the genome, and including expressed region-derived markers (expressed sequence tag polymorphisms). Twenty seven and 23 linkage groups of at least four markers were obtained for the female and the male parent maps, respectively. A subset of these linkage groups coalesced into 13 bi-parental linkage groups through markers shared between the two maps. This map was used to investigate the frequency of each marker type over chromosomes and the distribution of marker types relative to each other, using autocorrelation techniques. Our results show that, while the composition of chromosomes is homogeneous, low- and high-copy-number markers tend to occupy separate regions of the linkage groups, and that expressed sequences are preferentially associated with microsatellites and separated from retrotransposons. These results indicate that the spatial structure of Norway spruce chromosomes is not homogeneous
ISSN: 1614-2942

hal-01032033
https://hal.archives-ouvertes.fr/hal-01032033
DOI : 10.1007/s11295-005-0012-2

Éditeur(s) : HAL CCSD Springer Verlag/EDP Sciences
Résumé : Four populations of Norway spruce (Picea abies Karst.) were screened using nine nuclear microsatellite markers (three trinucleotides and six dinucleotides) and four chloroplast markers (all mononucleotides). Marker classes were compared for their variability, mutation rate and ability to detect differentiation between stands. Dinucleotide markers proved to be the most variable group and chloroplast stretches the least variable, with differences in mutation rate between the former and the latter spanning over two orders of magnitude. Variability correlated to the number of repeats but not to the absolute length of the microsatellite region. The different marker classes were combined with two different measures of genetic distance in order to investigate the performance of markers and evolutionary models for the study of genetic variation in natural populations of Norway spruce. Weir and Cockeram's F$_{rm ST}$ generally performed better in this clear-cut, four-population model study. Chloroplast haplotypes turned out to be the most sensitive marker system, being able to differentiate populations and to detect differences in genetic variability between sub-regions.
ISSN: 1286-4560

hal-01032048
https://hal.archives-ouvertes.fr/hal-01032048
DOI : 10.1051/forest:2006029

Éditeur(s) : HAL CCSD Elsevier
Résumé :  
The within-population spatial structure of genetic diversity is shaped by demographic processes, including historical accidents such as forest perturbations. Information drawn from the analysis of the spatial distribution of genetic diversity is therefore inherently linked to demographic-historical processes that ultimately determine the fate of populations. All adult trees and saplings in a 1.4-ha plot within a mixed Norway spruce (Picea abies [L.] Karst) stand were characterised by means of chloroplast (paternally inherited) markers, and a large sub-sample of these were genotyped at mitochondrial (maternally inherited) molecular markers. These data were used to analyse the spatial distribution of genetic variation and to compare the patterns corresponding to the two marker types. The plot presented non-homogeneous local stem density in the younger cohorts, and the indirect effect of this source of variation on the spatial genetic structure was investigated. Results suggest that (i) spatially limited seed dispersal induced patchiness in genotype distribution, while pollen flow had a homogenising effect; (ii) deviations from random spatial structure were stronger in the demographically most stable portions of the stand, while they were weaker where sudden bursts of regeneration occurred; (iii) spatially overlapping adult and sapling cohorts displayed the same spatial genetic structure (stronger on stable areas, weaker in portions of the stand undergoing events of intense regeneration), which was substantiated by the influence of local demographic processes. Regeneration dynamics as modulated by demography thus influences the distribution of genetic diversity within the stand both in the younger life stages and in the adult population.
ISSN: 0378-1127

hal-01032063
https://hal.archives-ouvertes.fr/hal-01032063
DOI : 10.1016/j.foreco.2008.03.023