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Author  |
Scotti-Saintagne, C.; Bodenes, C.; Barreneche, T.; Bertocchi, E.; Plomion, C.; Kremer, A. |
| Title |
Detection of quantitative trait loci controlling bud burst and height growth in Quercus robur L |
Type |
Journal Article |
| Year |
2004 |
Publication |
Theoretical and Applied Genetics |
Abbreviated Journal |
Theor. Appl. Genet. |
| Volume |
109 |
Issue |
8 |
Pages |
1648-1659 |
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| Abstract |
Genetic variation of bud burst and early growth components was estimated in a full-sib family of Quercus robur L. comprising 278 offspring. The full sibs were vegetatively propagated, and phenotypic assessments were made in three field tests. This two-generation pedigree was also used to construct a genetic linkage map (12 linkage groups, 128 markers) and locate quantitative trait loci (QTLs) controlling bud burst and growth components. In each field test, the date of bud burst extended over a period of 20 days from the earliest to the latest clone. Bud burst exhibited higher heritability (0.15-0.51) than growth components (0.04-0.23) and also higher correlations across field tests. Over the three tests there were 32 independent detected QTLs (Pless than or equal to5% at the chromosome level) controlling bud burst, which likely represent at least 12 unique genes or chromosomal regions controlling this trait. QTLs explained from 3% to 11% of the variance of the clonal means. The number of QTLs controlling height growth components was lower and varied between two and four. However the contribution of each QTL to the variance of the clonal mean was higher (from 4% to 19%). These results indicate that the genetic architecture of two important fitness-related traits are quite different. On the one hand, bud burst is controlled by several QTLs with rather low to moderate effects, but contributing to a high genetic (additive) variance. On the other hand, height growth depends on fewer QTLs with moderate to strong effects, resulting in lower heritabilities of the trait. |
| Address |
INRA, UMR Biodivers Genes & Ecosyst, F-33612 Cestas, France, Email: antoine.kremer@pierroton.inra.fr |
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0040-5752 |
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ISI:000225054800012 |
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EcoFoG @ eric.marcon @ |
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260 |
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| Author |
Scotti-Saintagne, C.; Bertocchi, E.; Barreneche, T.; Kremer, A.; Plomion, C. |
| Title |
Quantitative trait loci mapping for vegetative propagation in pedunculate oak |
Type |
Journal Article |
| Year |
2005 |
Publication |
Annals of Forest Science |
Abbreviated Journal |
Ann. For. Sci. |
| Volume |
62 |
Issue |
4 |
Pages |
369-374 |
| Keywords |
vegetative propagation; QTL; Quercus robur |
| Abstract |
Vegetative propagation is one of the main methods used for the deployment of improved genetic forest tree species. The objective of this paper was to study the genetic architecture of vegetative propagation by detecting Quantitative Trait Loci (QTL) in pedunculate oak ( Quercus robur). The mapping population consisted on an F-1 family of 278 offspring. Assessment of rooting ability over three years permitted the detection of 10 QTLs explaining between 4.4 and 13.8% of phenotypic variance, of which the two strongest were stable across years. Ongoing genomics programs in trees and in Arabidopsis are starting to shed light on the nature of the underlying genes. |
| Address |
Equipe Genet, INRA, UMR 1202, BIOGECO, F-33612 Cestas, France, Email: christophe.plomion@pierroton.inra.fr |
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E D P SCIENCES |
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1286-4560 |
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ISI:000229668600010 |
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EcoFoG @ eric.marcon @ |
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255 |
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| Author |
Scotti, I.; Paglia, G.; Magni, F.; Morgante, M. |
| Title |
Population genetics of Norway spruce (Picea abies Karst.) at regional scale: sensitivity of different microsatellite motif classes in detecting differentiation |
Type |
Journal Article |
| Year |
2006 |
Publication |
Annals of Forest Science |
Abbreviated Journal |
Ann. For. Sci. |
| Volume |
63 |
Issue |
5 |
Pages |
485-491 |
| Keywords |
conifers; SSR; divergence; statistical testing; genetic distance |
| Abstract |
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-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. |
| Address |
INRA, UMR ECOFOG, Kourou 97387, French Guiana, Email: ivan.scotti@kourou.cirad.fr |
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EDP SCIENCES S A |
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1286-4560 |
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ISI:000240514800005 |
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no |
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EcoFoG @ eric.marcon @ |
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177 |
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| Author |
Scotti, I.; Montaigne, W.; Cseke, K.; Traissac, S. |
| Title |
RaBoT: A rarefaction-by-bootstrap method to compare genome-wide levels of genetic diversity |
Type |
Journal Article |
| Year |
2013 |
Publication |
Annals of Forest Science |
Abbreviated Journal |
Ann. Forest Sci. |
| Volume |
70 |
Issue |
6 |
Pages |
631-635 |
| Keywords |
Diversity comparison; Genome scan; Genome-level diversity; Population genetics; Statistical testing |
| Abstract |
Context: No efficient method is available to compare multi-locus estimates of diversity while taking into account inter-locus and inter-population stochastic variance. The advent of genome scan approaches makes the development of such tests absolutely necessary. Aims: We developed a method to compare genome-wide diversity estimates while taking into account – and factoring out – variation in census size and making use of inter-locus variance to assess significance of differences in diversity levels. Methods: An approach based on rarefaction with bootstrap re-sampling (RaBoT) was implemented into a test of multi-locus comparison of diversity coded in R. The properties of the test were studied by applying it to simulated populations with varying diversity levels and varying differences in diversity levels. The test was then applied to empirical data from disturbed and undisturbed populations of Virola michelii (Myristicaceae) genotyped at 693 amplified fragment length polymorphism (AFLP) markers. Results: RaBoT was found to be rather conservative, with large numbers of false negatives when the diversity in the compared populations was similar, and false positives mostly associated to comparisons of populations with extremely high levels of diversity. When applied to empirical data, RaBoT detected higher genetic diversity in a post-disturbance than in an undisturbed population and lower genetic diversity in a seedling than in the corresponding adult population, but it also revealed differences in diversity between subgroups within the disturbed and undisturbed plots. Conclusion: RaBoT is a sensitive method to compare multi-locus levels of diversity that can be applied both at the genotype level for dominant markers (e.g. AFLP) and at the allele level for biallelic codominant markers (e.g. single-nucleotide polymorphisms). © 2013 INRA and Springer-Verlag France. |
| Address |
Unité Mixte de Recherche ecologie des Forêts de Guyane (EcoFoG), AgroParisTech, Kourou, French Guiana |
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12864560 (Issn) |
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Export Date: 30 August 2013; Source: Scopus; Coden: Afosf; doi: 10.1007/s13595-013-0302-z; Language of Original Document: English; Correspondence Address: Scotti, I.; Unité Mixte de Recherche ecologie des Forêts de Guyane (EcoFoG), INRA, Institut National de la Recherche Agronomique, BP 709, 97387 Kourou cedex, French Guiana; email: ivan.Scotti@ecofog.gf |
Approved |
no |
| Call Number |
EcoFoG @ webmaster @ |
Serial |
498 |
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| Author |
Scotti, I.; Montaigne, W.; Cseke, K.; Traissac, S. |
| Title |
Life after disturbance (II): the intermediate disturbance hypothesis explains genetic variation in forest gaps dominated by Virola michelii Heckel (Myristicaceae) |
Type |
Journal Article |
| Year |
2015 |
Publication |
Annals of Forest Science |
Abbreviated Journal |
Annals of Forest Science |
| Volume |
72 |
Issue |
8 |
Pages |
1035-1042 |
| Keywords |
Amazon; Bayesian clustering; Demogenetics; Guiana shield; Parentage analysis; Regeneration; Spatial genetic structure; Tropical rainforest |
| Abstract |
Key message: Genetic diversity appears to be unaffected by disturbance in a stand of the light-demanding Neotropical treeV. michelii. Although spatial genetic structure is modified in post-disturbance cohorts, mixing of seeds from different mother trees in canopy gaps appears to efficiently maintain genetic admixture. Context: The interplay between genetic and demographic processes has major consequences on population viability. Population size affects demographic trends, while genetic diversity insures viability by reducing risks of inbreeding depression and by maintaining adaptive potential. Yet, the consequences of increases in census size (as opposed to effective size) on genetic diversity of forest populations are poorly known. Aims: We have studied the structure of genetic diversity in populations of saplings of the light-responsive tree, Virola michelii (Myristicaceae, the nutmeg family), in two plots having undergone different levels of canopy-gap opening disturbance. This allowed us to test the “intermediate disturbance” hypothesis, which generally applies to species diversity, at the intra-specific scale. Methods: Levels and distribution of genetic diversity were compared between plots and between life stages. Sapling parentage was analysed to infer each adult tree’s contribution to regeneration. Results: Genetic diversity was higher, and spatial genetic structure was stronger in the post-disturbance than in the control seedling population. Parentage analysis suggested that a limited number of parents contributed to most of the regeneration, but that efficient mixing of their progeny may have enhanced the diversity of saplings occupying canopy gaps. Conclusion: A mixture of demo-genetic processes may contribute to maintain genetic diversity in spite of, or possibly due to, ecosystem disturbance in V. michelii. © 2015, INRA and Springer-Verlag France. |
| Address |
Solicaz, Guyane Technopôle, 16 bis Rue du 14 Juillet, Cayenne, French Guiana |
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Export Date: 14 December 2015 |
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no |
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EcoFoG @ webmaster @ |
Serial |
642 |
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| Author |
Scotti, I.; Gugerli, F.; Pastorelli, R.; Sebastiani, F.; Vendramin, G.G. |
| Title |
Maternally and paternally inherited molecular markers elucidate population patterns and inferred dispersal processes on a small scale within a subalpine stand of Norway spruce (Picea abies [L.] Karst.) |
Type |
Journal Article |
| Year |
2008 |
Publication |
Forest Ecology and Management |
Abbreviated Journal |
For. Ecol. Manage. |
| Volume |
255 |
Issue |
11 |
Pages |
3806-3812 |
| Keywords |
chloroplast microsatellites; mitochondrial minisatellites; pollen/seed dispersal; demography; spatial autocorrelation |
| Abstract |
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. (C) 2008 Elsevier B.V. All rights reserved. |
| Address |
[Scotti, I.] INRA, UMR 0745, ECOFOG, F-97387 Kourou, France, Email: ivan.scotti@kourou.cirad.fr |
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ELSEVIER SCIENCE BV |
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0378-1127 |
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ISI:000257019100019 |
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no |
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EcoFoG @ eric.marcon @ |
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137 |
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Scotti, I.; González-Martínez, S.C.; Budde, K.B.; Lalague, H. |
| Title |
Fifty years of genetic studies: what to make of the large amounts of variation found within populations? |
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Journal Article |
| Year |
2016 |
Publication |
Annals of Forest Science |
Abbreviated Journal |
Annals of Forest Science |
| Volume |
73 |
Issue |
1 |
Pages |
69-75 |
| Keywords |
Intra-specific variation; Microgeography; Natural selection; Population genomics |
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INRA, UMR745 Ecologie des Forêts de Guyane, Campus Agronomique, Kourou, French Guiana |
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Export Date: 7 March 2016 |
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no |
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EcoFoG @ webmaster @ |
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667 |
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Scotti, I.; Delph, L.F. |
| Title |
Selective trade-offs and sex-chromosome evolution in Silene latifolia |
Type |
Journal Article |
| Year |
2006 |
Publication |
Evolution |
Abbreviated Journal |
Evolution |
| Volume |
60 |
Issue |
9 |
Pages |
1793-1800 |
| Keywords |
antagonistic genes; linkage map; quantitative trait loci; sex-specific expression; Y chromosome |
| Abstract |
Alleles of sexually antagonistic genes (i.e., genes with alleles affecting fitness in opposite directions in the two sexes) can avoid expression in the sex to which they are detrimental via two processes: they are subsumed into the nonrecombining, sex-determining portion of the sex chromosomes or they evolve sex-limited expression. The former is considered more likely and leads to Y-chromosome degeneration. We mapped quantitative trait loci of major effect for sexually dimorphic traits of Silene latifolia to the recombining portions of the sex chromosomes and found them to exhibit sex-specific expression, with the Y chromosome in males controlling a relatively larger proportion of genetic variance than the X in females and the average autosome. Both reproductive and ecophysiological traits map to the recombining region of the sex chromosomes. We argue that genetic correlations among traits maintain recombination and polymorphism for these genes because of balancing selection in males, whereas sex-limited expression represses detrimental alleles in females. Our data suggest that the Y chromosome of S. latifolia plays a major role in the control of key metabolic activities beyond reproductive functions. |
| Address |
Indiana Univ, Dept Biol, Bloomington, IN 47405 USA, Email: ivan.scotti@kourou.cirad.fr |
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SOC STUDY EVOLUTION |
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0014-3820 |
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ISI:000241226800005 |
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no |
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EcoFoG @ eric.marcon @ |
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174 |
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Scotti, I.; Calvo-Vialettes, L.; Scotti-Saintagne, C.; Citterio, M.; Degen, B.; Bonal, D. |
| Title |
Genetic variation for growth, morphological, and physiological traits in a wild population of the Neotropical shade tolerant rainforest tree Sextonia rubra (Mez) van der Werff (Lauraceae) |
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Journal Article |
| Year |
2010 |
Publication |
Tree Genetics & Genomes |
Abbreviated Journal |
Tree Genet. Genomes |
| Volume |
6 |
Issue |
2 |
Pages |
319-329 |
| Keywords |
Ecophysiological traits; Heritability; Guiana shield; Amazon; Ecological genetics |
| Abstract |
Quantitative genetic diversity is a fundamental component of the interaction between natural populations and their environment. In breeding programmes, quantitative genetic studies on tropical trees have so far focused on fast-growing, light-demanding species, but no information exists on shade-tolerant, slow-growing species. For this study, 27 3-year-old open-pollinated families of the Neotropical shade-tolerant rainforest tree Sextonia rubra were measured in semicontrolled conditions for 20 morphological, growth, and photosynthesis traits; the effect of genetic relatedness, habitat of provenance, and mother tree status on seedling traits was analysed. Nine traits displayed significant genetic effects, while mother tree status and habitat effects were not significant (P > 0.05) for an y trait. Estimated heritability varied between 0.14 and 0.28, with growth-related traits having the highest values. Additive genetic variation correlated positively with nonheritable variation, suggesting that ecological-evolutionary factors increasing or decreasing additive genetic variance may also affect nonheritable variation in the same direction. Our results suggest that quantitative genetic variability should be taken into account in ecological studies on, and in the management of, natural tropical rainforests; further research is needed to investigate genetic x environment interactions, in particular from the point of view of the genetic response of shade-tolerant plant species to variations in light availability. |
| Address |
[Scotti, Ivan; Scotti-Saintagne, Caroline; Bonal, Damien] INRA, Unite Mixte Rech Ecol Forets Guyane, Kourou 97387, French Guiana, Email: ivan.scotti@ecofog.gf |
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SPRINGER HEIDELBERG |
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1614-2942 |
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ISI:000274112600015 |
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no |
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EcoFoG @ eric.marcon @ |
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68 |
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Scotti, I.; Burelli, A.; Cattonaro, F.; Chagne, D.; Fuller, J.; Hedley, P.E.; Jansson, G.; Lalanne, C.; Madur, D.; Neale, D.; Plomion, C.; Powell, W.; Troggio, M.; Morgante, M. |
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Analysis of the distribution of marker classes in a genetic linkage map: a case study in Norway spruce (Picea abies karst) |
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Journal Article |
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2005 |
Publication |
Tree Genetics & Genomes |
Abbreviated Journal |
Tree Genet. Genomes |
| Volume |
1 |
Issue |
3 |
Pages |
93-102 |
| Keywords |
Picea abies; conifers; linkage map; genome structure; molecular markers; autocorrelation |
| Abstract |
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 retrotranspo sons. These results indicate that the spatial structure of Norway spruce chromosomes is not homogeneous. |
| Address |
INRA, UMR ECOFOG, Kourou 97387, French Guiana, Email: ivan.scotti@kourou.cirad.fr |
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SPRINGER HEIDELBERG |
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1614-2942 |
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ISI:000244896200002 |
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EcoFoG @ eric.marcon @ |
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167 |
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