The impact of genomic selection on genetic diversity and genetic gain in three French dairy cattle breeds

International audienceAbstractBackgroundIn France, implementation of genomic evaluations in dairy cattle breeds started in 2009 and this has modified the breeding schemes drastically. In this context, the goal of our study was to understand the impact of genomic selection on the genetic diversity of bulls from three French dairy cattle breeds born between 2005 and 2015 (Montbéliarde, Normande and Holstein) and the factors that are involved.MethodsWe compared annual genetic gains, inbreeding rates based on runs of homozygosity (ROH) and pedigree data, and mean ROH length within breeds, before and after the implementation of genomic selection.ResultsGenomic selection induced an increase in mean annual genetic gains of 50, 71 and 33% for Montbéliarde, Normande and Holstein bulls, respectively, and in parallel, the generation intervals were reduced by a factor of 1.7, 1.9 and 2, respectively. We found no significant change in inbreeding rate for the two national breeds, Montbéliarde and Normande, and a significant increase in inbreeding rate for the Holstein international breed, which is now as high as 0.55% per year based on ROH and 0.49% per year based on pedigree data (equivalent to a rate of 1.36 and 1.39% per generation, respectively). The mean ROH length was longer for bulls from the Holstein breed than for those from the other two breeds.ConclusionsWith the implementation of genomic selection, the annual genetic gain increased for bulls from the three major French dairy cattle breeds. At the same time, the annual loss of genetic diversity increased for Holstein bulls, possibly because of the massive use of a few elite bulls in this breed, but not for Montbéliarde and Normande bulls. The increase in mean ROH length in Holstein may reflect the occurrence of recent inbreeding. New strategies in breeding schemes, such as female donor stations and embryo transfer, and recent implementation of genomic evaluations in small regional breeds should be studied carefully in order to ensure the sustainability of breeding schemes in the future

Sunlight-Exposed Biofilm Microbial Communities Are Naturally Resistant to Chernobyl Ionizing-Radiation Levels

BACKGROUND: The Chernobyl accident represents a long-term experiment on the effects of exposure to ionizing radiation at the ecosystem level. Though studies of these effects on plants and animals are abundant, the study of how Chernobyl radiation levels affect prokaryotic and eukaryotic microbial communities is practically non-existent, except for a few reports on human pathogens or soil microorganisms. Environments enduring extreme desiccation and UV radiation, such as sunlight exposed biofilms could in principle select for organisms highly resistant to ionizing radiation as well. METHODOLOGY/PRINCIPAL FINDINGS: To test this hypothesis, we explored the diversity of microorganisms belonging to the three domains of life by cultivation-independent approaches in biofilms developing on concrete walls or pillars in the Chernobyl area exposed to different levels of radiation, and we compared them with a similar biofilm from a non-irradiated site in Northern Ireland. Actinobacteria, Alphaproteobacteria, Bacteroidetes, Acidobacteria and Deinococcales were the most consistently detected bacterial groups, whereas green algae (Chlorophyta) and ascomycete fungi (Ascomycota) dominated within the eukaryotes. Close relatives to the most radio-resistant organisms known, including Rubrobacter species, Deinococcales and melanized ascomycete fungi were always detected. The diversity of bacteria and eukaryotes found in the most highly irradiated samples was comparable to that of less irradiated Chernobyl sites and Northern Ireland. However, the study of mutation frequencies in non-coding ITS regions versus SSU rRNA genes in members of a same actinobacterial operational taxonomic unit (OTU) present in Chernobyl samples and Northern Ireland showed a positive correlation between increased radiation and mutation rates. CONCLUSIONS/SIGNIFICANCE: Our results show that biofilm microbial communities in the most irradiated samples are comparable to non-irradiated samples in terms of general diversity patterns, despite increased mutation levels at the single-OTU level. Therefore, biofilm communities growing in sunlight exposed substrates are capable of coping with increased mutation rates and appear pre-adapted to levels of ionizing radiation in Chernobyl due to their natural adaptation to periodical desiccation and ambient UV radiation

Variabilité spatio-temporelle de la reproduction chez une espèce pérenne monoïque: Le cas du sapin pectiné, Abies alba Miller, en limite sud de son aire de répartition

This study focuses on the spatio-temporal variability of reproduction in silver fir(Abies alba), in its French rear edge populations in the Mont Ventoux and Lure mountain. Usually, marginal populations contrast from core populations with lower and more variable densities. In our populations of rs, we found that lower density leads to higher selfing rates through a mass-action law at both population and individual levels. As a consequence, germinative abilities were lower for seeds from lower density populations, mainly because of inbreeding depression. But this was balanced by a higher survival rates at the seedling stage. A more efficient genetic purge could explain this. However, in our populations, a lower density also induced a lower effective seed production, through an increased rate of empty seeds. This can result from pollen limitation. Indeed, genetic analyses revealed a rather high spatial genetic structure of pollen pool, indicating a limited dispersal with a mean dispersal distance between 20 and 50m. This limited dispersal also induced a high inter-individual variability of the mating system mainly due to variations of local density and individual pollen production. Finally, we found strong inter-annual variations of the pollen pools : giving an inter-mothers differentiation of 8%, we obtained an inter-annual différenciation of 13% within mothers. The year with the higher pollen productions also presented the lower overall genetic diversity. Thus this study confirms the necessity to consider multiple years in studies on the reproduction of a perennial tree such as fir, either for theoretical concerns of for practical questions focused on the management of genetic diversity.Cette thèse s'intéresse aux variations spatio-temporelles de la reproduction du sapin pectiné (Abies alba), en limite sud de son aire de répartition dans les populations du mont Ventoux et de la montagne de Lure. En général, les populations marginales présentent des densités faibles et variables. Pour nos populations de sapins, nous avons montré que les densités faibles entraînent une augmentation des taux d'autofécondation par loi d'action de masse, à l'échelle de la population mais également individuelle. Les populations moins denses présentent également une réduction du taux de germination par expression de la dépression de consanguinité, mais qui est compensée par une meilleure survie des semis pouvant provenir d'une purge plus efficace du fardeau génétique. Cependant, la diminution de la densité entraîne dans nos populations une baisse de la production efficace de graines par augmentation du taux de graines vides, probablement à cause d'une dispersion du pollen limitée. En effet, nos analyses génétiques conduisent à une distance de dispersion moyenne estimée de 20 à 50m. Cette faible dispersion induit également une forte variabilité individuelle du régime de reproduction liée aux variations locales de densité et de productions individuelles de pollen. Finalement, nous avons trouvé des variationsinter-annuelles importantes de la structure génétique spatiale du nuage de pollen avec une différenciation entre arbres-mères de 8% et une différenciation entre années au sein des mères de 13%. Les années avec les plus fortes productions de pollen étaient également celles avec la plus faible diversité génétique globale. Cette étude confirme donc la nécessité de considérer de multiples années quand on s'intéresse à la reproduction d'une espèce pérenne comme le sapin, à la fois pour des études théoriques et pour des questions centrées sur la gestion de la diversité

Variabilité spatio-temporelle de la reproduction chez une espèce pérenne monoïque: le cas du sapin pectiné, Abies alba Miller, en limite sud de son aire de répartition

Diplôme : Dr. d'UniversitéThis study focuses on the spatio-temporal varibility of reproduction in silver fir (Abies alba), in its French rear edge populations in the Mont Ventoux and Lure mountain. Usually, marginal populations contrast from core populations with lower and more variable densities. In our populations of firs, we found that lower densitiy leads to higher selfing rates through a mass-action law at both population and individual levels. As a consequence, germinative abilities were lower for seeds from lower density populations, mainly because of inbreeeding depression. But this was balanced by a higher survival rates at the seedling stage. A more efficient genetic purge could explain this. However, in our populations, a lower density also induced a lower effective seed production, through an increased rate of empty seeds. This can result from pollen limitation. Indeed, genetic analyses revealed a rather high spatial genetic structure of pollen pool, indicating a limited dispersal with a mean dispersal distance between 20 and 50m. This limited dispersal also induced a high interindividual variability of the mating system mainly due to variations of local density and individual pollen production. Finally, we found strong inter-annual variations of the pollen pools : giving an inter-mothers differentiation of 8%, we obtained an inter-annual differenciation of 13% within mothers. The year with the higher pollen productions also presented the lower overall genetic diversity. Thus this study confirms the necessity to consider multiple years in studies on the reproduction of a perennial tree such as fir, either for theoretical concerns of for practical questions focused on the management of genetic diversityCette thèse s'intéresse aux variations spatio-temporelles de la reproduction du sapin pectiné (Abies alba), en limite sud de son aire de répartition dans les populations du mont Ventoux et de la montagne de Lure. En général, les populations marginales présentent des densités faibles et variables. Pour nos populations de sapins, nous avons montré que les densités faibles entraînent une augmentation des taux d'autofécondation par loi d'action de masse, à l'échelle de la population mais également individuelle. Les populations moins denses présentent également une réduction du taux de germination par expression de la dépression de consanguinité, mais qui est compensée par une meilleure survie des semis pouvant provenir d'une purge plus efficace du fardeau génétique. Cependant, la diminution de la densité entraîne dans nos populations une baisse de la production efficace de graines par augmentation du taux de graines vides, probablement à cause d'une dispersion du pollen limitée. En effet, nos analyses génétiques conduisent à une distance de dispersion moyenne estimée de 20 à 50m. Cette faible dispersion induit également une forte variabilité individuelle du régime de reproduction liée aux variations locales de densité et de productions individuelles de pollen. Finalement, nous avons trouvé des variations inter-annuelles importantes de la structure génétique spatiale du nuage de pollen avec une différenciation entre arbres-mères de 8% et une différenciation entre années au sein des mères de 13%. Les années avec les plus fortes productions de pollen étaient également celles avec la plus faible diversité génétique globale. Cette étude confirme donc la nécessité de considérer de multiples années quand on s'intéresse à la reproduction d'une espèce pérenne comme le sapin, à la fois pour des études théoriques et pour des questions centrées sur la gestion de la diversit

Genome-wide detection of positive and balancing signatures of selection shared by four domesticated rainbow trout populations (Oncorhynchus mykiss)

Abstract Background Evolutionary processes leave footprints along the genome over time. Highly homozygous regions may correspond to positive selection of favorable alleles, while maintenance of heterozygous regions may be due to balancing selection phenomena. We analyzed data from 176 fish from four disconnected domestic rainbow trout populations that were genotyped using a high-density Axiom Trout genotyping 665K single nucleotide polymorphism array, including 20 from the US and 156 from three French lines. Using methods based on runs of homozygosity and extended haplotype homozygosity, we detected signatures of selection in these four populations. Results Nine genomic regions that included 253 genes were identified as being under positive selection in all four populations Most were located on chromosome 2 but also on chromosomes 12, 15, 16, and 20. In addition, four heterozygous regions that contain 29 genes that are putatively under balancing selection were also shared by the four populations. These were located on chromosomes 10, 13, and 19. Regardless of the homozygous or heterozygous nature of the regions, in each region, we detected several genes that are highly conserved among vertebrates due to their critical roles in cellular and nuclear organization, embryonic development, or immunity. We identified new candidate genes involved in rainbow trout fitness, as well as 17 genes that were previously identified to be under positive selection, 10 of which in other fishes (auts2, atp1b3, zp4, znf135, igf-1α, brd2, col9a2, mrap2, pbx1, and emilin-3). Conclusions Using material from disconnected populations of different origins allowed us to draw a genome-wide map of signatures of positive selection that are shared between these rainbow trout populations, and to identify several regions that are putatively under balancing selection. These results provide a valuable resource for future investigations of the dynamics of genetic diversity and genome evolution during domestication

Détection de signatures de sélection entre trois populations françaises domestiquées et une population nord-américaines de truites arc-en-ciel.

International audienc

Comment varie la reproduction du sapin (Abies alba Mill.) dans le temps et l'espace

National audienc

Anthropogenic effects on population genetics of phytophagous insects associated with domesticated plants

The hypothesis of isolation by distance (IBD) predicts that genetic differentiation between populations increases with geographic distance. However, gene flow is governed by numerous factors and the correlation between genetic differentiation and geographic distance is never simply linear. In this study, we analyze the interaction between the effects of geographic distance and of wild or domesticated status of the host plant on genetic differentiation in the bean beetle Acanthoscelides obvelatus. Geographic distance explained most of the among-population genetic differentiation. However, IBD varied depending on the kind of population pairs for which the correlation between genetic differentiation and geographic distance was examined. Whereas pairs of beetle populations associated with wild beans showed significant IBD (PP = 0.2992). This latter result can be explained by long-distance migrations of beetles on domesticated plants resulting from human exchanges of bean seeds. Beetle populations associated with wild beans were also significantly more likely than those on domesticated plants to contain rare alleles. However, at the population level, beetles on cultivated beans were similar in allelic richness to those on wild beans. This similarity in allelic richness combined with differences in other aspects of the genetic diversity (i.e., IBD, allelic diversity) is compatible with strongly contrasting effects of migration and drift. This novel indirect effect of human actions on gene flow of a serious pest of a domesticated plant has important implications for the spread of new adaptations such as resistance to pesticides