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The objective of the present study was to evaluate the resistance of 10 accessions to P. infestans, by in-vitro inoculation of detached leaflets with a complex isolation of the fungus. Late blight, caused by the fungus Phytophthora infestans Mont. De Bary, is one of the most important diseases of the potato crop, and can destroy complete plantations in a short space of time. Chile is considered as a sub-centre of the origin of cultivated potatoes with many native potato varieties in the country. The different resistance components demonstrated that within the material of Chilean native Solanum, there was a wide range of variation to late blight. The resistant control (R-8906384) and the accessions UCT-34-Cor presented the lowest infection efficiency, small sizes of the lesions and low levels of sporulation classifying them as the most resistant. This suggests low efficiency of the infection and high resistance to penetration in these materials. The more susceptible accessions often presented a good level of resistance for one or few components. It would be of great interest to go into the genetic control of the different resistance components to know if the same level of resistance expressed for a component by different accessions is under the same genetic control or not.

Allopolyploidy, combining interspecific hybridization with whole genome duplication, has had significant impact on plant evolution. Its evolutionary success is related to the rapid and profound genome reorganizations that allow neoallopolyploids to form and adapt. Nevertheless, how neoallopolyploid genomes adapt to regulate their expression remains poorly understood. The hypothesis of a major role for small noncoding RNAs (sRNAs) in mediating the transcriptional response of neoallopolyploid genomes has progressively emerged. Generally, 21-nt sRNAs mediate posttranscriptional gene silencing by mRNA cleavage, whereas 24-nt sRNAs repress transcription (transcriptional gene silencing) through epigenetic modifications. Here, we characterize the global response of sRNAs to allopolyploidy in Brassica, using three independently resynthesized Brassica napus allotetraploids originating from crosses between diploid Brassica oleracea and Brassica rapa accessions, surveyed at two different generations in comparison with their diploid progenitors. Our results suggest an immediate but transient response of specific sRNA populations to allopolyploidy. These sRNA populations mainly target noncoding components of the genome but also target the transcriptional regulation of genes involved in response to stresses and in metabolism; this suggests a broad role in adapting to allopolyploidy. We finally identify the early accumulation of both 21- and 24-nt sRNAs involved in regulating the same targets, supporting a posttranscriptional gene silencing to transcriptional gene silencing shift at the first stages of the neoallopolyploid formation. We propose that reorganization of sRNA production is an early response to allopolyploidy in order to control the transcriptional reactivation of various noncoding elements and stress-related genes, thus ensuring genome stability during the first steps of neoallopolyploid formation.

Transposable elements (TEs) represent a major component of plant genomes and may provide the host genome with the necessary plasticity for its adaptative response. Polyploidy has played a major role in the evolution of plants (Wendel, 2000) and its success can be explained by the fact that a polyploid genome is not only the strict addition of the progenitor genomes, but that polyploidisation induces structural and functional modifications which represent important sources of novelty (Adams and Wendel, 2005). Our study aims at evaluating the implication of TEs in the genomic modifications that occur during the formation of a polyploid genome. Our plant model is oilseed rape (Brassica napus, AACC) originating from interspecific hybridization between B. rapa (AA) and B. oleracea (CC), and we dispose of newly synthesized B. napus allotetraploids resulting from independent AA x CC crosses. We developed sequence-specific amplification polymorphism (S-SAP) markers anchored in two different families of Brassica-specific TEs, an Athila-like retrotransposon and a MITE, which are contrasting TEs regarding their genomic organisation, dynamics of evolution, and mode of replication. Comparison of the S-SAP profiles and characterization of the polymorphism identified in the newly synthesized allotetraploids will provide new insights into the putative role of TEs during the creation of an allopolyploid species.

Microsatellite markers are extensively used to evaluate genetic diversity in natural or experimental evolving populations. Their high degree of polymorphism reflects their high mutation rates. Estimates of the mutation rates are therefore necessary when characterizing diversity in populations. As a complement to the classical experimental designs, we propose to use experimental populations, where the initial state is entirely known and some intermediate states have been thoroughly surveyed, thus providing a short timescale estimation together with a large number of cumulated meioses. In this article, we derived four original gene genealogy-based methods to assess mutation rates with limited bias due to relevant model assumptions incorporating the initial state, the number of new alleles, and the genetic effective population size. We studied the evolution of genetic diversity at 21 microsatellite markers, after 15 generations in an experimental wheat population. Compared to the parents, 23 new alleles were found in generation 15 at 9 of the 21 loci studied. We provide evidence that they arose by mutation. Corresponding estimates of the mutation rates ranged from 0 to 4.97 × 10−3 per generation (i.e., year). Sequences of several alleles revealed that length polymorphism was only due to variation in the core of the microsatellite. Among different microsatellite characteristics, both the motif repeat number and an independent estimation of the Nei diversity were correlated with the novel diversity. Despite a reduced genetic effective size, global diversity at microsatellite markers increased in this population, suggesting that microsatellite diversity should be used with caution as an indicator in biodiversity conservation issues.

Strong selection within a given population locally reduces genetic variability not only in the selected gene itself but also in neighbouring loci. This so-called hitch-hiking effect is related to the initial linkage disequilibrium between markers and the selected gene, and depends mainly on the number of copies of the beneficial allele at the start of the selection phase. Contrary to the classical case, in which selection acts on a single, newly arisen beneficial mutation, we considered selection from standing variation (soft selective sweeps) on a gene (Rht-B1) with a major effect on plant height, a selected trait in an experimental wheat population grown for 17 generations, and we documented the evolution of gene diversity and linkage disequilibrium near this gene. As expected, Rht-B1 was found to be under strong selection (s = 0.15) and its variation in frequency accounted for 15% of the total trait evolution. This led to a smaller genetic effective population size at Rht-B1 (N-eg = 18) compared to the whole genome estimation (N-eg = 167). When compared with expectations under genetic drift only, no significant decrease in gene diversity was found at the closest loci. We computed expected di-locus frequencies for any linked marker-Rht-B1 pair due to hitch-hiking effects. We found that hitch-hiking was expected to affect the two most closely linked loci, but expected reduction in gene diversity was not greater than that due to genetic drift, which was consistent with the observations. Such limited effect was attributed to the low level of linkage disequilibrium (0.16) estimated after parental intercrosses, together with a relatively high initial frequency of the gene. This situation is favourable to candidate gene approaches where small linkage disequilibrium around selected genes is expected.

International audience; The objective of this work was to evaluate the resistance of 30 Chilean potato landraces to natural infection by Phytophthora infestans during two growing seasons in Southern Chile. Control cultivars were 'Desiree', which has moderate susceptibility to late blight, and 'Karu', which is characterized by moderate resistance to the disease. The response of the potato landraces to late blight infection was assessed weekly by scoring the percentage of foliage destruction during the growing season. Subsequently, the relative area under the disease progress curve (AUDPCr) was calculated. A wide response variation was observed among the landraces during the occurrence of late blight. The comparative analysis of the AUDPCr showed that three landraces achieved high resistance to the disease (low AUDPCr values). These were UCT-34Cor (0.05), UCT-26Ach (0.06) and UCT-27Mu (0.10). Most of the potato landraces were classified into the range moderately resistant to moderately susceptible. The estimated values of heritabilities of the means were moderate to high for the joint analysis of the two years tested (0.65). The wide range of AUDPCr observed within potato landraces suggests the presence of partial resistance in response to the complex virulence pattern of the P. infestans populations present in Southern Chile.

In order to investigate further the interest of using the Chilean gene pool in potato breeding programmes, the genetic diversity and population structure of a collection ofSolanum tuberosumL. genotypes including 350 worldwide varieties or breeders' lines (referred to as the modern group) and 30 Chiloé Island landraces were examined using simple sequence repeat markers. The close genetic proximity of the Chiloé Island landraces to the modern group was confirmed using several structure analysis methods: principal coordinate analysis; hierarchical clustering analysis; analysis of molecular variance; Bayesian model-based clustering analysis. The latter analysis, in particular, revealed no clear genetic structure between the modern group and the Chiloé Island landraces. The Chiloé Island germplasm appears to represent an interesting gene pool that could be exploited in potato breeding programmes using an association mapping approach.

International audience; The role played by whole-genome duplication (WGD) in evolution and adaptation is particularly well illustrated in allopolyploids, where WGD is concomitant with interspecific hybridization. This Genome Shock', usually accompanied by structural and functional modifications, has been associated with the activation of transposable elements (TEs). However, the impact of allopolyploidy on TEs has been studied in only a few polyploid species, and not in Brassica, which has been marked by recurrent polyploidy events. Here, we developed sequence-specific amplification polymorphism (SSAP) markers for three contrasting TEs, and compared profiles between resynthesized Brassica napus allotetraploids and their diploid Brassica progenitors. To evaluate restructuring at TE insertion sites, we scored changes in SSAP profiles and analysed a large set of differentially amplified SSAP bands. No massive structural changes associated with the three TEs surveyed were detected. However, several transposition events, specific to the youngest TE originating from the B.oleracea genome, were identified. Our study supports the hypothesis that TE responses to allopolyploidy are highly specific. The changes observed in SSAP profiles lead us to hypothesize that they may partly result from changes in DNA methylation, questioning the role of epigenetics during the formation of a new allopolyploid genome.

We characterized a Brassica miniature inverted repeat transposable element (MITE) from the Stowaway superfamily, designated BraSto (Bra ssica Sto waway). BraSto copy number was assessed using real-time quantitative PCR in the two diploid species B. rapa (genome A) and B. oleracea (genome C) and the corresponding allotetraploid species B. napus (genome AC). Phylogenetic relationships among a set of 131 BraSto copies were then analyzed. BraSto appears to have been only moderately amplified in the Brassica genome and was still active recently with marks of proliferation in both diploid Brassica species, which diverged 3.75 million years ago, but also in the allotetraploid species after reuniting of the two differentiated genomes. We characterized insertion sites for low-divergence BraSto copies among the gene space of the B. rapa genome using bioinformatics approaches. For BraSto copies localized nearby or within genes, we observed frequent associations of BraSto with putative promoters and regulatory regions of genes, but exclusion from coding regions. In addition, BraSto was significantly similar to several Brassica expressed sequence tags (ESTs), including stress-induced ESTs. We also demonstrated the enrichment of BraSto sequences in binding sites for transcription factors and other regulatory elements. Our results lead to the question of a role for BraSto in the regulation of gene expression: this putative role, if further confirmed experimentally, would help to obtain a new insight into the significance of MITEs in the functional plant genome.

Summary •Polyploidy, or whole genome duplication, is a major evolutionary process that has shaped eukaryotic genomes, notably those of flowering plants. The mechanisms underlying the regulation of, and sharing of functions between, the duplicated genes originating from polyploidy events, which lead to novel phenotypes, remain to be elucidated. •A previous comparative proteomic study identified 360 proteins that were differentially regulated between the diploid Brassica progenitors and their synthetic allotetraploid derivatives. For 102 of these proteins, using the same resynthesized Brassica napus allotetraploids, we assayed the accumulation of the transcripts of the corresponding genes. We compared transcript levels quantified in the synthetic allotetraploids with the mid-parent expression values. •Although all of the genes surveyed encoded nonadditive proteins, we found that two-thirds of them had additive transcript levels, indicating that most of the differential protein regulation is not explained by transcriptional changes. •Our data suggest that differential protein regulation is mainly governed by post-transcriptional modifications. Summarizing available data from transcriptomic studies of other synthetic allopolyploid models, we describe the general trends of transcript regulation in an allopolyploid genome and discuss putative underlying molecular mechanisms, with particular emphasis on the small RNA pathway for the post-transcriptional control of gene expression.

Background Allopolyploidy is a preeminent process in plant evolution that results from the merger of distinct genomes in a common nucleus via inter-specific hybridization. Allopolyploid formation is usually related to genome-wide structural and functional changes though the underlying mechanisms operating during this "genomic shock" still remain poorly known. The aim of the present study was to investigate the modifications occurring at the proteomic level following an allopolyploidization event and to determine whether these changes are related to functional properties of the proteins. In a previous report, we applied comparative proteomics to synthetic amphiploids of Brassica napus and to its diploid progenitors B. rapa and B. oleracea. Although several hundred polypeptides displayed additivity (i.e. mid-parent values) in the amphiploids, many of them showed non-additivity. Here, we report the in silico functional characterization of the "non-additive" proteins (the ones with a non-additive pattern of regulation) in synthetic B. napus. Results The complete set of non-additive proteins (335 in the stem and 205 in the root), as well as a subset of additive polypeptides (200 per organ), was identified by mass spectrometry. Several protein isoforms were found, and most of them (~55%) displayed "different" or "opposite" patterns of regulation in the amphiploids, i.e. isoforms of the same protein showing both up-regulation and down-regulation in the synthetic B. napus compared to the mid-parent value. Components of protein complexes were identified of which ~50% also displayed "different" or "opposite" patterns of regulation in the allotetraploids. In silico functional categorization of the identified proteins was carried out, and showed that neither functional category nor metabolic pathway were systematically affected by non-additivity in the synthetic amphiploids. In addition, no subcellular compartment was found to be over- or under-represented among the proteins displaying non-additive values in the allopolyploids. Conclusion Protein identification showed that functionally related polypeptides (isoforms and complex subunits) could be differentially regulated in synthetic B. napus in comparison to its diploid progenitors while such proteins are usually expected to display co-regulation. The genetic redundancy within an allopolyploid could explain why functionally related proteins could display imbalanced levels of expression. No functional category, no metabolic pathway and no subcellular localization was found to be over- or under-represented within non-additive polypeptides, suggesting that the differential regulation of gene products was not related to functional properties of the proteins. Thus, at the protein level, there is no evidence for the "genomic shock" expected in neo-polyploids and the overall topology of protein networks and metabolic pathways is conserved in synthetic allotetraploids of B. napus in comparison to its diploid progenitors B. rapa and B. oleracea.

POLYPLOIDY is a major evolutionary process of speciation in eukaryotes and particularly in plants where several economically important crop species including oilseed rape, wheat, and sugarcane are polyploid (Grant 1981; Wendel 2000). Moreover, an increasing number of diploid-considered species are shown to actually be paleopolyploids, such as maize (Gaut and Doebley 1997), Arabidopsis (Arabidopsis Genome Initiative 2000), and rice (Zhang et al. 2005). The high occurrence of polyploid plants has been the source of considerable interest, notably to determine why polyploidy represents such an indisputable evolutionary success. Several authors have noted that polyploidy must confer an immediate selective advantage (Osborn et al. 2003; Comai 2005) and have underlined the necessity to analyze the very first stages of polyploid formation. Accordingly, the study of newly synthesized polyploids has led to the description of structural changes such as chromosomal rearrangements (Pontes et al. 2004) and gains or losses of DNA sequences (Song et al. 1995; Liu et al. 1998; Madlung et al. 2005). Additionally, investigations have demonstrated the occurrence of modifications at the level of gene expression. Several studies on resynthesized Arabidopsis suecica (Comai et al. 2000; Wang et al. 2004, 2006), Gossypium allotetraploids (Adams et al. 2003, 2004), and allotetraploids and allohexaploids of wheat (Ni et al. 2000; Kashkush et al. 2002, 2003; He et al. 2003; Wu et al. 2003) have shown that some genes are silenced after polyploidization, while others are derepressed. Nearly all of these approaches were undertaken at the transcript level and most of them used qualitative or semiqualitative techniques like cDNA–AFLP display that allowed the detection of gene silencing or novel expression patterns, but lacked precision for more subtle variations (up- or downregulation). Other innovating techniques like cDNA–SSCP (Adams et al. 2003) give quantitative information on homeologous gene expression, but are restricted to a small number of genes. Genomewide analyses can now be undertaken using the promising cDNA microarray technology. This approach is planned for Brassica polyploids (Chen et al. 2004; Lee et al. 2004; Wang et al. 2005) and has been recently applied to the synthetic allopolyploids Senecio cambrensis (Hegarty et al. 2005) and A. suecica (Wang et al. 2006), revealing several modifications of gene expression. Proteomic tools complement transcriptomic approaches: cellular biochemistry is essentially modulated by proteins rather than by transcripts, and the correlation between mRNA abundance and protein amounts is erratic due to post-transcriptional regulations (Gygi et al. 1999). Additionally, post-translational modifications play a key role in the cell as they modulate protein activity, turnover, subcellular location, or interactions with proteins or nucleic acids and can be investigated only at the protein level. Comparative proteomics can be achieved using the two-dimensional electrophoresis (2-DE) technique that allows the resolution of hundreds of polypeptides in a single gel. Accurate and reproducible quantification of the corresponding spots can be performed using dedicated software and the relevant proteins identified by mass spectrometry. Comparative proteomics provides pertinent and reliable quantitative results on genomewide expression and it is becoming more and more popular in plant research (Thiellement et al. 1999, 2002). In this study, we used the Brassica napus model system to investigate the early consequences of allopolyploid formation on gene expression. Four independent neosynthesized B. napus amphidiploids, their diploid progenitors B. oleracea and B. rapa, as well as the amphihaploid hybrids were submitted to comparative proteomics. The additivity hypothesis (predicting a midparent proteome for the amphiploids) was tested in two distinct organs, the stem and root, and polypeptides displaying nonadditive patterns were identified using mass spectrometry.

DOI: 10.1002/pmic.200401092; Polyploidization is a major evolutionary process in eukaryotes. In plants, genetic and epigenetic changes occur rapidly after formation of allopolyploids. Hybridization, rather than genome doubling itself, is considered as the main cause for the resulting differential gene expression. We studied the consequences of genome doubling alone in an autopolyploid model, by comparing two-dimensional gel electrophoresis (2-DE) gels of haploid, diploid, and tetraploid Brassica oleracea cabbages. Two fully homozygous lines, HDEM and RC, as well as two organs, leaf and stem, were studied. For the 558 common spots found present in all the 29 2-DE gels of the experiment, inter-organ and -genotype differences were the major sources of the variation in protein amounts: 41 and 10-13%, respectively. HDEM leaf and stem proteomes were not significantly affected by the ploidy level, since no qualitative variation was detected and since the number of quantitative variations could be due to chance. For RC, no qualitative variations were observed, but a few spots were significantly variable in protein amount. However, the number of inter-ploidy variations was of the same range as the number of intra-ploidy variations. In conclusion, whatever the ploidy level, leaf and stem proteomes remained globally unchanged in both cabbage lines.

International audience; Single-row plots (SRP) are often used in early generation selection. For wheat, in such trials, it has already been demonstrated that inter-plot competition leads to highly biased estimations of grain yield. An experiment including one SRP trial and one reference 6-row-plot trial were conducted over two consecutive years in order to compare two statistical models for correcting competition effects. The neighbourhood covariate model relying on plant height proved to be more efficient than the more general producer-competitor model. It provided significant improvement in yield estimation, slightly greater using height measured at heading than using final height as covariate. Moreover, relative efficiency of selection in SRP when corrected for competition effects always reached about 85% , whatever the intensity of competition. The neighbouring covariate model based on plant height should be used for routine analysis of single-row-plot trials.; Modèles de correction de la compétition inter-génotypique chez le blé. Les parcelles monorang sont souvent utilisées dans les schémas de sélection précoce. Dans de tels dispositifs, il a été montré que la compétition entre parcelles adjacentes introduisait un biais dans l'évaluation du rendement. Afin de comparer l'efficacité de plusieurs modèles pour corriger les effets de la compétition, une expérimentation comprenant un essai constitué de parcelles monorang et un essai de référence constitué de parcelles de 6 rangs a été conduite deux années consécutives. Le modèle incluant la covariable de voisinage utilisant la hauteur des plantes s'est révélé plus efficace que le modèle producteur-compétiteur pour corriger le biais introduit par la compétition dans l'évaluation du rendement en parcelles monorang. La correction effectuée par la covariable est faiblement mais significativement meilleure dans le cas où la hauteur est mesurée à l'épiaison qu'à la récolte. D'autre part, l'efficacité relative de la sélection en parcelles monorang, une fois corrigés les effets de la compétition, atteint toujours 85 % , quelle que soit l'intensité de la compétition. La covariable de voisinage utilisant la hauteur des plantes est proposée pour l'analyse en routine des dispositifs d'essais en parcelles monorang.

The mating system is of major concern for the dynamic management of genetic resources. We investigated the outcrossing rate of six experimental wheat populations, derived from two genetic pools (PA and PB) which have been cultivated at four French sites. The replicates of the two segregating populations have undergone 10 years of multiplication in isolation, with no artificial selection. For each population, 78 individuals were randomly sampled and genotyped for 25 codominant loci revealed by 15 restriction fragment length polymorphism (RFLP) probes. Outcrossing rates were estimated on the basis of the multilocus heterozygote deficiency. Estimates ranged from 2.4 to 10.1 %, depending on the population. The outcrossing rate appeared to be affected by the cultivation site, and also by the interaction between the genetic pool and the cultivation site. No significant pool effect was found over sites. The use of natural or modified outcrossing rates is suggested for the management of gene flows between the subpopulations of a metapopulation. Consequences of recombination events within and between populations are discussed in the context of short-term adaptive response of populations and long-term elimination of weakly deleterious mutations., Le régime de reproduction est un paramètre essentiel pour le pilotage d’un programme de gestion dynamique des ressources génétiques. Cet article s’attache à l’estimation du taux d’allogamie dans six populations expérimentales de blé tendre, issues de deux pools génétiques différents (PA et PB) cultivés dans quatre sites distincts. Chaque population a subi dix années de multiplication en isolement, sans sélection consciente. Dans chacune d’elles, 78 individus ont été aléatoirement échantillonnés et génotypés pour vingt-cinq locus codominants, grâce à quinze sondes RFLP. Les taux d’allogamie ont été estimés à partir de l’hétérozygotie résiduelle multilocus. Un niveau d’allogamie élevé pour cette espèce cléistogame a été observé. Les estimations varient de 2,4 à 10,1 % suivant les populations. Ces taux d’allofécondation dépendent d’une part du site de culture, et d’autre part d’une interaction entre composition génétique initiale et site de culture. L’intérêt de l’allogamie tant pour la génération de nouvelles combinaisons génétiques que pour la purge des mutations faiblement délétères est discuté. L’utilisation des taux naturels d’allogamie pour instaurer des flux de gènes entre les populations est proposée dans l’optique d’une gestion en métapopulation.

The overall objective was to assess the genetic diversity of a collection of native potato varieties originating from the island of Chiloe, to characterize the resistance of these varieties to late blight (Phytophthora infestans) and to inquire about the status of in-situ conservation. The following specific topics was developed: a) conservation in-situ of native Solanum within the great isle of Chiloe and its impact on diversity, b) evaluation of the morphological diversity of the native potatoes that we have collected c) assessment of genetic diversity of the collection by the mean of microsatellite and AFLP markers, d) characterization of field and in-vitro resistances to late blight. Based on the results of the surveys, we can conclude that in-situ maintenance of native potato diversity i is not well preserved, due to strong social and economic changes on the island of Chiloe. There is a clear process of replacing native varieties for commercial cultivars in response to market conditions. Native varieties are present in 80.5% of the farms of Chiloe, but the diversity of varieties has been significantly reduced. The results morphological diversity showed the formation of groups under the popular name and local attributes assigned by the farmers themselves. Molecular evaluation of the collection (SSRs and AFLP) reveals a high degree of genetic diversity. Both markers were consistent in classifying Solanum fernandezianum as the more distant genotype compared to all the others. The SSRs allowed the estimation of the polymorphic information content for seven loci which values ranged between 0.63 to 0.89. Both types of markers, did not provide the same groupings among the accessions. The SSR-based study showed a low differentiation between native potatoes and improved cultivated varieties. The analysis of diversity based on the AFLP was not inconsistent with this result because despite containing only one cultivar (Desiree), the cultivar was grouped with the native varieties. In relation to resistance to late blight, most accessions of native potato fall into the ranks moderately resistant to moderately susceptible., L'objectif global était d'évaluer la diversité génétique d'une collection de variétés de pommes de terre indigènes originaires de l'île de Chiloé, pour caractériser la résistance de ces variétés au mildiou (Phytophthora infestans) et pour en savoir davantage sur l'état de conservation in-situ. Les sujets suivants a été élaboré: a) la conservation in situ de Solanum indigènes à l'île la grande de Chiloé et son impact sur la diversité, b) l'évaluation de la diversité morphologique des pommes de terre indigènes que nous avons recueillis c) l'évaluation de la diversité génétique par marqueurs microsatellites et AFLP, d) la caractérisation du terrain et des résistances in-vitro au mildiou. Sur la base des résultats des enquêtes, nous pouvons conclure que le maintien in situ de la diversité de pommes de terre indigènes n' est pas bien conservé, en raison des forts changes sociaux et économiques sur l'île de Chiloé. Il y a un processus clair de remplacer les variétés indigènes pour les cultivars commerciaux en réponse aux conditions du marché. Les variétés natives sont présents dans 80,5% des fermes de Chiloé, mais la diversité a été considérablement réduite. Les résultats de la diversité morphologique ont montré la formation de groupes sous le nom populaire et des attributs locaux affectés par les agriculteurs eux-mêmes. L'évaluation moléculaire de la collection (SSRs et AFLP) révèle un haut degré de diversité génétique. Les deux marqueurs ont été uniformes dans la classification Solanum fernandezianum comme le génotype plus éloigné. La SSR a permis l'estimation de la teneur des informations polymorphes pour sept loci dont les valeurs se situaient entre 0,63 à 0,89. Les deux types de marqueurs, n'a pas fourni les mêmes groupes parmi les accessions. L'étude SSR basé a montré une faible différenciation entre les pommes de terre indigènes et l'amélioration des variétés cultivées. L'analyse de la diversité sur la base des AFLP n'était pas incompatible avec ce résultat parce que, malgré contenant un seul cultivar (Désirée), le cultivar a été regroupée avec les variétés indigènes. En ce qui concerne la résistance au mildiou, la plupart des accessions sont dans les rangs modérément résistante à modérément sensible.

In situ conservation of crop genetic resources is widely recommended but, as yet, no methods have been developed to rank the genetic entities to preserve and the social organisations to involve. Increased knowledge of the dynamic of agrobiodiversity is essential for the integration of conservation and valorization in the strategies of crop productivity improvement in traditional agrosystems. The highlands of Madagascar have been identified as a key site for rice, Oryza sativa, genetic diversity. To define conservation strategies, we performed multidisciplinary analysis of rice genetic diversity and factors shaping its distribution in the Vakinankaratra region of Madagascar. Individual and collective surveys, collect and characterization of samples of cultivated rice varieties in 1050 farms located in 32 villages were realized. Averages numbers of rice varieties used per village (10.9) and per farm (2.2) are comparables with other traditional agrosystems, nevertheless great regional variability is observed. The determinants of this variability are altitude, production system of villages, type of rice cultivation system and farm economic richness. An important disparity in the frequency of the use of varieties was observed with large proportion of "minor" varieties used by less than 10% of farms. Local seed management is characterized by the lack of selection for varietal purity. The adoption of new practices of seed and variety management, associated with the recent development of upland rice in this region, shows the capacity of the system to innovations. Along with the indica and japonica rice subspecies of O. sativa, we confirmed the presence of an atypical rice group with a preferential habitat of 1250-1750 m. Spatial distribution of genetic diversity was uneven. The most determining factor of this unevenness was the altitude authorising or not the presence of different rice cropping systems and the associated types of varieties. Village and individual farmer's wealth also had a determining role on the amount of rice diversity they hosted. While molecular variance between villages in a given interval of altitude represented 16% of the total variance, within-village variance represented more than 75% of the total, and within-farm variance 70% of within-village variance. This hierarchical distribution of molecular variance suggests that a small number of samples per scale (altitude interval, village and farm) could allow to capture most of the genetic diversity observed. However, within-variety diversity was also important making ex situ conservation strategies impractical and costly. Implications of the within-variety diversity are discussed in terms of adaptive advantages, evolutionary processes, and need for in situ conservation., Mieux connaître les dynamiques de l'agrobiodiversité est indispensable pour détecter les évolutions défavorables et élaborer des stratégies de conservation, en particulier dans les agrosystèmes traditionnels, encore peu affectés par l'intensification agricole. Une étude de la dynamique de la diversité et de la gestion des variétés et semences de riz a été entreprise dans la région de Vakinankaratra. Celle-ci, située au centre des hauts plateaux de Madagascar, se caractérise par une grande diversité agroécologique, des systèmes de production et des systèmes de culture du riz liée, notamment, aux variations de l'altitude (750-1950m). L'étude s'est appuyée, d'une part, sur des enquêtes (collectives et individuelles) auprès de 1050 exploitations réparties dans 32 villages, d'autre part, sur la collecte systématique et la caractérisation des variétés de riz maintenues dans ces villages, au moyen de descripteurs agro-morphologiques et moléculaires. La région héberge non seulement les 3 groupes majeurs d'O. sativa (indica, japonica tropical et japonica tempéré) mais aussi un groupe atypique, non répertorié ailleurs dans le monde. Ces derniers sont des riz irrigués plus proches des indica que des japonica ; leur habitat préférentiel est l'intervalle d'altitude 1250-1750m. La distribution éco-géographique de la diversité est façonnée par, respectivement, l'altitude, les systèmes de production et la richesse des exploitations. Elle est organisée en 4 strates : intervalle d'altitude, village, exploitation et parcelle. A chaque strate, la différentiation génétique entre les sous-ensembles représente jusqu'à 70% de la diversité totale. Les variétés locales ont une structure multi-lignées ; la fréquence des lignées constituantes varie entre exploitations et entre villages. Leurs distributions régionales peuvent être assimilées à des métapopulations fragmentées. Les variétés locales de riz sont des biens communautaires quasi sacrées. Les variétés améliorées cohabitent avec elles sans constituer de véritables menaces. Il existe une grande disparité dans la fréquence d'utilisation des variétés. Dans chaque village, 1-2 " variétés majeures " sont utilisées par plus de 50% des agriculteurs et plusieurs " variétés mineures " par moins de 10% d'entre eux. Les échanges de variétés et de semences sont limités entre villages, plus intenses à l'intérieur de chaque village. Les semences ne se vendent pas mais s'échangent. Un système de valeurs culturelles incite à la sélection pour l'homogénéité. Le système de constitution des lots de semences conduit à une sélection involontaire d'adaptation GxE. Le système vernaculaire de nomination, assez sophistiqué, n'est plus opérationnel qu'à l'échelle village ; il en résulte une faible consistance des noms de variétés entre villages ; et le nombre de variétés n'est plus un bon indicateur de la diversité régionale. L'introduction récente de la riziculture pluviale a engendré une nouvelle dynamique qui bouscule les pratiques traditionnelles de gestion des variétés et des semences. Les signes d'érosion observés parmi les variétés locales, incitent à l'analyse de l'évolution récente (4-5 dernières décennies) de la diversité et à la mise en place d'un observatoire pour le suivi des évolutions à venir. La conservation in-situ de la diversité doit s'inscrire dans des actions intégrées de développement rural. La recherche peut y contribuer par la valorisation des variétés locales dans des schémas de sélection participative et par une conservation dynamique de ces ressources sous forme de populations à large base génétique.