Éditeur(s) : INRA : Institut National de la Recherche Agronomique Université des Antilles. Service commun de la documentation
Extrait de : 52e congrès annuel de la Société caribéenne des plantes alimentaires / 52nd annual meeting of the Caribbean food crops society (CFCS), du 10 au 16 juillet 2016. INRA, CFCS
Description : The Creole pig has always been part of the rural and suburban landscape of Martinique. Currently, this breed is not integrated into a research and conservation program. The Natural Park of Martinique Region (PNRM) has the objective to maintain and valorize the genetic heritage of Martinique?s Creole pig and develop a niche business. Based on PNRM knowledge, some Creole pigs live freely in the mountains in the North, in the South coast and in a few disparate traditional breeders located in the countryside. It is essential to carry out an inventory of the local pig population to propose a scheme for conservation and economic development. In order to favour the appropriation of the Creole pig niche, the PNRM, as a decision maker, acts in a systemic and holistic way by considering the whole Martinican territory and the pig sub-sector: producers involved in the COOPMAR pig farmers? cooperative, researchers of INRA (FWI), the food chain and at least (in a second phase) the consumers and the Martinican society. First of all, the pig farmers are involved (private family farms and specialised pig producers). Researchers and technicians from PNRM and INRA- URZ (Animal production research unit) and INRA-PTEA (Tropical platform in animal experimentation) are performing experimental studies both in controlled conditions and in farms, in order to: i) determine phenotypic and genetic characteristics of Martinique?s Creole pigs in comparison with other pig breeds from the Caribbean area; ii) help at designing genetic management to maintain the population and avoiding inbreeding; iii) help at defining feeding management by a) establishing, at the whole territorial food chain, an inventory of co or by-products available for pig feeding; b) implementing experimental studies in technology for conservation; c) implementing feeding and growing experiments and finally iv) help at defining eco-friendly production systems a) aiming at generate an adequate revenue and b) focusing on ecosystem services such as meat quality, socio-cultural services and circular economy. Le porc créole a toujours fait partie du paysage rural et suburbain de la Martinique. Actuellement, cette race n'est pas intégrée dans un programme de recherches et de conservation. Le parc naturel de la région de la Martinique (PNRM) a l'objectif pour maintenir et valoriser l'héritage génétique du porc créole de la Martinique et pour développer des créneaux. Basé sur la connaissance de PNRM, quelques porcs créoles vivent librement dans les montagnes dans le nord, dans la côte sud et chez quelques éleveurs traditionnels disparates situés dans la campagne. Il est essentiel d'effectuer un inventaire de la population locale de porc pour proposer un plan pour la conservation et le développement économique. Afin de favoriser l'appropriation du créneau créole de porc, le PNRM, comme décideur, agit d'une manière systémique et holistique en considérant tout le territoire de la Martinique et sous-secteur de porc : producteurs impliqués dans la coopérative d'agriculteurs de porc de COOPMAR, les chercheurs d'AICN (FWI), la chaîne alimentaire et au moins (dans une deuxième phase) les consommateurs et la société Martiniquaise. Tout d'abord, les agriculteurs de porc sont impliqués (les fermes privées de famille et les producteurs de porc spécialisés). Les chercheurs et les techniciens de PNRM et AICN URZ (unité de recherches de production animale) et INRA-PTEA (plate-forme tropicale chez l'expérimentation animale) réalisent des études expérimentales dans des conditions commandées et dans les fermes : i) déterminent des caractéristiques phénotypiques et génétiques des porcs créoles de la Martinique en comparaison d'autres races de porc à partir du secteur des Caraïbes ; ii) aide à concevoir la gestion génétique pour maintenir la population et à éviter l'endogamie ; iii) aide à définir la gestion de alimentation a) en établissant, à la chaîne alimentaire territoriale de totalité, à un inventaire de Co ou aux sous-produits disponibles pour l'alimentation de porc ; b) mise en oeuvre des études expérimentales en technologie pour la conservation ; c) mettant en application des expériences de alimentation et croissantes et finalement iv) aide à définir viser qui respecte l'environnement des systèmes de production a) produisent de à revenu approprié et b) se concentrant sur des services d'écosystème tels que la qualité de viande, des services socioculturels et l'économie circulaire.
Siècle(s) traité(s) : 21
Droits : CC-BY-NC-ND - Attribution - Pas d'utilisation commerciale - Pas de modification
Permalien : http://www.manioc.org/fichiers/V16263
V16263

Éditeur(s) : HAL CCSD National Academy of Sciences
Résumé : International audience
Natal philopatry, the return of individuals to their natal area for reproduction, has advantages and disadvantages for animal populations. Natal philopatry may generate local genetic adaptation, but it may also increase the probability of inbreeding that can compromise persistence. Although natal philopatry is well documented in anadromous fishes, marine fish may also return to their birth site to spawn. How philopatry shapes wild fish populations is, however, unclear because it requires constructing multigenerational pedigrees that are currently lacking for marine fishes. Here we present the first multigenerational pedigree for a marine fish population by repeatedly genotyping all individuals in a population of the orange clownfish (Amphiprion percula) at Kimbe Island (Papua New Guinea) during a 10-y period. Based on 2927 individuals, our pedigree analysis revealed that longitudinal philopatry was recurrent over five generations. Progeny tended to settle close to their parents, with related individuals often sharing the same colony. However, successful inbreeding was rare, and genetic diversity remained high, suggesting occasional inbreeding does not impair local population persistence. Local reproductive success was dependent on the habitat larvae settled into, rather than the habitat they came from. Our study suggests that longitudinal philopatry can influence both population replenishment and local adaptation of marine fishes. Resolving multigenerational pedigrees during a relatively short period, as we present here, provides a framework for assessing the ability of marine populations to persist and adapt to accelerating climate change.
ISSN: 0027-8424

hal-01417471
https://hal-univ-perp.archives-ouvertes.fr/hal-01417471
DOI : 10.1073/pnas.1611797113

Éditeur(s) : Elsevier
Résumé : Correlation between DNA microsatellite heterozygosity and growth rate was investigated in two hatchery-propagated stocks of the shrimp Penaeus stylirostris, which had been genetically isolated from wild founders for 17 generations, and from each other for five more generations. presumed demographic history of these populations suggested that they were maintained at small effective population sizes. and this was confirmed by significant changes in allelic frequencies between the two stocks. Despite a small sample size (n = 60) and a small number of loci screened, a significant positive correlation was detected between microsatellite tri-locus heterozygosity and growth rate in one of the two stocks (r = 0.3, P = 0.02). In the other stock (n = 48), the positive correlation was not significant, but the combined test of single locus heterozygote advantage over the three loci was significant (P = 0.005).Use of DNA microsatellite markers, whose selectively neutral status is generally accepted, allowed us to reject the hypothesis of direct overdominance at marker loci as an explanation for an association of growth rate with heterozygosity. The average depression associated with one locus in our case is above or equivalent to the amount observed for a 10% increase of inbreeding in other species. These results suggest that heterozygosity at neutral marker loci is sufficiently well correlated with individual inbreeding coefficients to reveal a significant residual inbreeding load for growth rate in Tahitian P. stylirostris stocks. Inbreeding during hatchery propagation was, thus, insufficient to purge the ancestral load.
Aquaculture (0044-8486) (Elsevier), 2000-04 , Vol. 184 , N. 3-4 , P. 203-219

Droits : 2000 Elsevier Science B.V. All rights reserved
http://archimer.ifremer.fr/doc/2000/publication-753.pdf
DOI:10.1016/S0044-8486(99)00331-2
http://archimer.ifremer.fr/doc/00000/753/

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé :  
In this paper, we report a study of the mating system and gene flow of Symphonia globulifera, a hermaphroditic, mainly bird-pollinated tree species with a large geographic distribution in the tropical Americas and Africa.Using three microsatellites, we analysed 534 seeds of 28 open pollinated families and 164 adults at the experimental site 'Paracou' in French Guiana. We observed, compared to other tropical tree species, relatively high values for the effective number of alleles. Significant spatial genetic structure was detected, with trees at distances up to 150 m more genetically similar than expected at random. We estimated parameters of the mating system and gene flow by using the mixed mating model and the TwoGener approach. The estimated multilocus outcrossing rate, tm, was 0.920. A significant level of biparental inbreeding and a high proportion of full-sibs were estimated for the 28 seed arrays. We estimated mean pollen dispersal distances between 27 and 53 m according to the dispersal models used. Although the adult population density of S. globulifera in Paracou was relatively high, the joint estimation of pollen dispersal and density of reproductive trees gave effective density estimates of 1.6 and 1.3trees/ha. The parameters of the mating system and gene flow are discussed in the context of spatial genetic and demographic structures, flowering phenology and pollinator composition and behaviour.
ISSN: 0018-067X

hal-01032178
https://hal.archives-ouvertes.fr/hal-01032178
DOI : 10.1038/sj.hdy.6800560

Éditeur(s) : HAL CCSD
Résumé : il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : ACTIVITY_REPORT
Understanding genomic evolution in wild populations is of particular importance because evolution is a central process in our understanding of populations’ history and their future response to global changes. In addition to fundamental knowledge, the study of populations’ evolution has wide applications such as conservation/restoration genetics or epidemiology. Indeed, genetic diversity is the ‘fuel’ for populations’ evolution and adaptation to new conditions, and estimating the extent and the geographic structure of genetic diversity, as well as identifying the evolutionary forces behind (demography, gene flow, and adaptation) are thus major challenges in the current context of global changes. [br/]A particular attention is currently devoted to the process of genetic divergence in wild populations, with emphases on gene flow, local adaptation, and their interactions. Indeed, adaptation in wild populations is supported in many species by many kinds of experiments based on both quantitative phenotypic traits and molecular data. However, the processes governing populations’ evolution are poorly understood in the tropical rainforest of Amazonia, and the relative influence of neutral and adaptive processes are continuously discussed. [br/]I am a young scientist interested in the process of genomic divergence in wild (tree) populations. I aimed at understanding how evolution structures the genetic diversity and governs molecular divergence in wild populations, with particular emphases on gene flow and local adaptation. During five years as a young scientist, I worked on answering the following questions, focusing on two tree species occupying vulnerable areas: mainly [i]Eperua falcata[/i] in Amazonia and, to a lesser extent, [i]Abies alba[/i] in the Mediterranean area.[br/][u]Scientific questions:[/u][br/]- Which evolutionary drivers are responsible of the structure of genetic diversity in wild populations occupying wide areas? This question was addressed at different geographical scales: from large (regional) to very local (microgeographic) scales. [br/]- What is the relative influence of neutral (gene flow, inbreeding) and adaptive drivers in the process of genetic divergence?[br/]- Is microgeographic adaptation possible in spite of extensive gene flow between populations occupying the extreme boundaries of an ecological gradient? [br/]- What is the extent of natural selection in the (whole) genome of wild populations? [br/][br/]My research work is at the interface between three promising disciplines: Evolutionary genomics (i.e. the study of populations evolution and the evolutionary drivers behind), Bioinformatics (i.e. the treatment of next-generation data), and Bayesian modelling (i.e. the empirical calibration of complex mechanistic model). I intend to take advantage of the recent advances in sequencing and informatic technologies to bring up to date the field of ecological genetics and evolutionary biology, by developing modern research strategies to study the process of genomic divergence in wild populations.
https://hal.archives-ouvertes.fr/hal-01204218

hal-01204218
https://hal.archives-ouvertes.fr/hal-01204218
PRODINRA : 286326

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
In French Guiana, severe cases of toxoplasmosis in immunocompetent patients are associated with atypical strains of Toxoplasma gondii linked to a wild neotropical rainforest cycle and a higher genetic diversity than usually observed for T. gondii isolates from anthropized environment. This raises the question of the impact of anthropization of the natural environment, on genetic diversity and on the population structure of T. gondii. However, few data are available on strains circulating in the anthropized areas from French Guiana. Seropositive animals originating mainly from anthropized sub-urban areas and punctually from wild environment in French Guiana were analyzed for T. gondii isolation and genotyping. Thirty-three strains were obtained by bioassay in mice and compared with 18 previously reported isolates chiefly originating from the Amazon rainforest. The genotyping analysis performed with 15 microsatellite markers located on 12 different chromosomes revealed a lower genetic diversity in the anthropized environment. Results were analyzed in terms of population structure by clustering methods, Neighbor-joining trees reconstruction based on genetic distances, F(ST,) Mantel's tests and linkage disequilibrium. They clearly showed a genetic differentiation between strains associated to the anthropized environment and those associated to the wild, but with some inbreeding between them. The majority of strains from the anthropized environment were clustered into additional lineages of T. gondii that are common in the Caribbean. In conclusion the two environmental populations "wild" and "anthropized" were genetically well differentiated. The anthropization of the environment seems to be accompanied with a decreased diversity of T. gondii associated with a greater structure of the populations. We detected potential interpenetration and genetic exchanges between these two environmental populations. As a higher pathogenicity in human of "wild" genotypes has been described, the interpenetration of both environments leads to hybridization between strains that may be at risk for human health.
ISSN: 1567-1348

pasteur-00654105
https://hal-riip.archives-ouvertes.fr/pasteur-00654105
https://hal-riip.archives-ouvertes.fr/pasteur-00654105/document
https://hal-riip.archives-ouvertes.fr/pasteur-00654105/file/Mercier_et_al_IGE2011.pdf
DOI : 10.1016/j.meegid.2011.05.003

Éditeur(s) : Springer
Résumé : The great fecundity and very high larval mortality of most marine invertebrates and fish make possible substantial variance in the number of offspring contributed by adults to subsequent generations. The reproductive success of such organisms may thus resemble a sweepstakes lottery, in which a minority of progenitors succeeds in replacing an entire population, while the majority fails to procreate. One specific prediction of this hypothesis, that genetic diversity of newly settled cohorts should be less than that of the adult population, is tested in the present study. Microsatellite DNA markers were examined in naturally spawned juvenile European flat oysters Ostrea edulis (L.), collected over a 12-day period in 1993 from the western Mediterranean Sea, near Sete, France (43 degrees 32'N, 3 degrees 56'E) and grown out for a period of up to 10 months. Variation in these juveniles was compared to that in a pooled sample of adults collected in 1994 from two locations (Thau Lagoon and Port St. Louis) that had statistically homogeneous allelic frequencies. Though nearly twice as large as the pooled adult sample, the juvenile sample had only 60% of the adult allelic diversity. Analyses of linkage disequilibrium and kinship, as well as estimation of the effective number of parents, suggested that 10-20 adults produced this juvenile cohort. This observation supports the hypothesis of sweepstakes reproductive success and suggests that partial inbreeding may occur even in species with large populations and dispersing planktonic larvae.
Marine Biology (0025-3162) (Springer), 2007-03 , Vol. 150 , N. 6 , P. 1173-1182

Droits : 2007 Springer
http://archimer.ifremer.fr/doc/2007/publication-2616.pdf
DOI:10.1007/s00227-006-0441-y
http://archimer.ifremer.fr/doc/00000/2616/

Éditeur(s) : Actes du 6e colloque national BRG, La Rochelle, 2-3-4 octobre 2006
Résumé : Previous studies have shown heritable variation in larval developmental traits in the Pacific oyster Crassostrea gigas. In order to study the genetic consequences of production of oyster larvae in hatcheries, two factors, specific to hatcheries, were examined: the effect of discarding the smallest larvae (i.e. culling) and the effect of temperature (20°C versus 26°C). A mixed-family approach was used in order to infer the genetic composition of larval populations and family assignment, limiting possible environmental bias and allowing the study of a relatively large number of families using a limited number of larval tanks. Our results show that three multiplexed highly polymorphic microsatellite markers are a powerful tool for family assignment and, consequently, for the study of bivalve larvae genetics. Culling, by selective sieving of the smallest larvae is an advantageous practice at a phenotypic scale as it reduced variance in larval size, variance of developmental rate and time to settlement. Culling of 50% of the larval population only led to 15% less spat, showing a positive phenotypic correlation between larval growth and settlement success. However, culling represents a substantial risk for diversity loss, because it increases the variance of reproductive success among parental oysters. The effective population sizes of early settling cohorts of settlement were lower than those of later ones. Our results show that the settlement of slow growing larvae significantly contributes to minimizing the variability of reproductive success and therefore to maximizing genetic diversity. These results corroborate the low estimations of variability of broodstocks sampled in several French commercial hatcheries, relative to natural populations. The genetic composition of the larval population and the resulting spat was significantly different between the two tested temperatures, revealing genotype x environment interaction for survival. Similarly, genotype x environment interaction was also observed for larval growth as a higher temperature exerted a positive influence on the expression of genetic variability for this trait. Consequently, we can conclude that a temperature of 26°C coupled with culling, to common practice in oyster hatcheries, is likely to amplify the selection pressure for fast growing larvae. To test for this hypothesis, we compared larval developmental traits in the progeny of a hatchery broodstock closed for 7 generations, with the progeny of wild oysters and the two possible hybrids. Our results show that selection of fast growing larvae can counteract presumed inbreeding depression, due to higher mean relatedness among hatchery broodstock than in the wild. Genetic effects of intensive rearing conditions at larval stage are significant and should be taken into account in hatchery practices, especially in terms of genetic diversity management.
Afin d'étudier les conséquences génétiques des pratiques de production en écloserie d'huître creuse, deux facteurs ont été examinés : l'élimination des petites larves et la température. Nos résultats montrent que l'assignation de parenté par marqueurs microsatellites est un outil performant pour les études génétiques en phase larvaire de familles élevées en mélange. Bien qu'avantageux d'un point de vue phénotypique, le tamisage sélectif représente un risque de perte de diversité. La fixation des larves à croissance lente permet en effet de minimiser la variabilité du succès reproducteur et de fait, de maximiser la variabilité génétique. Ces résultats corroborent les estimations de variabilité sur les stocks d'écloseries françaises où l'on constate une diversité allélique inférieure à celle de populations issues du milieu naturel. La température exerce également une influence sur la précocité de l'expression de la variabilité génétique pour la croissance larvaire. Ainsi une température élevée associée à une procédure de tamisage peut amplifier l'effet sélectif. Enfin, la sélection de larves à croissance rapide semble démontrée, s'opposant à la dépression de consanguinité présumée. Les conditions d'élevage peuvent donc avoir un effet génétique significatif qui devrait être pris en considération dans les pratiques d'écloserie, notamment dans la gestion de la diversité génétique.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2006/acte-1505.pdf
http://archimer.ifremer.fr/doc/00000/1505/

Éditeur(s) : Elsevier
Résumé : Two populations of the Latin American shrimp Penaeus (Litopenaeus)stylirostris domesticated in Hawaii and in New Caledonia were previously shown to be genetically differentiated and proven highly inbred. In New Caledonia, where different Vibriosis affect shrimp production and antibiotic use is banned in growing ponds, the Hawaiian population was introduced to increase the allelic variability available for local shrimp farmers and start a genetic improvement program. Growth and survival rates of the two pure populations and the two-way F-1-hybrids obtained by breeding Hawaiian animals with New Caledonian animals were assessed in several simple experiments (earthen ponds, floating cages and experimental infection challenges) during two years on two successive generations. Results were very consistent: F-1-hybrids growth rates in earthen ponds were 37% (+/-7% SD) higher than for pure populations. Cage experiments demonstrated no competition between the different populations when reared together or separately in a common environment. The F-1-hybrids also showed better survival rates in all experiments. Combining the results on growth and survival rates leads to the conclusion that biomass production is much higher with F-1-hybrid populations than with pure populations using the same quantity of juveniles stocked: biomass production in ponds was increased 1.4 and 2.3 times on year I and year 2 respectively, and 1.9 times in floating cages. The advantage of growing F-1-hybrids appeared proportionally higher when environmental and sanitary conditions led to poorer survival (34% in year 2 vs. 56% in year 1). These results are a good example of performance improvement by heterosis effect and/or of performance loss due to inbreeding in the pure populations. This study demonstrates that aquaculture industries which cannot afford large selection programs may benefit from using two different inbred parental stocks to produce F-1-hybrids for each commercial growout. This is notably true when only inbred populations are available, or when introduction of genetic variability from the wild or from other genetic resources represents a zoo-sanitary risk. In our case, the expected increase in L stylirostris production could be around 85% (according to our average results) if producers keep stocking their ponds at their current densities using F-1-hybrids. However, for sustainability reasons, it is advisable to stock F-1-hybrid animals at lower densities, the gain in performance allowing producing the same amount of biomass with less input. (C) 2008 Elsevier B.V. All rights reserved.
Aquaculture (0044-8486) (Elsevier), 2008-06 , Vol. 278 , N. 1-4 , P. 43-50

Droits : 2008 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/2008/publication-4316.pdf
DOI:10.1016/j.aquaculture.2008.03.018
http://archimer.ifremer.fr/doc/00000/4316/

Éditeur(s) : Caribbean & Latin American Aquaculture 2007, 6 - 9 novembre 2007, San Juan, Puerto Rico
Résumé : The Pacific blue shrimp Litopenaeus stylirostris was introduced in New Caledonia thirty years ago. Because of its high inbreeding, a SPF strain domesticated in Hawaii, genetically differentiated from the Caledonian strain, had to be imported. The two strains’ reproductive performances were compared at different periods and cross breedings were assessed. The average results show that Caledonian animals give twice as many nauplii than the Hawaiian animals. The best cross breeding is obtained with Caledonian male x Hawaiian female. A possible explanation is the later age or weight of maturity for the Hawaiian strain compared to the Caledonian strain, difference which could come from the geographical origins and/or the zootechnical and climatic domestication conditions.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00198/30881/29249.pdf
http://archimer.ifremer.fr/doc/00198/30881/

Éditeur(s) : HAL CCSD Springer Verlag/EDP Sciences
Résumé : International audience
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.
ISSN: 1286-4560

hal-01502942
https://hal-agroparistech.archives-ouvertes.fr/hal-01502942
https://hal-agroparistech.archives-ouvertes.fr/hal-01502942/document
https://hal-agroparistech.archives-ouvertes.fr/hal-01502942/file/art_10.1007_s13595-015-0508-3-1_%7B869D58F4-272C-491F-A903-DAD6CDBDC042%7D.pdf
DOI : 10.1007/s13595-015-0508-3

Résumé : Genetic consequences of production of Pacific oyster larval in hatchery: drift and selective pressures related to rearing practices. In order to study the genetic consequences of production of oyster larvae in hatcheries, two factors were examined: the effects of discarding the smallest larvae (i.e. culling) and temperature effects. A mixed-family approach was used in order to infer the genetic composition of the larval population. The results show that high polymorphic microsatellite-based family assignment is a powerful tool for the study of bivalve larvae genetics. Culling by selective sieving is an advantageous practice at a phenotypic scale, but also represents a substantial risk for diversity loss if parentage assignment is not introduced as a breeding practice. Settlement of slow growing larvae contributes to minimizing the variability of reproductive success and therefore to maximizing genetic diversity. These results corroborate the lower estimations of variability made on broodstocks from French commercial hatcheries relative to natural populations. Temperature exerts an influence on the expression of genetic variability for larval growth. A temperature of 26°C, coupled with culling could amplify the selective effect. Furthermore, selection of fast growing larvae has proven to counteract inbreeding depression at this stage. Genetic effects of intensive rearing conditions are significant and should be taken into account in hatchery practices, especially in terms of genetic diversity management.
Afin d'étudier les conséquences génétiques des pratiques de production de larves en écloserie d'huître creuse, deux facteurs ont été examinés : l'effet de l'élimination des plus petites larves et l'effet de la température. Une approche de familles élevées en mélange a été utilisée afin d'avoir accès à l'information génétique au stade larvaire. Les résultats obtenus montrent que l'assignation de parenté basée sur des marqueurs microsatellites hautement discriminants est un outil performant pour les études génétiques en phase larvaire. Bien qu'avantageuse d'un point de vue phénotypique, la pratique de tamisage sélectif représente un risque substantiel de perte de diversité si cette pratique n'est pas associée à une assignation de parentée par empreintes génétiques. La fixation des larves à croissance lente permet de minimiser la variabilité du succès reproducteur et de fait, de maximiser la variabilité génétique. Ces résultats corroborent les estimations de variabilité sur les stocks d'écloseries commerciales françaises où l'on constate une diversité allélique inférieure à celle de populations issues du milieu naturel. La température exerce également une influence sur la précocité de l'expression de la variabilité génétique pour la croissance larvaire. Ainsi une température élevée (26°C) associée à une procédure de tamisage peut amplifier l'effet sélectif. Enfin, la sélection de larves à croissance rapide semble démontrée, s'opposant à la dépression de consanguinité présumée en phase larvaire. Les conditions d'élevage peuvent donc avoir un effet génétique significatif qui devrait être pris en considération dans les pratiques d'écloserie, notamment dans la gestion de la diversité génétique.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2006/rapport-1459.pdf
http://archimer.ifremer.fr/doc/00000/1459/

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : Background. In wild plant populations, genetic divergence within continuous stands is common, sometimes at very short geographical scales. While restrictions to gene flow combined with local inbreeding and genetic drift may cause neutral differentiation among subpopulations, microgeographical variations in environmental conditions can drive adaptive divergence through natural selection at some targeted loci. Such phenomena have recurrently been observed in plant populations occurring across sharp environmental boundaries, but the interplay between selective processes and neutral genetic divergence has seldom been studied.[br/]Methods. We assessed the extent of within-stand neutral and environmentally-driven divergence in the Neotropical tree [i]Eperua falcate Aubl[/i]. (Fabaceae) through a genome-scan approach. Populations of this species grow in dense stands that cross the boundaries between starkly contrasting habitats. Within-stand phenotypic and candidate-gene divergence have already been proven, making this species a suitable model for the study of genome-wide microgeographic divergence. Thirty trees from each of two habitats (seasonally flooded swamps and well-drained plateaus) in two separate populations were genotyped using thousands of AFLPs markers. To avoid genotyping errors and increase marker reliability, each sample was genotyped twice and submitted to a rigorous procedure for data cleaning, which resulted in 1196 reliable and reproducible markers.[br/]Results. Despite the short spatial distances, we detected within-populations genetic divergence, probably caused by neutral processes, such as restrictions in gene flow. Moreover, habitat-structured subpopulations belonging to otherwise continuous stands also diverge in relation to environmental variability and habitat patchiness: we detected convincing evidence of divergent selection at the genome-wide level and for a fraction of the analyzed loci (comprised between 0.25% and 1.6%). Simulations showed that the levels of differentiation for these outliers are compatible with scenarios of strong divergent selection
ISSN: 1932-6203

hal-01204220
https://hal.archives-ouvertes.fr/hal-01204220
https://hal.archives-ouvertes.fr/hal-01204220/document
https://hal.archives-ouvertes.fr/hal-01204220/file/journal.pone.0121394.PDF
PRODINRA : 287494

Éditeur(s) : HAL CCSD
Résumé : In this paper we report a study of the mating system and gene flow of Sextonia rubra, a hermaphroditic, insect pollinated tropical tree species with a geographic distribution in the Guyana Plateau and the Amazon. Using five microsatellites we analysed 428 seeds of 27 open pollinated families at the experimental site "Paracou" in French Guiana. We observed, compared to other tropical tree species, a high level of genetic diversity. We estimated parameters of the mating system and gene flow by using the mixed mating model and the TwoGenerapproach. The estimated multilocus outcrossing rate, tm, was 0.992 indicating nearly complete outcrossing. A significant level of biparental inbreeding and a small proportion of full-sibs were estimated for the 27 seed arrays. The differentiation of allelic frequencies among the pollen pools was ΦFT = 0.061. We estimated mean pollen dispersal distances between 65 m and 89 m according to the dispersal models used. The joint estimation of pollen dispersal and density of reproductive trees gave an effective density estimate of 2.1-2.2 trees/ha
Silvae genetica

hal-01031483
https://hal.archives-ouvertes.fr/hal-01031483

Résumé : The tropical seabass Lates calcarifer was introduced in Tahiti in 1984 and then was domesticated without other introduction. Three successive generations have been obtained in captivity. Tissue samples of the 38 animaIs which represent the total Tahitian broodstock were preserved in alcohol to be genotyped with four microsatellite markers (Yue et al., 2001). Three of four described markers were successfully transferred to the laboratory of genetics of Tahiti (marker LcaM01, LcaM02, LcaM03), as the revelation technology available locally did not allow the use of LcaM04 in routine. The results show that the genetic diversity of the tahitian broodstock is not equivalent of the one of the species, which could be explained by the small size of the founder population, which is consistant with the history of the Tahitian population. The structuration of the 4th generation into several batches obtained from different parents appears to be the minimum management procedure to limit inbreeding.
Le loup tropical Lates calcarifer a été introduit à Tahiti en 1984 puis domestiqué sans apport d'animaux extérieurs. Trois générations successives ont été obtenues en captivité. Des prélèvements de tissus sur les 38 géniteurs qui constituent l'intégralité du stock de reproducteurs tahitiens sont conservés dans l'alcool pour être génotypés à l'aide de quatre marqueurs microsatellites (Yue et al., 2001). Trois des quatre marqueurs décrits ont pu être transférés avec succès au laboratoire de génétique de Tahiti (marqueurs LcaM01, LcaM02, LcaM03), la technique de révélation disponible localement ne permettant pas d'utiliser LcaM04 en routine. Les résultats montrent qu'on ne dispose pas à Tahiti de toute la variabilité génétique de l'espèce, ce qui pourrait s'expliquer, compte tenu de l'histoire de cette population, par un faible nombre de géniteurs fondateurs. La structuration de la 4ème génération en plusieurs lots issus de parents différents apparaît comme la mesure de gestion minimale pour limiter la consanguinité au sein de cette population.

Droits : 2003 Ifremer
http://archimer.ifremer.fr/doc/00142/25300/23372.pdf
http://archimer.ifremer.fr/doc/00142/25300/

Éditeur(s) : PSIC 11 - 11th Pacific Science Inter-Congress : Pacific Countries and their Ocean: Facing Local and Global Changes / 2nd Symposium on French Research in the Pacific. March 2 - 6, 2009 Tahiti, French Polynesia
Résumé : Shrimp farming in New Caledonia relies on the culture of a domesticated strain of Litopenaeus stylirostris introduced from Mexico at a time when genetic principles were of little or no consideration. Since then, advances in agriculture and for some aquatic species of importance led caledonian shrimp farmers to reconsider the appropriateness of a genetic improvement strategy adapted to local biotechnical and economical constraints. This questioning involves many different and interrelated aspects: scientific and technologic (genetics, biosecurity, quarantine, ), economic and organizational (financing, diffusion of genetic improvement) and pedagogic (awareness of farmers). Local institutions, producers associations, research centre and sanitary services associated to carry on the test of a first improvement strategy based on the crossing of different strains of L. stylirostris. This conceptually simple approach aimed at eliminating inbreeding, the first genetic limitating factor of improvement in captive populations. A second domesticated strain was obtained from Hawaii by the caledonian farmers, imported through a quarantine under the control of the zoosanitary local authorities, and reproduced and tested as pure or crossbred stocks by Ifremer within the framework of an interdisciplinary research project financed by caledonian institutions. Present results for hybrids (better growth and survival in the absence of virus) demonstrate the validity of this approach. They also bring out the importance to simultaneously integrate in a development scheme, a breeding centre to maintain and reproduce disease free breeders. This strategy and organization, tested in New Caledonia, could possibly be of benefit to other small scale aquaculture activities in the pacific islands.
La filière crevetticole de Nouvelle-Calédonie s’est développée jusqu’à aujourd’hui à partir d’un stock domestiqué de Litopenaeus stylirostris introduit d’Amérique à une époque où les principes de base en génétique n’étaient pas ou peu appliqués en aquaculture. Les avancées récentes en agriculture et chez quelques espèces aquacoles d’importance mondiale ont conduit les acteurs de cette filière à se poser la question de la mise en place d’une stratégie d’amélioration génétique adaptée aux contraintes biotechniques et économiques locales. Cette réflexion comportait à la fois des aspects scientifiques et technologiques (génétique, biosécurité, quarantaine, conservatoire), économiques et organisationnels (coût de l’opération, modalité de diffusion du progrès attendu), pédagogiques (sensibilisation des fermiers). Des acteurs d’horizons différents (institutions locales, association de producteurs, centre de recherche, police zoosanitaire) se sont associés pour monter une opération de testage d’une première stratégie d’amélioration par croisement de souches de la même espèce. Cette stratégie conceptuellement simple visait l’élimination du premier facteur génétique de limitation des performances d’élevage d’une population captive, à savoir une consanguinité d’autant plus élevée que le nombre de géniteurs fondateurs était faible. Une seconde souche domestiquée a ainsi été acquise à Hawaii par les producteurs calédoniens, contrôlée en quarantaine par les services vétérinaires calédoniens en charge de la réglementation sanitaire, reproduite et testée pure et en croisement par l’Ifremer dans le cadre d’un projet de recherche pluridisciplinaire plus large financé par les institutions du Pays. Les résultats obtenus démontrent l’intérêt de la démarche (meilleure croissance, meilleure survie en l’absence de virus). Mais ils montrent aussi l’utilité d’intégrer simultanément dans le plan de développement de la filière une stratégie de conservation des souches parentales afin de disposer de géniteurs exempts de pathogènes. Cette stratégie et cette organisation testées en Nouvelle-Calédonie pourraient vraisemblablement être profitables à d’autres filières aquacoles modestes, en particulier dans les pays insulaires du Pacifique.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00198/30879/29247.pdf
http://archimer.ifremer.fr/doc/00198/30879/

Éditeur(s) : Elsevier
Résumé : The Latin American shrimp Litopenaeus stylirostris was introduced in three different Pacific islands (Tahiti, New Caledonia via Tahiti, and Hawaii) and hatchery-propagated for 7-25 generations to develop shrimp farming based on these domesticated stocks. Three microsatellite markers have been used in an attempt to assess the genetic bases of the populations available to start a selective breeding program. The comparison of eight hatchery stocks (five New Caledonian, two Hawaiian and one Tahitian stocks) and one wild Ecuadorian population showed a much lower variability in the domesticated stocks than in the wild population, especially in New Caledonia and Tahiti (2-3.7 vs. 14-27 alleles per locus; 20-60% vs. 90% expected heterozygosity). The Tahitian and the New Caledonian stocks share the same alleles, suggesting that the loss of alleles occurred during the common past of these populations. On the contrary, New Caledonian and Hawaiian populations share only one common allele at the three loci studied. Although the low genetic variability and the resulting inbreeding of the New Caledonian stocks do not seem to affect their present performance, the results of this study demonstrate the usefulness of the introduction of new stocks in order to increase the potential responses to new controlled or uncontrolled selective pressures. The introduction in New Caledonia of the Hawaiian domesticated stocks, which would provide the local shrimp industry with 40% of the allelic diversity of the species, is advised and preferred to the one of wild animals in order to take advantage (i) of the spontaneous selection which occurred during domestication and (ii) of their favourable sanitary "specific pathogen free" status (no presence of four viruses: WSV, YHV, IHHNV, TSV) which limits the risk of introduction of pathogens.
La crevette d'Amérique latine Litopaenus stylirostris a été introduite dans trois îles du Pacifique (à Tahiti, en Nouvelle-Calédonie via Tahiti, et à Hawaii), et a été ensuite reproduite en écloserie pendant 7 à 25 générations à des fins d'aquaculture. Trois marqueurs microsatellites ont été utilisés pour évaluer les bases génétiques des populations disponibles pour le démarrage d'un programme d'amélioration génétique. L'étude comparative de 8 populations domestiquées (cinq néo-calédoniennes, deux hawaiiennes et une tahitienne) et d'une population sauvage d'Equateur révèle une variabilité très réduite dans les populations d'élevage, en particulier en Nouvelle-Calédonie et à Tahiti (2 à 3.7 allèles par locus au lieu de 14 à 27 en population sauvage ; 20% à 60% d'hétérozygotie au lieu de 90%). Les souches tahitiennes et calédoniennes disposent des mêmes allèles, ce qui suggère que la perte d'allèles a eu lieu lors de l'histoire commune des ces populations. A l'inverse, les populations néo-calédoniennes et hawaiiennes n'ont en commun qu'un seul allèle sur les 3 locus étudiés. Bien que la très faible variabilité génétique du cheptel calédonien ne semble pas affecter ses performances actuelles, les résultats de cette étude démontrent l'utilité de l'introduction de variabilité afin d'augmenter la capacité de réponse à de nouvelles pressions de sélection (contrôlées ou non). L'introduction des souches hawaiiennes en Nouvelle-Calédonie qui permettrait à la filière locale de disposer de 40% de la diversité allélique de l'espèce) est préconisée de préférence à celle d'animaux sauvages afin de bénéficier (i) de la sélection spontanée qu'elles ont subi lors de leur domestication et (ii) de leur statut sanitaire « specific pathogen free, SPF » (absence de 4 virus : WSV, YHV, IHHNV, TSV) qui limite les risques de transferts de pathogènes.
Aquatic Living Resources (0990-7440) (Elsevier), 2003-12 , Vol. 16 , N. 6 , P. 501-508

Droits : 2003 Published by Elsevier, Paris.
http://archimer.ifremer.fr/doc/2003/publication-596.pdf
DOI:10.1016/j.aquliv.2003.07.001
http://archimer.ifremer.fr/doc/00000/596/