Isabelle Bonnin

French National Institute for Agricultural Research, Avignon, Provence-Alpes-Cote d'Azur, France

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Publications (25)105.96 Total impact

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    ABSTRACT: Changing and more volatile climate conditions are leading to higher vulnerability and lower resilience for crop production. Recent studies indicate that crop diversity in agricultural fields may ensure pest control and yield stability in the face of environmental changes. However, few studies have evaluated crop diversity in the field, especially at the within-species level. Applying a new indicator, HT*, which integrates both the spatial evenness of different varieties and molecular genetic data (within and between variety genetic diversity), we followed the evolution of bread wheat genetic diversity on French agricultural landscapes during the 20th century. To our knowledge, the monitoring of crop genetic diversity at such a large but detailed spatial and temporal scale has never before been conducted. In comparison to two frequently used but less integrative indicators (the number of varieties grown in the field and their allelic diversity as measured by the Nei index), the HT* indicator revealed increasing genetic homogenization overall. This trend was due to the disappearance of diversity within varieties (initial replacement of landraces by more homogeneous old lines and later by modern pure lines), to the spatial homogenization occurring in the last period of the 20th century with the different ‘départements’ (French administrative territories) progressively cultivating the same varieties and to their increasing genetic similarities. This result calls into question the effects of plant breeding, seed system organization and seed regulation on wheat genetic diversity, especially in the context of current environmental changes.
    Agriculture Ecosystems & Environment 01/2014; 195:183–192. · 2.86 Impact Factor
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    ABSTRACT: Earliness is very important for the adaptation of wheat to environmental conditions and the achievement of high grain yield. A detailed knowledge of key genetic components of the life cycle would enable an easier control by the breeders. The objective of the study was to investigate the effect of candidate genes on flowering time. Using a collection of hexaploid wheat composed of 235 lines from diverse geographical origins, we conducted an association study for six candidate genes for flowering time and its components (vernalization sensitivity and earliness per se). The effect on the variation of earliness components of polymorphisms within the copies of each gene was tested in ANOVA models accounting for the underlying genetic structure. The collection was structured in five groups that minimized the residual covariance. Vernalization requirement and lateness tend to increase according to the mean latitude of each group. Heading date for an autumnal sowing was mainly determined by the earliness per se. Except for the Constans (CO) gene orthologous of the barley HvCO3, all gene polymorphisms had a significant impact on earliness components. The three traits used to quantify vernalization requirement were primarily associated with polymorphisms at Vrn-1 and then at Vrn-3 and Luminidependens (LD) genes. We found a good correspondence between spring/winter types and genotypes at the three homeologous copies of Vrn-1. Earliness per se was mainly explained by polymorphisms at Vrn-3 and to a lesser extent at Vrn-1, Hd-1 and Gigantea (GI) genes. Vernalization requirement and earliness as a function of geographical origin, as well as the possible role of the breeding practices in the geographical distribution of the alleles and the hypothetical adaptive value of the candidate genes, are discussed.
    Theoretical and Applied Genetics 07/2011; 123(6):907-26. · 3.66 Impact Factor
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    ABSTRACT: In fragmented populations, genetic drift and selection reduce genetic diversity, which in turn results in a loss of fitness or in a loss of evolvability. Genetic rescue, that is, controlled input of diversity from distant populations, may restore evolutionary potential, whereas outbreeding depression might counteract the positive effect of this strategy. We carried out self-pollination and crosses within and between populations in an experimental subdivided population of a selfing species, Triticum aestivum L., to estimate the magnitude of these two phenomena. Surprisingly, for a self-fertilizing species, we found significant inbreeding depression within each population for four of the six traits studied, indicating that mildly deleterious mutations were still segregating in these populations. The progeny of within- and between-population crosses was very similar, indicating low between-population heterosis and little outbreeding depression. We conclude that relatively large population effective sizes prevented fixation of a high genetic load and that local adaptation was limited in these recently diverged populations. The kinship coefficient estimated between the parents using 20 neutral markers was a poor predictor of the progeny phenotypic values, indicating that there was a weak link between neutral diversity and genes controlling fitness-related traits. These results show that when assessing the viability of natural populations and the need for genetic rescue, the use of neutral markers should be complemented with information about the presence of local adaptation in the subdivided population.
    Heredity 02/2011; 106(2):289-99. · 4.11 Impact Factor
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    ABSTRACT: In annual plant species, flowering time is a major adaptive trait that synchronizes the initiation of reproduction with favorable environmental conditions. Here, we aimed at studying the evolution of flowering time in three experimental populations of bread wheat, grown in contrasting environments (Northern to Southern France) for 12 generations. By comparing the distribution of phenotypic and presumably neutral variation, we first showed that flowering time responded to selection during the 12 generations of the experiment. To get insight into the genetic architecture of that trait, we then tested whether the distribution of genetic polymorphisms at six candidate genes, presumably involved in the trait expression, departed from neutral expectation. To that end, we focused on the temporal variation during the course of the experiment, and on the spatial differentiation at the end of the experiment, using previously published methods adapted to our experimental design. Only those genes that were strongly associated with flowering time variation were detected as responding to selection. For genes that had low-to-moderate phenotypic effects, or when there was interaction across different genes, we did not find evidence of selection using methods based on the distribution of temporal or spatial variation. In such cases, it might be more informative to consider multilocus and multiallelic combinations across genes, which could be the targets of selection.
    Evolution 02/2010; 64(7):2110-25. · 4.86 Impact Factor
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    ABSTRACT: Over the past few years, considerable progress has been made in high-throughput single nucleotide polymorphism (SNP) genotyping technologies, largely through the investment of the human genetics community. These technologies are well adapted to diploid species. For plant breeding purposes, it is important to determine whether these genotyping methods are adapted to polyploidy, as most major crops are former or recent polyploids. To address this problem, we tested the capacity of the multiplex technology SNPlex with a set of 47 wheat SNPs to genotype DNAs of 1314 lines that were organized in four 384-well plates. These lines represented different taxa of tetra- and hexaploid Triticum species and their wild diploid relatives. We observed 40 markers which gave less than 20% missing data. Different methods, based on either Sanger sequencing or the MassARRAY genotyping technology, were then used to validate the genotypes obtained by SNPlex for 11 markers. The concordance of the genotypes obtained by SNPlex with the results obtained by the different validation methods was 96%, except for one discarded marker. Furthermore, a mapping study on six markers showed the expected genetic positions previously described. To conclude, this study showed that high-throughput genotyping technologies developed for diploid species can be used successfully in polyploids, although there is a need for manual reading. For the first time in wheat species, a core of 39 SNPs is available that can serve as the basis for the development of a complete SNPlex set of 48 markers.
    Plant Biotechnology Journal 06/2009; 7(4):364-74. · 6.28 Impact Factor
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    ABSTRACT: The occurrence of populations exhibiting high genetic diversity in predominantly selfing species remains a puzzling question, since under regular selfing genetic diversity is expected to be depleted at a faster rate than under outcrossing. Fine-scale population genetics approaches may help to answer this question. Here we study a natural population of the legume Medicago truncatula in which both the fine-scale spatial structure and the selfing rate are characterized using three different methods. Selfing rate estimates were very high ( approximately 99%) irrespective of the method used. A clear pattern of isolation by distance reflecting small seed dispersal distances was detected. Combining genotypic data over loci, we could define 34 multilocus genotypes. Among those, six highly inbred genotypes (lines) represented more than 75% of the individuals studied and harboured all the allelic variation present in the population. We also detected a large set of multilocus genotypes resembling recombinant inbred lines between the most frequent lines occurring in the population. This finding illustrates the importance of rare recombination in redistributing available allelic diversity into new genotypic combinations. This study shows how multilocus and fine-scale spatial analyses may help to understand the population history of self-fertilizing species, especially to make inferences about the relative role of foundation/migration and recombination events in such populations.
    Heredity 06/2008; 100(5):517-25. · 4.11 Impact Factor
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    ABSTRACT: The transition from vegetative to floral meristems in higher plants is determined by the coincidence of internal and environmental signals. Contrary to the photoperiod pathway, convergent evolution of the cold-dependent pathway has implicated different genes between dicots and monocots. Whereas no association between natural variation in vernalization requirement and Flowering time locus T (FT) gene polymorphism has been described in Arabidopsis, recent studies in Triticeae suggest implication of orthologous copies of FT in the cold response. In our study, we show that nucleotide polymorphisms on A and D copies of the wheat FT gene were associated with variations for heading date in a collection of 239 lines representing diverse geographical origins and status (landraces, old or recent cultivars). Interestingly, polymorphisms in the non-coding intronic region were strongly associated to flowering variation observed on plants grown without vernalization. But differently from VRN1, no epistatic interaction between FT homeologous copies was revealed. In agreement with the results of association study, the A and D copies of FT were mapped in regions including major QTLs for earliness traits in hexaploid wheat. This work, by identifying additional homeoalleles involved in wheat vernalization pathway, will contribute to a better understanding of the control of flowering, hence providing tools for the breeding of varieties with enhanced adaptation to changing environments.
    Theoretical and Applied Genetics 03/2008; 116(3):383-94. · 3.66 Impact Factor
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    ABSTRACT: Experimental populations evolving under natural selection represent an interesting tool to study genetic bases of adaptation. Evolution of genes possibly involved in adaptive response can be followed together with the corresponding phenotypic traits. Using experimental populations of hexaploid wheat, we studied the evolution of flowering time, a major adaptive trait that synchronizes the initiation of reproduction and the occurrence of favourable environmental conditions. During 12 generations, three populations were grown in contrasted environments (Vervins North France, Le Moulon near Paris, Toulouse South France) under the influence of natural selection, drift, mutation and recombination. Evolution of diversity at the major gene VRN-1 involved in wheat vernalization response has been analysed jointly with earliness estimated in controlled conditions. Whatever the population, rapid phenotypic changes as well as parallel genotypic variations were observed in the first seven generations, probably as the result of selection acting on this major gene which explains 80% of the trait variation overall. Different allelic combinations at physically unlinked copies of VRN-1 located on distinct genomes (A, B and D) were selected between populations. As theoretically expected, due to population differentiation, a high level of genetic diversity was maintained overall in generation 12. Surprisingly, in two populations out of three, the emergence of new alleles by mutation or migration, coupled with temporal variable selection or frequency-dependent selection, allowed to maintain within-population diversity despite local genetic drift and natural selection. This result may plead for an evolutionary approach of wheat genetic resource conservation.
    Molecular Ecology 03/2008; 17(3):930-43. · 6.28 Impact Factor
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    ABSTRACT: Despite its significance in evolutionary and conservation biology, few estimates of effective population size (N(e)) are available in plant species. Self-fertilization is expected to affect N(e), through both its effect on homozygosity and population dynamics. Here, we estimated N(e) using temporal variation in allele frequencies for two contrasted populations of the selfing annual Medicago truncatula: a large and continuous population and a subdivided population. Estimated N(e) values were around 5-10% of the population census size suggesting that other factors than selfing must contribute to variation in allele frequencies. Further comparisons between monolocus allelic variation and changes in the multilocus genotypic composition of the populations show that the local dynamics of inbred lines can play an important role in the fluctuations of allele frequencies. Finally, comparing N(e) estimates and levels of genetic variation suggest that H(e) is a poor estimator of the contemporaneous variance effective population size.
    Journal of Evolutionary Biology 12/2007; 20(6):2349-60. · 3.48 Impact Factor
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    ABSTRACT: Although current knowledge about the overall distribution of zinc (Zn) tolerance in Arabidopsis halleri populations is scarce, the species is an emerging model for the study of heavy metal tolerance in plants. We attempted to improve this knowledge by testing the Zn tolerance of scattered European metallicolous (M) and nonmetallicolous (NM) populations of A. h. subsp. halleri and A. h. subsp. ovirensis in hydroponic culture. The occurrence of constitutive tolerance was unconditionally established in A. h. halleri and tolerance was extended to the subspecies ovirensis. M populations were the most tolerant but there was a continuous range of variation in tolerance from NM to M populations. Finally, relatively high levels of tolerance were detected in some NM populations, suggesting that enhanced tolerance could be present at high frequency in populations that have not experienced metal exposure. We used our results to argue the evolutionary dynamics and origin of Zn tolerance in A. halleri.
    Journal of Evolutionary Biology 12/2006; 19(6):1838-50. · 3.48 Impact Factor
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    ABSTRACT: Dynamic management (DM) of genetic resources aims at maintaining genetic variability between different populations evolving under natural selection in contrasting environments. In 1984, this strategy was applied in a pilot experiment on wheat (Triticum aestivum). Spatio-temporal evolution of earliness and its components (partial vernalization sensitivity, daylength sensitivity and earliness per se that determines flowering time independently of environmental stimuli) was investigated in this multisite and long-term experiment. Heading time of six populations from the tenth generation was evaluated under different vernalization and photoperiodic conditions. Although temporal evolution during ten generations was not significant, populations of generation 10 were genetically differentiated according to a north-south latitudinal trend for two components out of three: partial vernalization sensitivity and narrow-sense earliness. It is concluded that local climatic conditions greatly influenced the evolution of population earliness, thus being a major factor of differentiation in the DM system. Accordingly, a substantial proportion (approximately 25 %) of genetic variance was distributed among populations, suggesting that diversity was on average conserved during evolution but was differently distributed by natural selection (and possibly drift). Earliness is a complex trait and each genetic factor is controlled by multiple homeoalleles; the next step will be to look for spatial divergence in allele frequencies.
    Annals of Botany 11/2006; 98(4):805-17. · 3.45 Impact Factor
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    ABSTRACT: The population structure of the pseudo-metallophyte herb, Arabidopsis halleri, was studied using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) on chloroplast DNA (cpDNA). The history of metallicolous (M) populations showing increased zinc tolerance was investigated. Eight primer-enzyme combinations out of 72 tested were applied to a total of 625 individuals from 28 widespread populations, 14 of them being M. Eleven distinct chlorotypes were found: five were common to nonmetallicolous (NM) and M populations, whereas six were only observed in one edaphic type (five in NM and one in M). No difference in chlorotype diversity between edaphic types was detected. Computed on the basis of chlorotype frequencies, the level of population differentiation was high but remained the same when taking into account levels of molecular divergence between chlorotypes. Isolation by distance was largely responsible for population differentiation. Geographically isolated groups of M populations were more genetically related to their closest NM populations than to each other. Our results suggest that M populations have been founded separately from distinct NM populations without suffering founding events and that the evolution towards increased tolerance observed in the distinct M population groups occurred independently.
    Molecular Ecology 01/2006; 14(14):4403-14. · 6.28 Impact Factor
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    ABSTRACT: Arabidopsis halleri, a close wild relative of A. thaliana, is a clonal, insect-pollinated herb tolerant to heavy metals (Zn, Pd, Cd) and a hyperaccumulator of Zn and Cd. It is of particular interest in the study of evolutionary processes and phytoremediation. However, little is known about its population gene flow patterns and the structure of its genetic diversity. We used five microsatellite loci to investigate the genetic structure at a fine spatial scale (10 cm to 500 m) in a metallicolous population of A. halleri. We also studied the contributions made by clonal propagation and sexual reproduction (seed and pollen dispersal) to the genetic patterns. Clonal diversity was high (D(G) > 0.9). Clonal spread occurs only at short distances (< 1 m). Both clonal spread and limited dispersal, associated with sexual reproduction, contribute to the significant spatial genetic structure revealed by spatial autocorrelation analysis. The shape of the autocorrelogram suggests that seed dispersal is restricted and pollen flow extensive, which may be related to intense activity by insect pollinators. Clonal spread was more extensive in the lowly polluted zone than in the highly polluted zone. This cannot be interpreted as a strategy for promoting the propagation of adapted genotypes under the harshest ecological constraints (highest heavy metal concentrations). The higher fine-scale spatial genetic structure found in the lowly polluted zone can be ascribed to plant densities that were lower than in the highly polluted zone. No evidence of genetic divergence due to spatial heavy metal heterogeneity was found between lowly and highly polluted zones.
    Molecular Ecology 10/2004; 13(10):2959-67. · 6.28 Impact Factor
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    ABSTRACT: In endangered species, it is critical to analyse the level at which populations interact (i.e. dispersal) as well as the levels of inbreeding and local adaptation to set up conservation policies. These parameters were investigated in the endangered species Parnassia palustris living in contrasted habitats. We analysed population structure in 14 populations of northern France for isozymes, cpDNA markers and phenotypic traits related to fitness. Within population genetic diversity and inbreeding coefficients were not correlated to population size. Populations seem not to have undergone severe recent bottleneck. Conversely to pollen migration, seed migration seems limited at a regional scale, which could prevent colonization of new sites even if suitable habitats appear. Finally, the habitat type affects neither within-population genetic diversity nor genetic and phenotypic differentiation among populations. Thus, even if unnoticed local adaptation to habitats exists, it does not influence gene flow between populations.
    Molecular Ecology 07/2002; 11(6):979-90. · 6.28 Impact Factor
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    ABSTRACT: • The ability of metallicolous and nonmetallicolous populations of Arabidopsis halleri to accumulate zinc (Zn), cadmium (Cd) and lead (Pb) is compared here in order to explore the extent and variability of this trait in wild A. halleri plants.• Aerial plant parts and the soil around the harvested plants were collected and analysed for metal concentrations or total and extractable metal concentrations, respectively, for 20 metallicolous and 13 nonmetallicolous populations.• Results show that metallicolous and nonmetallicolous populations have the same ability to accumulate Zn and Cd but that neither population type is able to accumulate Pb. Between populations within type, an homogenous accumulating response is observed for Zn, whereas the ability to accumulate Cd is variable.• Zn and Cd accumulation to very high concentrations is a constitutive property of the species. The Zn and Cd hyperaccumulator trait of A. halleri from contaminated sites was confirmed. Interestingly, nonmetallicolous plants are Zn and Cd hyperaccumulators. The possibility of using A. halleri in phytoremediation is discussed.
    New Phytologist 06/2002; 155(1):47 - 57. · 6.74 Impact Factor
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    ABSTRACT: The genetic diversity of spores of two indigenous species of Glomus isolated from three soils of a long-term field experiment amended by different quantities of sewage sludges has been evaluated. Three populations of spores of Glomus claroideum (W2537) and three populations of spores of Glomus DAOM 225952 (W2538) were analysed using a microsatellite primer and aliquots of genomic DNA were obtained from single spores (Inter Simple Sequence Repeat (ISSR) fingerprints). 39 polymorphic bands were found for G. claroideum, and 43 in Glomus DAOM 225952. The intraspecific diversity was high, ranging from 22 to 33 different electrophoretic types for G. claroideum, and 15-27 for Glomus DAOM 225952 depending on the population. Resampling experiments showed that the number of polymorphic bands was sufficient to score all multilocus profiles in the populations and to describe the clonality structure within populations. On average, one multilocus profile was represented by about four spores whatever the population and the species. Partitioning of the within-species phenotypic variance showed that more than 92% of the variation was found within populations, while the among-population variance component accounted for less than 8%, even though it was statistically different from 0. This result is confirmed by the fact that only few multilocus profiles were shared by two populations of G. claroideum, and none by populations of Glomus DAOM 225952. In addition to the high level of diversity observed within populations, linkage disequilibria analyses and association indices calculated across loci indicates that reproduction cannot be solely clonal. Recombination or recombination-like events are likely to occur in these arbuscular mycorrhizal fungi. An 'epidemic' population structure was found for both fungal species in the soil that had received high amounts of sewage sludge.
    Heredity 09/2001; 87(Pt 2):243-53. · 4.11 Impact Factor
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    ABSTRACT: In order to elucidate the mechanisms underlying the large amount of RAPD polymorphism found in 1990 in a population of the selfing annual Medicago truncatula GAERTN. (Fabaceae), we have analysed most of the individuals (n = 363) from the same population 6 years later using microsatellite loci. We confirm the result of the earlier study, namely that this population is very polymorphic and highly subdivided, with approximately 37% of the variance distributed among subpopulations, only 50 m apart one from another. We use standard F-statistics analyses, linkage disequilibria, minimum spanning network, multilocus assignment tests and spatial autocorrelation analyses to test the hypotheses that spatial structure and outcrossing events are involved in maintaining the large amount of genetic diversity at the level of each subpopulation. Interestingly, fine-scale spatial structure could be observed in only one subpopulation suggesting that other mechanisms are acting elsewhere. To the best of our knowledge, this is the first study of fine spatial genetic structure in a predominantly selfing species.
    Molecular Ecology 07/2001; 10(6):1371-83. · 6.28 Impact Factor
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    ABSTRACT: In order to elucidate the mechanisms underlying the large amount of RAPD polymorphism found in 1990 in a population of the selfing annual Medicago truncatula GAERTN. (Fabaceae), we have analysed most of the individuals (n = 363) from the same population 6 years later using microsatellite loci. We confirm the result of the earlier study, namely that this population is very polymorphic and highly subdivided, with approximately 37% of the variance distributed among subpopulations, only 50 m apart one from another. We use standard F-statistics analyses, linkage disequilibria, minimum spanning network, multilocus assignment tests and spatial autocorrelation analyses to test the hypotheses that spatial structure and outcrossing events are involved in maintaining the large amount of genetic diversity at the level of each subpopulation. Interestingly, fine-scale spatial structure could be observed in only one subpopulation suggesting that other mechanisms are acting elsewhere. To the best of our knowledge, this is the first study of fine spatial genetic structure in a predominantly selfing species.
    Molecular Ecology 05/2001; 10(6):1371 - 1383. · 6.28 Impact Factor
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    ABSTRACT:  In this paper we compare mean values, heritability estimates, coefficient of genetic variation, and genetic correlations among several fitness components of two natural populations of a selfing plant species, Medicago truncatula L. It is shown that the population that had been found most polymorphic for molecular markers in a previous study was also the most variable for quantitative characters. Depending on the traits, the larger heritabilities in this population were due to either larger coefficients of genetic variances or smaller coefficients of environmental variances. Whereas genetic and phenotypic correlation matrices were very similar within each population, they were quite different between populations. In particular, although a positive correlation between age and size at maturity was found in both populations, the correlation between age at maturity and reproductive success was negative in the more variable population (late flowering plant, with a larger size at flowering, produced fewer pods), whereas no correlation was observed in the less variable population. We suggest that while in the less variable population all individuals have a high reproductive effort, several strategies coexist in the more variable population, with some early-flowering genotypes showing a high reproductive effort and other late-flowering genotypes showing a larger competitive ability through increased vegetative growth.
    Theoretical and Applied Genetics 01/1997; 94(5):641-651. · 3.66 Impact Factor
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    ABSTRACT:  About 40% (α=0.05) of the PCR-derived markers scored in a Medicago truncatula and M. tornata intraspecific cross departed from Mendelian expectations at α=0.05. This proportion is among the highest ever documented in the literature, notably for intraspecific crosses. Estimations of DNA amount were also implemented for the parental genotypes or parental lines, and significant variations were observed. Our results suggest that the parental genotypes have diverged for quite a while, and we propose that the level of distortion we documented is correlated with the genome size difference we measured.
    Theoretical and Applied Genetics 01/1997; 94(5):682-691. · 3.66 Impact Factor

Publication Stats

767 Citations
105.96 Total Impact Points

Institutions

  • 2002–2010
    • French National Institute for Agricultural Research
      • Génétique Végétale
      Avignon, Provence-Alpes-Cote d'Azur, France
  • 2001
    • Université des Sciences et Technologies de Lille 1
      • Laboratoire de Génétique et Evolution des Populations Végétales (GEPV)
      Lille, Nord-Pas-de-Calais, France
    • The University of York
      York, England, United Kingdom