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Cet article retrace les principales étapes et la contribution de l’INRA au développement de la génomique, qui révolutionne depuis deux décennies les connaissances sur la structure et le fonctionnement du génome des animaux d’élevage. L’élaboration, dans les années 90, des premières cartes de marqueurs microsatellites a rapidement permis de mettre en évidence de nombreux locus à effets quantitatifs et de localiser les premiers gènes majeurs. En parallèle, les travaux de cytogénétique et de génomique comparative permettaient de tirer parti de l’avancée des connaissances sur le génome de l’homme et de la souris. A la fin des années 90, la construction d’outils de cartographie à haute densité, cartes d’hybrides d’irradiation et banques de grands fragments, a permis l’essor des travaux de cartographie fine et l’identification des premières mutations causales. Le début des années 2000 a été marqué par le développement des outils d’étude systématique de l’expression des gènes, micro-réseaux et puces à ADN, le démarrage du séquençage des premiers génomes d’animaux d’élevage, et l’essor des bases de données génomiques et de la bioinformatique. La connaissance des séquences permet ensuite de détecter in silico leurs variations, en particulier les très nombreuses variations ponctuelles (SNP) et de caractériser finement la structure des génomes des populations animales. La génomique a également renouvelé les méthodes d’amélioration génétique des populations, avec la mise en place de programmes de sélection assistée par marqueurs, de caractérisation et de gestion de la variabilité génétique et le développement d’applications en matière de contrôle de généalogie ou de traçabilité., This article outlines the main steps and the contribution of INRA to the development of genomics, which has revolutionised over the last two decades the knowledge of livestock genome structure and function. The development in the 1990’s of the first microsatellite marker maps quickly allowed the first major genes to be localised and numerous quantitative trait loci to be detected. Meanwhile, cytogenetics and comparative genomics studies allowed livestock genomics to benefit from advances in the knowledge of human and mouse genomes. At the end of the 1990’s, the construction of high-density mapping tools such as radiation hybrid maps and large insert libraries made it possible to develop fine mapping programmes and to identify the first causative mutations. The early 2000’s have been marked by the development of systematic gene expression tools, i.e. micro-arrays and DNA chips, the start of the first animal genome sequencing projects, and the rise of genomic databases and bioinformatics. Available sequence data then made it possible to detect in silico their variations, in particular the numerous single point polymorphisms (SNP) and to finely characterise the structure of livestock population genomes. Genomics has also renewed breeding programmes, with the development of programmes for marker-assisted selection, for the characterisation and the management of genetic variability and of parentage control or traceability applications.

Characterisation of genetic diversity in a large number of European pig populations has been undertaken with EC support. The populations sampled included local (rare) breeds, national varieties of the major international breeds, commercial lines and the Chinese Meishan breed. A second phase of the project will sample a further 50 Chinese breeds. Neutral genetic markers (AFLP and microsatellites), with individual or bulk typing, were used and compared.DNA from 59 European pig populations was extracted on samples of about 50 individuals per population. Individuals were typed for 50 microsatellites and for 148 AFLP bands. A subset of 25 populations was typed for 20 microsatellites on pools of DNA. Allele frequencies were estimated by direct allele counting for the co-dominant markers. Frequencies of AFLP negative alleles (absent bands) were obtained by taking the square root of absent band frequencies. Within-breed variability was summarised using standard statistics: expected and observed heterozygosity, mean observed and effective numbers of alleles, and F statistics. Between-breed diversity analysis was based on a bootstrapped Neighbor-Joining (NJ) tree derived from Reynolds distances (DR). The standard distance of Nei (DS) was also calculated.

Two genes coding for Na[sup +],K[sup +] -ATPase [alpha] and [beta] subunits are localized on pig chromosome 4, to the q1.6[yields]q2.3 and 1.3[yields]q2.1 regions, respectively, by radioactive in situ hybridization. According to nucleotide and amino acid sequence comparisons with different human isoforms of Na[sup +] ,K[sup +]-ATPase, these pig [alpha] and [beta] ATPase genes show strong homologies with human [alpha]1 and [beta] subunit ATPase genes, respectively. These results are discussed with respect to comparative mapping data of conserved genes in mammalian species. We showed that the pig cDNA probes encoding ATPase [alpha] and, [beta] genes reveal DNA polymorphism in Meishan an Large White pigs. 35 refs., 4 figs., 2 tabs.

Chantier qualité GA; International audience; Atlantic salmon Salmo salar microsatellite markers from a large database were analysed and selected with technical, economic and genetic criteria to provide an optimized set of polymorphic DNA markers for the analysis of the genetic diversity and the structure of anadromous Atlantic salmon populations. A set of 37 microsatellite markers was identified that are easy to use and provide a high level of differentiation power.

We investigate the use of markers to hasten the recovery of the recipient genome during an introgression breeding program. The effects of time and intensity of selection, population size, number and position of selected markers are studied for chromosomes either carrying or not carrying the introgressed gene. We show that marker assisted selection may lead to a gain in time of about two generations, an efficiency below previous theoretical predictions. Markers are most useful when their map position is known. In the early generations, it is shown that increasing the number of markers over three per non-carrier chromosome is not efficient, that the segment surrounding the introgressed gene is better controlled by rather distant markers unless high selection intensity can be applied, and that selection on this segment first can reduce the selection intensity available for selection on non-carrier chromosomes. These results are used to propose an optimal strategy for selection on the whole genome, making the most of available material and conditions (e.g., population size and fertility, genetic map).

Un aperçu des méthodes de caractérisation des ressources génétiques basées sur les marqueurs moléculaires est présenté. La variabilité génétique entre races s’exprime généralement, à partir d’un ensemble de fréquences alléliques, sous la forme d’indices de fixation et de diversité génique, ainsi que de distances génétiques entre races. Ces dernières peuvent être converties en phylogénie, classification ou mesure globale de diversité. La richesse allélique est une information complémentaire intéressante à prendre en compte. La planification expérimentale des études de diversité et leur fiabilité statistique sont brièvement discutées.

National audience; La base de données Mapgena a un double objectif : regrouper et gérer les informations utiles aux programmes d’étude du génome (cartographie, détection de QTL, analyse de populations) et ses applications ; créer des interfaces entre ces données et les outils d’analyse (crimap, linkage, qtlmap, phylip, génépop, fstat...). Elle est multi-espèce et contient des typages variés (protéines, hémotypes, gènes, microsatellites, RFLP...) ainsi que des caractères divers pour les performances. Cette base de données sous Oracle et son application développée avec l’AGL Uniface sont accessibles sur le serveur dga5 au Centre de Traitement de l’Information Génétique. A ce jour, les programmes de recherches gérés dans Mapgena sont : les programmes de détection de QTL dans plusieurs espèces (bovins laitiers, porcs, poule), le programme international de cartographie génétique chez le cheval ainsi que les données de typage dans le programme de sélection des reproducteurs chez les caprins.

Les données biologiques, en particulier les séquences d’ADN, s’accumulent extrêmement rapidement. Pour exploiter toutes ces données, une nouvelle science est née, la bioinformatique. Accéder de manière rapide et fiable aux données disponibles dans les banques internationales et analyser les données expérimentales produites à grande échelle nécessitent des outils informatiques puissants et en perpétuel développement. Assembler les séquences brutes, trouver les unités fonctionnelles des séquences génomiques, comparer les séquences entre elles, prédire les structures et les fonctions des macromolécules, comprendre les interactions entre les gènes et leurs produits en termes de réseaux métaboliques mais aussi d’évolution des espèces : toutes ces questions nécessitent l’utilisation de la bioinformatique et son développement.

La cartographie génétique chez les animaux domestiques consiste d’abord à établir le long du génome un réseau de marqueurs génétiques espacés entre eux de 20 cM et dont certains sont localisés avec précision sur les chromosomes. Parmi les différentes sources de polymorphisme disponibles sur le génome, les microsatellites sont les plus intéressants à utiliser. Ils sont très polymorphes, bien répartis le long du génome et leur étude peut être automatisée. Les connaissances recueillies sur le génome seront intégrées aux analyses quantitatives actuelles grâce à la mise en œuvre de nouveaux concepts d’analyse génétique. Elles permettront une évaluation précoce des génotypes, la mise en évidence de régions du génome intervenant dans la variabilité de caractères quantitatifs ou QTL (pour quantitative trait loci), une amélioration des méthodes d’identification des animaux et de vérification des filiations et une appréciation de la diversité génétique des races. L’analyse des parties codantes du génome complète le réseau de marqueurs. Elle permet de comparer les génomes des différents mammifères et en particulier de profiter des informations disponibles sur la carte humaine. Le but final de la cartographie est d’isoler des gènes d’intérêt zootechnique repérés sur le génome., Gene mapping of economically important animal species involves first defining a network of genetic markers evenly spaced along the genome, some of which should be precisely localized on the chromosomes. Of the different sources of polymorphism available on the genome, microsatellites are the most interesting. They are highly polymorphic, spread along the genome and their study can be automated. This knowledge will provide new tools and need the development of new concepts in the fields of quantitative and population genetics. The first expected applications are: an early evalution of genotypes; the discovery of genome regions involved in the variability of quantitative characters; an improvement of the methods of animal identification and relationship verification; and an estimation of breed genetic diversity. The analysis of the genome coding parts completes this marker network. It allows different mammalian genomes to be compared and information concerning the human map to be used. The final goal is to isolate genes important for animal production.

Nous présentons ici les travaux s’inscrivant dans le cadre du projet «Mathématiques et marqueurs moléculaires», en abrégé «MMM». Ces travaux ont pour objet l’identification et l’utilisation de gènes contrôlant des caractères quantitatifs - ou QTL (quantitative trait loci) - à partir de l’information issue des phénotypes, de la généalogie et de marqueurs moléculaires. Une première partie concerne la mise en évidence de gènes à effet majeur et l’utilisation de ces gènes en sélection, à partir d’informations phénotypiques (mesures sur le caractère dont le contrôle génétique est recherché) et généalogiques (relations de parenté entre individus de la population mesurée). La deuxième partie concerne l’utilisation conjointe de ces informations phénotypiques et généalogiques avec celles issues du marquage moléculaire dans la détection, la localisation de QTL, et en amélioration génétique., We present in this paper the results of the project "Mathematics and Molecular Markers" (MMM). These results concern the identification and use of genes that control quantitative characters or QTL (quantitative trait loci), using phenotypic, genealogical and molecular marker information. The first section concerns identification of major genes using information of a phenotypic (measures of the character) and genealogical (relationships between individuals) type and use of these genes in selection. The second section concerns the use of this information jointly with molecular marker information for detection and localisation of QTL, and for genetic improvement.

We investigated protocol designs for gene mapping in livestock. The optimization of the population structure was based on the empirical variance of the recombination rate estimator. We concluded that a mixture of half-sib and full-sib families is preferred to half-sib families; a knowledge of parental phases does not improve the quality of the estimation for typical livestock families with five offspring or more; and measurements of the genotype of the mates in half-sib families are not useful. Graphs and algebraic approximations for the practical choice of family size and structure are given.

Following Robertson (1970a) it is generally considered that for mass selection the selected proportion that maximises ultimate response is 0.5. This prediction has been partly tested by different authors. Here we explicitly address the question using computer simulations of selection in finite populations with linkage. The results show that the response achieved is always lower than the one predicted by standard methods, and that optimum selection intensity may be much lower than predicted unless population size is small.

Cet article rappelle tout d’abord les conditions expérimentales qui ont permis, chez les plantes, la localisation de gènes ayant des effets sur des caractères quantitatifs, en soulignant l’importance de la notion de déséquilibre de liaison. Les situations qui permettent de s’en rapprocher dans les populations animales sont ensuite évoquées : croisement entre races éloignées, localisation d’un gène majeur attribué à une mutation récente, déséquilibre aléatoire induit par la consanguinité ou déséquilibre systématique dû à la sélection, études de ségrégation intra-familiales. L’ordre de grandeur des effectifs d’animaux qu’il sera nécessaire de typer et d’observer est indiqué, en fonction du nombre et de l’importance des gènes quantitatifs à détecter.

The M13.13 minisatellite probe, consisting of a polymer of the M13 VNTR consensus sequence, cross-hybridized to ovine DNA and allowed detection of several polymorphic loci. Individual specific patterns were obtained in sheep using this probe. Pedigree analysis showed that individuals were heterozygous for most of the DNA fragments detected (88%). By studying the segregation of male's variable DNA fragments, a minimum of 10 loci were defined. The ovine DNA 'fingerprint' obtained with M13.13 is polymorphic enough to be used efficiently in animal identification, paternity testing, and possibly as a source of genetic markers for linkage analysis.

Predicting the genetic drift in small populations is considered over a short interval of time. A detailed description of the dynamic and spatial structure of the population is used, together with several measures of the change of genetic variability with time: mean inbreeding and kinship coefficients within and between groups of animals; percentages of genes contributed by the various foundation groups that made up the initial population; rate of loss of founder genes; joint distribution and random fluctuations of allelic frequencies. This approach is illustrated by means of two theoretical populations that model actual cattle breeds, and is applied to two problems: the conservation of a small population with or without freezing of semen, and the conflict between diffusion of genetic progress and random drift in a selected population conducted with or without superovulation and embryo transfer. Two main conclusions were drawn from these examples: 1. (a) Drift should not be characterized by single values (genetic effective size, or mean inbreeding coefficients), but rather by a set of criteria that have differentiated sensitivities to variations in demographic structure, mating scheme and gene diffusion. 2. (b) Quite large random variations in gene frequencies can be promoted by selection in seemingly large populations.

The syntenic α and β casein genes were localized in the rabbit by chromosomal in situ hybridization, using a mixture of two radioactive cDNA probes corresponding to these two genes. Highly significant labeling was observed on chromosome 12. A total of 175 silver grains was found on chromosomes in the 193 mitoses studied; 18% of the grains were on chromosome 12, and 42% of the grains on this chromosome were localized to the 12q24 region. Statistical analysis revealed that this labeling was highly significant.

Properties of identity relation between genes are discussed, and a derivation of recurrent equations of identity coefficients in a random mating, diploid dioecious population is presented. Computations are run by repeated matrix multiplication. Results show that for effective population size (Ne) larger than 16 and no mutation, a given identity coefficient at any time t can be expressed approximately as a function of (1—f), (1—f)3 and (1—f)6, where f is the mean inbreeding coefficient at time t. Tables are presented, for small Ne values and extreme sex ratios, showing the pattern of change in the identity coefficients over time. The pattern of evolution of identity coefficients is also presented and discussed with respect to N eu, where u is the mutation rate. Applications of these results to the evolution of genetic variability within and between inbred lines are discussed.

Data on the segregation of human markers in somatic hybrids between permanent rodent cell lines and primary human cells were gathered and statistically analyzed, using various criteria of association. The analysis provides evidence that human chromosomes do not segregate independently in somatic cell hybrids. A statistical decision rule concerning synteny or independence between markers is proposed, and its utility in developing the gene maps of other species by means of somatic cell hybridization is explored.

The syntenic alpha and beta casein genes were localized in the rabbit by chromosomal in situ hybridization, using a mixture of two radioactive cDNA probes corresponding to these two genes. Highly significant labeling was observed on chromosome 12. A total of 175 silver grains was found on chromosomes in the 193 mitoses studied; 18% of the grains were on chromosome 12, and 42% of the grains on this chromosome were localized to the 12q24 region. Statistical analysis revealed that this labeling was highly significant.

International audience

Two genes in a pedigree are identical by descent if they are two copies of a common ancestor gene. To obtain an unambiguous definition of the set of genes, at some autosomal locus, any gene is defined as an ordered pair of zygotes: the zygote who carries the gene, and the parent who transmitted it. The natural ordered structure on the set of zygotes yields an ordered structure upon the set of genes. Any event of the mendelian segregation splits down the set of genes into non-overlaping classes of identical genes: when considered as an ordered sub-set of genes, each class is shown to have the algebraic properties of a tree. Given a sub-set 𝔗 of genes, a family of exclusive events ensuring identity between all genes of 𝔗 is identified as a family of genic trees with some property. This relationship between segregational events and genic trees is extended to the case where two sub-sets 𝔗 and 𝔗′ of genes are considered together. As a consequence, a general method is obtained to compute either identity coefficients involving any number of genes splitted into one or two identity classes, or the fifteen coefficients defined among four genes, whichever the relationships between zygotes and genes might be. Using this approach to deal with the allelic structure in a set of genes carried by related zygotes is suggested.

In the south-east of France, local honey bees possess only the B allele at the MDH locus, whereas the races which are usually imported into this area do not have this allele. The proportion of non-B genes in a sample of drones was used to measure the “genetic pollution” in the local population. Within the course of a breeding scheme of local bees, 99 queens, whose genotypes are BB, were naturally mated between April 25 and June 10, 1985 at la Tave (Gard, France). Twenty daughters-workers of each queen were analysed at the MDH locus. The frequency of the B allele in drones that mated with these queens is estimated by the proportion of workers with genotype BB and the genetic pollution by the cumulated frequency of the other alleles. The sampling variances of these frequencies involve a coefficient which is a function of the average number of drones mated with a queen. This latter parameter is estimated through the maximum likelihood method. In addition to the three well-known alleles, a rare allele (frequency=0.0055), possibly equivalent to the S1 allele described by Badino et al. (1983), has been found in three different colonies. Cumulating the frequencies of the non-B alleles results in an estimation of the genetic pollution equal to 0.0394 (±0.0071). This low value allows us to proceed to the next step of the selection project. The mean number of drones mated to a queen is 12.4 with a (10.4–19.3) confidence interval at the 90% level.

On décrit une méthodologie pour contrôler la consanguinité dans des petites populations d’animaux domestiques, en tenant compte des contraintes d’élevage. On considère une population divisée en groupes de reproduction comprenant un ou plusieurs mâles et des femelles. Un groupe est divisé en classes d’âge, chaque sous-ensemble de la population, défini par le sexe, le groupe de reproduction, et la classe d’âge est décrit par 3 nombres qui désignent l’effectif, les réformes et le renouvellement. La structure génétique est décrite par les coefficients de consanguinité et de parenté moyens calculés sur ces sous-ensembles de la population. Des conditions sont établies pour minimiser l’accroissement du coefficient de consanguinité pendant les premières générations : (1) le nombre de groupes est supérieur à 10 ; (2) le schéma d’accouplement comporte la circulation des mâles de chaque groupe sur les femelles de tous les autres groupes ; (3) le nombre de mâles effectivement utilisés chaque année est aussi grand que possible et leur rythme de renouvellement est rapide. La démarche est illustrée dans le cas de 3 populations composées respectivement de 80 mâles et 2 000 femelles, 44 mâles et 616 femelles, 20 mâles et 80 femelles. Ces règles provoquent une réduction de la variabilité des coefficients de consanguinité moyens. Une structure génétique induite par le schéma d’accouplement se substitue à la structure initiale. Pour des populations de quelques dizaines de mâles et de quelques centaines de femelles, le respect de ces règles permet de limiter l’augmentation du coefficient de consanguinité à 0,3 p. 100 par génération., A method is proposed for controlling inbreeding rates in small populations, taking account of usual breeding constraints. A population is divided into breeding groups ; each group is divided into age classes, the demographic structure of which are defined by parameters stating their rates of renewal and their reproducing capabilities. At any time, the genetic description is made up of the set of mean inbreeding coefficients of the subsets (sex X breeding group X age) and of mean kinship coefficients between these subsets. General conditions are given, that minimize inbreeding rates over the first few generations : (i) the number of breeding groups should be at least 10 ; (ii) the mating scheme should involve the circulation of males from any group over females of all other groups ; (iii) the number of males used per year, and their rate of turnover should be maximised. The approach is illustrated by considering three model populations made up of 80 and 2 000, 44 and 616, 20 and 80 males and females respectively. The proposed rules lead to a reduction in the variance of inbreeding coefficients, and induce a genetic structure independent of the initial relationships between founder individuals. With such rules, the rate of inbreeding does not exceed 0.3 p. 100 per generation, for populations with a few tens of males and a few hundreds of females.

National audience