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International audience; As part of the European Union project GEroNIMO, a broad survey was conducted with stakeholders (breeders, managers, advisers and processors) involved in preserving local pig breeds (LB) to collect their perceptions and involve them in the project. It was designed in seven languages including English and was carried out online. An overall descriptive analysis of the responses of 339 participants is presented; results by country or breed are also mentioned. The data collected covers 11 countries and 32 breeds, with unequal representation by breed and country. Preserving genetic diversity is the main motivation stated by the stakeholders surveyed, followed by the economic activities associated with LB. The animals are raised purebred in small (median size: nine sows) and quite recent farms (median existence: 7 years); their selection is based mainly on phenotypic features (breed standards, number and quality of the teats). Participants expressed interest in selection, particularly for reproductive traits, but there are many barriers to the implementation of breeding programmes. Most of them expressed concern about the sustainability of LB, especially for economic reasons. Concerns about compliance with health regulations and fears of infection by pathogens came next. Stakeholders expected support from public authorities, especially to improve productivity and to protect the use of breed names.; Dans le cadre du projet européen GEroNIMO, une vaste enquête a été menée auprès des acteurs (éleveurs, techniciens, gestionnaires ou transformateurs) impliqués dans la conservation des races locales de porcs (RL) pour recueillir leurs perceptions et les associer au projet. Elle a été traduite en sept langues dont l'anglais et s’est déroulée en ligne. Une analyse descriptive globale des réponses de 339 participants est présentée ; des résultats par pays ou par race sont aussi mentionnés. Les données collectées couvrent 11 pays et 32 races, avec des représentations déséquilibrées par race et par pays. Les acteurs interrogés placent en tête de leurs motivations la préservation de la diversité génétique puis les activités économiques associées aux RL. Les animaux sont élevés en race pure dans de petits ateliers (effectif médian de neuf truies), assez récents (durée médiane de 7 ans). La sélection des reproducteurs repose principalement sur des caractéristiques phénotypiques : standard des races, nombre et qualité des tétines. Les participants manifestent de l’intérêt pour la sélection, particulièrement pour les caractères de reproduction, mais de nombreux freins à la mise en oeuvre de programmes de sélection existent. Ils expriment majoritairement des inquiétudes sur la pérennité des RL, surtout pour des raisons économiques. Les préoccupations liées au respect des normes sanitaires et aux craintes d’infection par des pathogènes viennent après. Les acteurs impliqués dans la préservation des RL attendent un soutien des pouvoirs publics, notamment pour améliorer la productivité et pour protéger l’utilisation du nom des races.

Additional file 3: Figure S3. Classification of different genetical links with the Naif bull for the 2017 cohort. Red: individuals with no genetic family link to Naif (0_LWN); purple: individuals with a recent genetic link with Naif through one of their parents (1_LWN_R); green: individuals with an old link with Naif through one of their parents (1_LWN_O); orange: individuals related to the first use of Naif by both parents (2_LWN_O); magenta: individuals related to the recent use of Naif by both parents (2_LWN_R); blue: individuals with one old and one recent genetic link with Naif (2_LWN_OR).

Additional file 4: Figure S4. Annual evolution of the equivalent number of generations from the pedigree data.

Additional file 10: Figure S8. Inbreeding depression on reproduction index in 2017 for individuals resulting or not from the reintroduction of the Naif bull. Blue: individuals not resulting from the recent use of Naif—Green: individuals resulting from the recent use of Naif. Regression lines were estimated using an ANCOVA model considering reproduction index (REPRO) as the response variable, and the inbreeding level based on ROH (FROH), the link to the recent use of Naif (NoRECENT_LWN if no link and RECENT_LWN if resulting for reintroduction of Naif) and its interaction as explanatory variables. In blue, $$REPRO_{noRECENT\_LWN} = 0.25 - 1.99F_{ROH}$$ R E P R O n o R E C E N T _ L W N = 0.25 - 1.99 F ROH . In green, $$REPRO_{noRECENT\_LWN} = 0.29 - 1.36F_{ROH}$$ R E P R O n o R E C E N T _ L W N = 0.29 - 1.36 F ROH . The slopes of the regression lines were not significantly different between the two groups (p = 0.63).

Additional file 8: Figure S6. Evolution of GEBV for the three indices (INEL, ISU, REPRO) in the Abondance breed. GEBV were assessed in 2017 for all genotyped individuals. Error bars correspond to standard errors.

Additional file 5: Figure S5. Principal component analysis of genotyping data for Cohort 2. Green: individuals with no genetic link to Naif (noLWN); and red: individuals with a genetic link to Naif (LWN). Naif is represented by the blue dot.

Additional file 2: Figure S2. Distribution of birth years for the four female cohorts. The 2443 cows in Cohort 1a are represented in pink, the 4092 cows in Cohort 2a are represented in blue, the 37 cows in Cohort 1b are represented in green and the 25 cows in Cohort 2b are represented in purple.

Additional file 2: Table S2. Marginal estimated means of each diversity index per group of populations. The letters and grey color stand for significant pairwise differences between groups (Tukey correction for multiple tests).

Additional file 3: Figure S1. Correlation matrix of population molecular or demographic diversity indices for breeds involved in a management program (Group 1). Values correspond to Pearson’s correlation coefficients. Colored cells stand for significant correlations (p < 0.05) either positive (blue) or negative (red), the intensity depending on the strength of the correlation between estimates. White cells represent non-significant correlations. Nb.Generation stands for the number of generations since the start of the management program and Fixed for the proportion of fixed alleles.

Additional file 5: Figure S3. Mean assignment probability of populations to each of the two clusters. The Asian and European clusters are colored in red and blue, respectively.

Additional file 4: Figure S2. Matrix of pairwise Fst between populations. Darker blue indicates a stronger pairwise Fst.

Native from North America, rainbow trout has been domesticated since the 1870s and introduced on all continents. Domestication and selective breeding have led to genetic changes due to inbreeding, genetic drift and selection. To address evolutionary biology questions, we used variant databases from USDA and INRAE to develop a 665K SNP array* (HD chip) for rainbow trout from a subset of the 32,372,492 SNPs. We prioritized the most variable SNPs in both databases with homogenous repartition over the genome. Of the 664,531 HD chip SNPs, 65% and 61% passed quality control and were polymorphic in samples of 288 and 175 genotyped fish from two commercial French lines (LB and LC respectively). Then, a subset of 72 LB and 67 LC genotypes of weakly related fish was pooled with the HD genotypes of 14 fish from the INRAE synthetic line (SY) and of 20 fish coming from rivers of the North West of USA (HA). These genotypes were used to reveal regions of the genome with low genetic diversity among various populations, likely to involve genes positively selected during either domestication or selection. The three French lines were moderately differentiated (Fst ~ 0 .10-0.12), but strongly differed from the HA population (Fst ~ 0 .27-0.29). A run of homozygosity (ROH) study revealed homozygous regions shared by all populations on Omy2, Omy12 and Omy15. These ROH islands included 26 annotated genes related to key roles in reproduction, embryonic development, genome stability and immunity.

As part of the European multi-actor project GEroNIMO (Genome and Epigenome eNabled breedIng in MOnogastrics) a survey was conducted with actors and stakeholders (breeders, advisers…) of the local pig breeds’ sector to collect their perceptions. The objective was to describe the farms, their levels of productivity, their economic viability and the breeding programs. It also aimed to identify stakeholders’ concerns about the future of local breeds and the overall impact of the sanitary crisis on them. A dedicated online survey was designed in seven languages including English, with emphasis on six European countries: Croatia, Italy, France, Portugal, Slovenia and Spain. In some cases, face-to-face interviews were also conducted. A total of 374 responses were collected, of which the most complete (n=337) were included in the analysis. Results show that local pig breeds are mainly reared on small farms, using outdoor rearing, locally available feed resources and natural mating. Preserving genetic diversity and maintaining breeds’ standard characteristics are the main motivations stated by the surveyed stakeholders. For one third of the surveyed breeders, activities related to local breeds are economically unbalanced, with deteriorating profitability due to the sanitary crisis. Genetic evaluation is performed in very few local breeds, but stakeholders demonstrated their interest for selective breeding, especially for reproductive traits. They expect the public authorities to protect the use of breed names and introduce incentives to increase productivity. A similar survey was also conducted for local chicken breeds.

Additional file 6: Figure S4. Unrooted neighbor-joining tree of the Hergnie breed. The colors of the surrounding circle represent the different breeders.

Genomic selection (GS) is commonly used in livestock and increasingly in plant breeding. Relying on phenotypes and genotypes of a reference population, GS allows performance prediction for young individuals having only genotypes. This is expected to achieve fast high genetic gain but with a potential loss of genetic diversity. Existing methods to conserve genetic diversity depend mostly on the choice of the breeding individuals. In this study, we propose a modification of the reference population composition to mitigate diversity loss. Since the high cost of phenotyping is the limiting factor for GS, our findings are of major economic interest. This study aims to answer the following questions: how would decisions on the reference population affect the breeding population, and how to best select individuals to update the reference population and balance maximizing genetic gain and minimizing loss of genetic diversity? We investigated three updating strategies for the reference population: random, truncation, and optimal contribution (OC) strategies. OC maximizes genetic merit for a fixed loss of genetic diversity. A French Montbéliarde dairy cattle population with 50K SNP chip genotypes and simulations over 10 generations were used to compare these different strategies using milk production as the trait of interest. Candidates were selected to update the reference population. Prediction bias and both genetic merit and diversity were measured. Changes in the reference population composition slightly affected the breeding population. Optimal contribution strategy appeared to be an acceptable compromise to maintain both genetic gain and diversity in the reference and the breeding populations.

International audience

Additional file 7: Table S6. Number of bulls and offspring for each birth period in the dataset.

PCR and sequencing primers for sequencing MC1R gene. (PDF 185Â kb)

Mutations in MC1R. Mutations found in MC1R region in Noire du Velay, Romanov and Suffolk sheep. (PDF 187Â kb)

Principal component analysis. PCA using 500Â K SNP genotypes of all French breeds in this study except MĂŠrinos de Rambouillet and Ouessant sheep. (PDF 19Â kb)

La biodiversité aviaire régresse ces dernières années en lien avec la réduction voire l'arrêt des accompagnements financiers de la part des collectivités locales envers les collectifs de races locales, la non-inclusion en 2010 des volailles dans le dispositif pour la Protection des Races Menacées (PRM) et l’évolution incontrôlée de la consanguinité, faute de gestion génétique appropriée pour certaines races. La caractérisation de la diversité des races locales apporte des informations nouvelles sur la gestion génétique et l’organisation structurelle, et permet de construire un argumentaire pour le développement de politiques de conservations adaptés. D’une part, grâce à la remontée des données généalogiques, des outils de gestion génétique adaptés aux races locales ont pu être mis en place : procéder au choix des reproducteurs en conciliant une amélioration du niveau génétique des candidats sélectionnés avec une stabilisation de l’apparentement moyen et établir des plans d’accouplement limitant l’évolution de la consanguinité attendue à la génération suivante. D’autre part, le dispositif PRM a été adapté aux volailles permettant un accompagnement financier des collectifs de races locales avec deux mesures : la première pour les races en phase de valorisation économique, la seconde pour les races en phase de relance comptant un cheptel de reproducteurs réduit., Aviary biodiversity has been regressing these past few years with the reduction or even closure of local authority funding towards local breed associations, the non-inclusion of poultry in the Protection of Endangered Breeds (PEB) Program, and the uncontrolled evolution of coancestry for some breeds which lack proper genetic management. The characterization of diversity of local breeds brings new information on genetic management and structural organization, making it possible to build argument to develop proper conservation policies. On the one side, with genealogic data feedback, genetic management tools suitable for local breeds have been set up: choosing breeding stock by balancing improvement of genetic level of selected candidates with stabilization inbreeding rate and designing mating plans while limiting expected coancestry evolution for the next generation. On the other side, PEB Program was adjusted for poultry allowing a financial support for local breeds associations with two measures: one for breeds currently experiencing economic valorization, the other one for breeds experiencing a recovery plan with a limited breeding stock.

FLK results. FLK regions under selection, SNP frequencies, haplotype cluster frequencies and SNP and haplotype local trees. (PDF 14210Â kb)

F3 test results for migration events detected in the population tree estimated using treemix. (PDF 111Â kb)

The small population sizes of French local breeds raise the question of their in- or ex-situ conservation. For thatgoal the characterization of their genetic diversity with molecular tools appears as a preliminary key step. 22local breeds along with 4 control widespread lines with an average of 60 individuals per breed were genotypedusing a 57K DNA SNP chip leading to a total sample made of 26 breeds and 1516 individuals. Within breedgenetic diversity was good but variable among them (mean F comprised between 3 and 28%), inbreedingcoefficients being related to the population sizes. Among breed diversity was large (Fst=0.25) allowing for aclear genetic identification of breeds. Relationships among breeds figured out their history (origin, breeders) orusage (broilers, layers...). Finally combining these genetic analyses with morphological data could help detectinggenomic region of interest in a selection perspective. To conclude, French local breeds appeared to be largelydiversified genetically and morphologically making them a good example of a successful management by bothbreeders and selection centers. Nevertheless much attention should be paid for their long term conservation.; Les faibles effectifs observés chez les races traditionnelles, locales et/ou anciennes posent la question de leurconservation in- ou ex-situ. La caractérisation de leur diversité génétique est un des déterminants essentiels deleur maintien et les analyses moléculaires s’avèrent être l’outil idéal pour cela. 22 races locales de poules ontdonc été génotypées à raison de 60 individus par population en moyenne avec une puce à ADN haute densité(57K). 4 lignées commerciales témoin ont également été intégrées, soit un total de 26 populations et 1516individus. La diversité intra-race est bonne, avec un niveau de consanguinité correct mais variable entre races (Fmoyen compris entre 3 et 28%), le niveau de consanguinité d’une race étant logiquement lié avec ses effectifs. Ilexiste également une grande diversité entre races (Fst=0.25), qui se différencient bien les unes des autres. Deplus, les relations observées entre races sont cohérentes avec leurs histoires. La structuration génétiques’explique ensuite principalement par la conduite des élevages. L’usage des races (pondeuses, de chair,commerciales) affecte aussi leur structure génétique. Finalement, ces analyses, combinées à la descriptionmorphologique des races, pourraient permettre de détecter des zones du génome d’intérêt pour la sélection. Enconclusion, les races locales françaises de poules présentent une grande diversité génétique, avec des spécificités,permettant de les distinguer très clairement les unes des autres. De plus leur gestion semble bien menée par leséleveurs et centres de sélection avec le maintien d’une diversité intra et inter-population relativement importante.

International audience

International audience