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Chantier qualité GA; International audience; Undernutrition before and after calving has a detrimental effect on the fertility of dairy cows. The effect of nutritional stress was previously reported to influence gene expression in key tissues for metabolic health and reproduction such as the liver and the genital tract early after calving, but not at breeding, that is, between 70 and 90 days post-partum. This study investigated the effects of pre- and post-partum mild underfeeding on global gene expression in the oviduct, endometrium and corpus luteum of eight multiparous Holstein cows during the early and middle phases of an induced cycle 80 days post-partum. Four control cows received 100% of energy and protein requirements during the dry period and after calving, while four underfed received 80% of control diet. Oestrous synchronization treatment was used to induce ovulation on D80 post-partum. Oviducts, ovaries and the anterior part of each uterine horn were recovered surgically 4, 8, 12 and 15 days after ovulation. Corpora lutea were dissected from the ovaries, and the endometrium was separated from the stroma and myometrium in each uterine horn. The oviduct segments were comprised of ampulla and isthmus. RNAs from ipsi- and contralateral samples were pooled on an equal weight basis. In each tissue, gene expression was assessed on a custom bovine 10K array. No differentially expressed gene (DEG) in the corpus luteum was identified between underfed and control, conversely to 293 DEGs in the oviduct vs 1 in the endometrium under a false discovery rate (FDR)

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Chantier qualité spécifique "Auteurs Externes" département de Génétique animale : uniquement liaison auteur au référentiel HR-Access; absent

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Genomics has brought with it a true biological revolution and has a great number of potential applications in all areas of life sciences. In animal sciences, it will become possible to improve the production of milk or meat according to consumer demands. Concerning food safety, molecular tools have already been commercialized for the detection of contaminants in meat. Genetic markers i.e. DNA markers, have also been marketed to detect the origins of individual bovine animals and their breed. For the genetic selection of cattle, DNA markers likely to be employed for the selection of tenderness or marbling traits of beef have been patented by Australian scientists. Several ongoing projects in France, Europe and the USA aim at studying the relevance of these markers and finding new ones. In muscle biology, tracking gene expression with DNA chips or by physically separating the expressed proteins has led to the identification of genes that play an important role in muscle development. These genes could in turn serve as new biological markers for tenderness, marbling or rearing practices. Large-scale projects both publicly and privately funded, in Europe, the South Sea Islands, and especially in North America aim at exploiting to a maximum new advances in genomics in favour of beef production.

Genomics has brought about in its wake a true biological revolution and can be applied to all areas of life sciences. Having sequenced the genomes of several different species, genomics techniques now allow us to study polymorphisms and the gene expression of proteins, enhancing our understanding of the biological functions of genes. The combined know-how of physicists and computer scientists, as well as of geneticists and physiologists is required to identify how genes control the dynamics of cell functions. Naturally enough, it is in the sphere of human medicine that the applications of genomics look most promising. Preventive and customized medicine, adapted to the genetic potential and to the way of life of each individual, will in all probability see the light of clay in the foreseeable future. in farm animals, there is no doubt that sequencing the bovine genome will give rise to new concepts and new molecular tools which will accelerate studies in bovine genomics. Comparing the bovine genome with that of other species, including humans, is also a potential source of huge progress for both human health and ruminant husbandry in general.

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Session 3: Génomique et qualités des viandes; absent

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International audience; The control and understanding of the nucleation and growth of nano-objects are key points for improving and/or considering the new applications of a given material at the nanoscale. Mastering the morphology is essential as the final properties are drastically affected by the size, shape, and surface structure. Yet, a number of challenges remain, including evidencing and understanding the relationship between the experimental parameters of the synthesis and the shape of the nanoparticles. Here we analyzed jointly and in detail the formation of anisotropic ZnO nanoparticles under different experimental conditions by using two different analytical tools enabling the analysis of TEM images: 2D size plots and multivariate statistical analysis. Well-defined crystalline ZnO nanorods were obtained through the hydrolysis of a dicyclohexyl zinc precursor in the presence of a primary fatty amine. Such statistical tools allow one to fully understand the effect of experimental parameters such as the hydrolysis rate, the mixing time before hydrolysis, the length of the ligand aliphatic chain, and the amount of water. All these analyses suggest a growth process by oriented attachment. Taking advantage of this mechanism, the size and aspect ratio of the ZnO nanorods can be easily tuned. These findings shed light on the relative importance of experimental parameters that govern the growth of nano-objects. This general methodological approach can be easily extended to any type of nanoparticle.

Up to now, genetic selection in cattle has been directed in favour of muscle growth, which changes muscle characteristics, and hence meat quality. One key concern, that now needs examination, is to understand the relationships between muscle growth and muscle characteristics related to meat quality. To achieve such a goal, muscles of divergently selected animals were analysed by three complementary approaches: (i) determination of muscle biochemical characteristics, (ii) identification of differentially expressed genes using transcriptomic and proteomic tools, (iii) identification of Single Nucleotide Polymorphisms (SNP) within candidate genes.

International audience; The aim of this study was to evaluate the genetic component of the locomotor jumping ability, via a wearable accelerometer sensor, and to estimate the genetic correlation with performance in competition, to introduce such criteria in selection schema. A sample of 1,056 young 3-year-old horses were equipped with a 3-dimensional accelerometer during a free jumping test, in regular breeding shows from 2015 to 2017. Seven variables were extracted from the dorso-ventral acceleration curve for the last three jumps over a double bar obstacle of 1.15 m for the front pole and 1.20 m for the back pole with a 1.20 m spread. Variables were the peaks of forelimbs, hindlimbs, and landing acceleration, the duration between peaks at take-off, the peak of forelimb acceleration and start of jump, jump duration and duration between the beginning of the impact of forelimbs and the peak at landing. During breeding shows, judges scored balance, strength, style, and reactivity for free jumping and jumping tests under saddle. Jumping competition results were recorded by logarithm of the sum of points earned in each competition. All horses in official competitions were included, i.e., 160,257 horses born in 1997 with a total of 649,491 annual performances. An animal mixed model with complete pedigree over four generations (353,236 horses) were used with fixed effects of jumping test location and date, morning/afternoon, gender, month of birth, rank of jump for accelerometric data, effect of year of competition, combined with age and gender for competition results. As a result, jump duration was the most heritable and repeatable for jump variables: h(2) = 0.16 (0.06), r = 0.52 (0.02), while accelerations were moderately heritable (h(2) = 0.05-0.09, r = 0.39-0.51). Judgement scores were heritable: 0.21 (0.07)-0.33 (0.09) and were highly correlated. Scores during free jumping were genetically correlated to jump duration: 0.71 (0.15)-0.88 (0.16). Both jump duration and judgement scores were genetically correlated to competition performance: 0.59 (0.13) for jump duration, from 0.60 (0.11) to 0.77 (0.12) for scores. Jump duration and judgement scores can be used as early selection criteria. The advantage of the accelerometric measurement is its objectivity and the ease of recording.

International audience

Cet article présente un bilan de la variabilité génétique dans les huit principales races bovines laitières françaises établi à partir de l’information généalogique. La stratégie d’ouverture diffère entre populations, les races Normande et Tarentaise étant fermées, les races Prim’Holstein, Pie Rouge des Plaines, Brune et Simmental Française faisant largement appel à des gènes extérieurs, tandis que les races Montbéliarde et Abondance ont procédé à une légère infusion de gènes Holstein rouge. Lorsque la qualité des généalogies et la structure de la population permet de le calculer correctement, le niveau de consanguinité est faible mais il s’accroît assez rapidement, de l’ordre de 1 % par génération, ce qui correspond à un effectif génétique réalisé de quelques dizaines de reproducteurs. Le nombre d’ancêtres efficace, dérivé des probabilités d’origine de gènes, est compris entre 17 et 64 et n’est pas corrélé avec le nombre de femelles dans la population. Les races bovines laitières, du fait de l’efficacité de l’insémination artificielle, sont donc des populations extrêmement réduites en terme d’origines génétiques. Des études plus approfondies devront rapidement proposer des solutions visant à préserver la variabilité génétique, mais restant compatibles avec les programmes de sélection actuels. Sans préjuger des réponses à apporter, il semble cependant nécessaire, d’une part, de maintenir toutes les populations existantes et, d’autre part, d’augmenter le nombre de pères à taureaux., This paper presents an overview of the genetic variability of the 8 main French dairy cattle breeds, estimated through pedigree information. The Normande and Tarentaise breeds are closed populations, the Montbeliarde and Abondance breeds recently introduced a limited amount of Red Holstein genes, whereas the Holstein, Brown Swiss, Pie Rouge des Plaines, and Simmental populations widely use foreign germplasm, sometimes until complete absorption. The estimation of inbreeding is strongly dependent on the population structure and on the quality of the pedigree information. When inbreeding can be correctly estimated, its level is found to increase by about 1 % per generation, and the realized effective size is close to or less than 50. The effective number of ancestors, derived from the probabilities of gene origins, varies from 17 to 64 according to the breed and is not related to the number of females in the population. Due to the efficiency of artificial insemination, the dairy cattle breeds are genetically small populations. Further investigations are needed to propose selection methods more favorable to the preservation of genetic diversity but still compatible with the selection programs. Two urgent proposals are to maintain all existing populations and to increase the number of bull sires in the breeds with the largest number of females.

International audience; Kadruka 23 is a relatively undisturbed funerary mound located in the Northern State of the Sudan, dating to the fifth millennium, also known as the Nubian Middle Neolithic. Begun in 2014, the excavations at the site have already brought to light nearly 40 burials, a majority of which belongs to juvenile subjects. A concentration and seemingly codified treatment of very young individuals was immediately remarked upon. With the knowledge that such practices have been observed elsewhere, this hypothesis about differential treatment based on age, is one we wish to develop in further detail. The demarcation of the very young deceased is underscored by several phenomena. We have identified a preferential placement within the cemetery (at the top of the mound), the association of mortuary goods not found with older individuals (bead waistbands, ceramic and shell spoons, etc.), consistent placement of ceramics (slightly above the burial level), as well as a variety of burial positions (not seen in the significantly more codified disposal of the older deceased). Our aim is to improve comprehension of the identity of the young dead, and their place in society before and after death.

International audience; Meta-analyses have been carried out to quantify the effect of dietary vitamin E on α-tocopherol accumulation and on lipid oxidation in porcine M. longissimus. Published results of 13 (vitamin E accumulation) and 10 (lipid oxidation) experiments respectively were used for the analyses. After a number of standardization procedures, a nonlinear relationship was found between the supplementary vitamin E and the accumulation of α-tocopherol in pork which approached a maximum value of 6.4 μg/g tissue. Pork lipid oxidation levels were described in terms of Thiobarbituric Acid Reacting Substances (TBARS) values. The statistical analysis revealed significant effect of vitamin E dose, muscle α-tocopherol concentration and supplementation time on TBARS, resulting in two prediction models for lipid oxidation. Meta-analysis has proven to be a valuable tool for combining results from previous studies to quantify the effects of dietary vitamin E. Further studies, carried out with standardized experimental protocols would be beneficial for model validation and to increase the predictive power of the derived models.

Summary The purpose of this study was to investigate the kinetics of blood lactate concentration in 5 saddle horses during an incremental test on an inclined treadmill (3%). In order to mimic field conditions, the exercise test consisted of five 3 min bouts at increasing speeds (7.5, 8.3, 9.2 and 10 m/s); each bout being followed by 1 min rest. Blood samples were taken prior to each step, every minute during each step and every 30 s during each rest period. At low intensities of exercise, stability of blood lactate concentration was sometimes observed during the first minutes of the bout, followed by an increase in the second part. At higher intensities, blood lactate concentration rose more quickly and no stability was observed. Lactate concentration in the blood sample taken at t3′30 during the rest period, often reached a higher value than in the preceeding bout. The VLa4 calculated from blood lactate concentrations obtained at t3′ and t3′30 were not significantly different (P>0.05); mean ± s.d. 9.8 ± 0.7 and 9.8 ± 0.6 m/s, respectively. By using the blood lactate concentrations obtained at t4', the VLa4 appeared higher (mean ± s.d. 10.1 ±0.7 m/s).

Summary The purpose of this study was to demonstrate the relationships between jumping technique and dorsoventral acceleration measured at the sternum. Eight saddle horses of various jumping abilities competed on a selective experimental show jumping course including 14 obstacles. An accelerometric belt fastened onto the thorax continuously measured the dorsoventral acceleration during the course. At each jump, 11 locomotor parameters (acceleration peaks, durations and stride frequency) were obtained from the dorsoventral acceleration-time curves. The type of obstacle significantly influenced the hindlimb acceleration peak at take-off and the landing acceleration peak (P

Chantier qualité GA; International audience; Within a population of Charolais young bulls, two extreme groups of longissimus thoracis muscle samples, classified according to Warner−Bratzler shear force (WBSF) of 55 °C grilled meat, were analyzed by 2D-electrophoresis. Muscle analyses were performed on 4 bulls of the “tender” group (WBSF = 27.7 ± 4.8 N) and 4 bulls of the “tough” group (WBSF = 41.2 ± 6.1 N), at 3 post-mortem times: D0, samples taken within 10 min post-mortem; D5 and D21, samples kept at 4 °C under vacuum during 5 and 21 days. Proteins of muscle samples were separated in two fractions based on protein solubility in Tris buffer: “soluble” and “insoluble”. Proteins of both fractions were separated by 2D-electrophoresis. Evolution of spots during the 3 post-mortem times was analyzed by hierarchical classification (HCA). Three clusters of proteins presenting similar evolution profiles provided accurate classification of post-mortem times and showed the translocation of some chaperone proteins and glycolytic enzymes from the soluble fraction to the insoluble fraction between D0 and D5. Cellular structure dismantlement and proteolysis was observed at D21. Effect of group (“tender” vs “tough”) on spot intensities was tested by ANOVA. At D0, higher quantity of proteins of the inner and outer membrane of mitochondria was found in the tender group suggesting a more extensive degradation of mitochondria that may be related to the apoptotic process.

International audience; Records of Holstein dairy cows in Hokkaido, Japan, were used to study the effects of environmental factors on length of productive life and to estimate genetic parameters for length of productive life. Each record was assigned to 1 of 3 data sets depending on the percent-age of type-scored cows in the herd. This percentage was considered to partly reflect the management policy in each herd, in particular regarding culling. The A, B, and C data sets consisted of herds with none, less than 60%, and more than 60% of type-scored cows, respectively, and included 158,719, 787,598, and 131,499 re-cords, respectively. Analyses of length of productive life were separately carried out on each data set using the Survival Kit software (Version 5.0). Nonparametric hazards estimates and the shape parameters of the baseline Weibull distribution differed between the 3 data sets. A cow having a sire originating from the United States or Canada had a relatively lower risk of being culled than a cow having Japanese sire in data set C. However, in data set A, a cow having a Canadian sire had a higher relative risk than a cow having a Japanese sire. The herd-year variance for data set A was about twice as large as for data set C. In contrast, the sire variance for data set A was about 40% of the one for data set C. As a result, heritability varied across data sets from 0.046 to 0.134. The results of this study suggest that it is important to consider factors related to herd management policy, such as the percentage of type-scored cows, in genetic analyses on length of productive life of Holstein cows in Hokkaido, Japan.

Segregation at the loci coding for the K88ab and K88ac small intestinal receptors to E. coli adhesins (K88abR, K88acR) and at the transferrin (TF) locus was studied in 38 pig families including 273 piglets. The TF locus showed a segregation deviation towards the B variant while each of the K88 receptors behaved as a single autosomal dominant gene. Recombinants between K88abR and K88acR provide evidence that they are under the control of two different loci. Thirty-two triple backcross families were selected to test linkage and estimate recombination rates (theta). Our results demonstrate that the two K88 receptor loci are closely linked (theta = 0.02) with a maximum lod score value (Zm) of 46.0. In addition, they are linked to the TF locus, theta = 0.14, Zm = 19.6 for the K88abR locus and theta = 0.16, Zm = 17.9 for the K88acR locus. The estimated recombination rates, smaller in males than in females, are consistent with the order TF-K88abR-K88acR. This linkage thus localizes the K88 loci, as the TF locus, on chromosome 13.

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.

International audience; French and Asian subsets of chicken breeds were first analysed using 22 microsatellites and then compared to the AVIANDIV European set using 14 loci. Positive correlations were observed between FIT or FST and typological values or variance of markers using the multivariate analysis MCOA. The first axis of the multivariate representation separated Asian from European breeds, revealing breeds with Asian ancestor. Using all or 14 loci, correct assignation rate was always higher than 93%. The Weitzman index and the aggregate diversity D were calculated using 22 loci within French and Asian breeds. The French breed Coucou de Rennes and the Hua-Tung breed seemed to contribute the most to the global diversity of each subset. This approach on French-only breeds and then on French with AVIANDIV domestic breeds (14 loci) showed that the Marans breed contributed the most. The AVIANDIV framework could be useful to evaluate the genetic diversity of local breeds and to help in connecting national and regional conservation policies.

A large number of environmental factors affect the daily milk production of a cow. Lactation curves included in the French test-day model are modelled as a function of days in milk with semi-parametric curves (splines). The proper modelling of environmental effects in the test-day analysis was investigated using test-day records collected from the first three lactations of French Montbéliarde cows from 1988 to 2005. Four lactation-curve effects describing calving month, length of dry period, age at calving and gestation defined within parity-class were fitted. The shape of lactation curves did not depend on year of calving, which can be modelled as a constant over the whole lactation. To reduce computational requirements and time, data were pre-adjusted in a first step for fixed effects with no year interaction, and then used for genetic evaluation. Correlations for each lactation between 305-day estimates of genetic and permanent environment effects computed using pre-adjustment factors obtained at a 4-year interval were virtually one. The use of a two-step procedure had a very limited impact on the estimates of genetic and permanent environment effects. The minimum correlations with values estimated with a one-step procedure were 0.9984 and 0.9974, respectively. The knowledge of systematic environmental effects affecting the cow daily yield through lactation curves offers interesting perspectives to predict future daily milk production.

Effects of selection for reproductive traits were estimated using data from 3 pig lines derived from the same Large White population base. Two lines were selected for 6 generations on high ovulation rate at puberty (OR line) or high prenatal survival corrected for ovulation rate in the first 2 parities (PS line). The third line was an unselected control line. Genetic parameters for age and BW at puberty (AP and WP); number of piglets born alive, weaned, and nurtured (NBA, NW, and NN, respectively); proportions of stillbirth (PSB) and survival from birth to weaning (PSW); litter and average piglet BW at birth (LWB and AWB), at 21 d (LW21 and AW21), and at weaning (LWW and AWW) were estimated using REML methodology. Heritability estimates were 0.38 +/- 0.03, 0.46 +/- 0.03, 0.16 +/- 0.01, 0.08 +/- 0.01, 0.09 +/- 0.01, 0.04 +/- 0.01, 0.04 +/- 0.02, 0.19 +/- 0.02, 0.10 +/- 0.02, 0.10 +/- 0.02, 0.36 +/- 0.02, 0.27 +/- 0.01, and 0.24 +/- 0.01 for AP, WP, NBA, PSB, NW, NN, PSW, LWB, LW21, LWW, AWB, AW21, and AWW, respectively. The measures of litter size showed strong genetic correlations (r(a) >/= 0.95) and had antagonistic relations with PSB (r(a) = -0.59 to -0.75) and average piglet BW (r(a) = -0.19 to -0.46). They also had strong positive genetic correlations with prenatal survival (r(a) = 0.67 to 0.78) and moderate ones with ovulation rate (r(a) = 0.36 to 0.42). Correlations of litter size with PSW were negative at birth but positive at weaning. The OR and PS lines were negatively related to PSW and average piglet BW. Puberty traits had positive genetic correlations with OR and negative ones with PS. Genetic trends were estimated by computing differences between OR or PS and control lines at each generation using least squares and mixed model methodologies. Average genetic trends were computed by regressing line differences on generation number. Significant (P < 0.05) average genetic trends were obtained in OR and PS lines for AP (respectively, 2.1 +/- 0.9 and 3.2 +/- 1.0 d/generation) and WP (respectively, 2.0 +/- 0.5 and 1.8 +/- 0.5 d/generation) and in the PS line for NBA (0.22 +/- 0.10 piglet/generation). Tendencies (P < 0.10) were also observed for LWB (0.21 +/- 0.12 kg/generation) and AWW (-0.25 +/- 0.14 kg/generation) in the PS line. Selection on components of litter size can be used to improve litter size at birth, but result in undesirable trends for preweaning survival.

Two-dimensional electrophoresis was used to compare Longissimus sarcoplasmic protein abundance between two groups (tough meat and tender meat), defined on the basis of extreme Warner-Bratzler shear force values measured on cooked pork. Fourteen protein spots differed in quantity (P0.05) between the two groups and were identified. Adypocyte fatty acid binding protein and acyl-CoA binding protein involved in lipid traffic and in the control of gene expression regulating cell proliferation and differentiation, and Enoyl-CoA hydratase, aldose reductase and triosephosphate isomerase indirectly related to lipid metabolism were overrepresented in the tender group. The tender group was further characterized by increased levels of proteins involved in protein folding and polymerization (initiation factor elf-3beta, chaperonin subunit 2, profilin II). The results suggest that the lower post-cooking shear force could at least in part be related to muscle adipogenetic and/or myogenetic status of which the possible underlying mechanisms are discussed.

The effects of season (hot vs. warm) in a tropical humid climate, parity (primiparous vs. multiparous) and breed (Creole: CR, Large White: LW) on rectal temperature (RT) were studied for a total of 222 lactations obtained in 85 sows (43 CR and 42 LW; 56 primiparous and 166 multiparous) over a 28-d lactation, between June 2002 and April 2005. Mean daily ambient temperature was higher during the hot season than during the warm season (26.0 vs. 24.1°C) and relative humidity was high and similar in both seasons (89% on average). At farrowing, BW was lower (172 vs. 233 kg) and backfat thickness was higher (37 vs. 21 mm) in CR than in LW sows (p

The racing careers of 2, 3, 4, and 5-year-old Thoroughbreds and French trotters born in France between 1995 and 1999 were analysed. The horses were evaluated on a set of traits, with particular attention to annual or career earnings and number of starts. As expected, the distributions of earnings corrected for year, age and sex are very skew and thus inappropriate for breeding value estimations. However, Log transformation results in near normal distributions more suitable for this purpose. Another problem of annual or career earnings required a more complex approach. As most horses did not win any money in France (67% of the trotters and 41% of the Thoroughbreds), it is difficult to correctly evaluate these horses. On the other hand, a linear adjustment of the Log of earnings by the Log of the number of starts (exponential adjustment of the earning index) leads to regression coefficients close to 1. It justified the use of the Log of earnings per start and explained its higher heritability in literature. A quadratic adjustment of the Log of earnings by the Log of the number of starts (sigmoid adjustment of the earning index) improves the adjustment for the Thoroughbred only and should be implemented for these horses. The probability of a horse to be placed according to the number of starts was also studied. It is shown that the observed percentage of non-placed horses ps according to the number of starts, s, is in all cases inferior to the expected percentage (ps

A new multiple trait strategy based on discriminant analysis was studied for efficient detection of linked QTL in outbred sib families, in comparison with a multivariate likelihood technique. The discriminant analysis technique describes the segregation of a linear combination of the traits in a univariate likelihood. This combination is calculated for each pair of positions depending on the inheritance of the pairs of QTL haplotypes in the progeny. The gains in power and accuracy for position estimations of multiple trait methods in grid searches were evaluated in reference to single trait detections of linked QTL. The methods were applied to simulated designs with two correlated traits submitted to various effects from the linked QTL. Multiple trait strategies were generally more powerful and accurate than the single trait technique. Linked QTL were distinguished when they were separated enough to identify informative recombinations: at least two genetic markers and 25 cM between the QTL under the simulated conditions. Except in a particular case, discriminant analysis was at least as powerful as the multivariate technique and its implementation was five times faster. Combining the advantages from both methodologies, we finally propose a complete strategy for rapid and efficient systematic multivariate detections in outbred populations.

The importance of variance modelling is now widely known for the analysis of microarray data. In particular the power and accuracy of statistical tests for differential gene expressions are highly dependent on variance modelling. The aim of this paper is to use a structural model on the variances, which includes a condition effect and a random gene effect, and to propose a simple estimation procedure for these parameters by working on the empirical variances. The proposed variance model was compared with various methods on both real and simulated data. It proved to be more powerful than the gene-by-gene analysis and more robust to the number of false positives than the homogeneous variance model. It performed well compared with recently proposed approaches such as SAM and VarMixt even for a small number of replicates, and performed similarly to Limma. The main advantage of the structural model is that, thanks to the use of a linear mixed model on the logarithm of the variances, various factors of variation can easily be incorporated in the model, which is not the case for previously proposed empirical Bayes methods. It is also very fast to compute and is adapted to the comparison of more than two conditions.

Human cutaneous melanoma is a complex trait inherited in about 10% of cases. Although 2 high-risk genes, CDKN2A and CDK4, and 1 low risk gene, MC1R, have been identified, susceptibility genes remain to be discovered. Here, we attempted to determine new genomic regions linked to melanoma using the pig MeLiM strain, which develops hereditary cutaneous melanomas. We applied quantitative trait loci (QTL) mapping method to a significant genome-wide scan performed on 331 backcross pigs derived from this strain. QTLs were detected at chromosome-wide level for a melanoma synthetic trait corresponding to the development of melanoma. The peak positions on Sus scrofa chromosomes (SSC) were at 49.4 and 88.0 cM (SSC1), 56.0 cM (SSC13), 86.5 cM (SSC15) and 39.8 cM (SSC17), and, on SSC2, at 16.9 cM, in families derived from F1 males only (p < 0.05, except for SSC13, p < 0.01). Analysis of 7 precise specific traits revealed highly significant QTLs on SSC10 (ulceration), on SSC12 (presence of melanoma at birth), on SSC13 (lesion type), and on SSC16 and SSC17 (number of aggressive melanomas) at the respective positions 42.0, 95.6, 81.0, 45.3 and 44.8 cM (p < 0.001 and p < 0.05 respectively at the chromosome- and genome-wide levels). We also showed that MeLiM MC1R*2 allele, which determines black coat colour in pigs, predisposes significantly to melanoma. Interactions were observed between MC1R and markers located on SSC1 (p < 0.05). Taken together, these results indicate that MeLiM swine is a model for human multigenic diseases. Comparative mapping revealed human regions of interest to search for new melanoma susceptibility candidates.

In a stochastic simulation study the effect of simultaneously changing the model for prediction of breeding values and changing the breeding goal was studied. A population of 100 000 cows with registrations on seven traits was simulated in two steps. In the first step of 15 years the population was selected for production and mastitis occurrence using a univariate model for prediction of breeding values for production and a trivariate model using information on mastitis treatments, udder depth and somatic cell score for prediction of breeding values for mastitis occurrence. In the second step six different scenarios were set up and simulated for 15 years combining two different breeding goals and three different models for prediction of breeding values in 20 replicates. Breeding goal 1 had relative economic value per genetic standard deviation on production (19.4) and mastitis occurrence ( - 50) whereas breeding goal 2 had a economic value on production (19.4), udder depth (4.2), mastitis occurrence ( - 50), non return rate (13.0) and days open ( - 16.75). Model 1 was a model similar to the one used in the first 15 years. Model 2 was an approximate multitrait model where solutions for fixed effects from a model corresponding to model 1 were subtracted from the phenotypes and a multitrait model with an overall mean, a year effect, an additive genetic and a residual effect were applied. Model 3 was a full multitrait model. Average genetic trends for total merit and each individual trait over 20 replicates were compared for each scenario. With the number of replicates the genetic responses using model 2 and 3 were not significant different. With a broad breeding goal using, model 2 or model 3 gave a significantly higher response in total merit than using model 1. Using a narrow breeding goal there was no significant difference between models used for prediction of breeding values. Results showed that with a breeding goal with a lot of emphasis on low heritable traits with a high economic value using a multitrait methodology for prediction of breeding values will redistribute the genetic progress in the total merit index. More gain will come from the low heritable traits in the breeding goal and less from traits with higher heritability. With a broad breeding goal and exploiting the available information in the data the inbreeding coefficient increased though not significantly.

BACKGROUND: To fulfil consumers' requirements for food traceability, it is necessary to have effective tools to differentiate food products according to their origin. The aim of the study was to identify a limited number of physico-chemical measurements that could differentiate rabbit meat from three different rearing systems: standard production system or a high quality norm system or a very low growth breeding system. RESULTS: The stepwise linear discriminant analysis (LDA) provided 14 physico-chemical variables, then combined into two discriminant factors. Most of them (n = 8) were related to bone traits, and especially (n = 5) to mechanical femur assessments. Mechanical characteristics of meat were also relevant in this analysis. Decision tree analysis (DTA) selected two variables only (femur stiffness, and ratio of femur weight to chilled carcass weight) to discriminate the three groups. A total of 96% and 90% of rabbits were correctly assigned to their original group according to LDA and DTA, respectively. CONCLUSION: This work demonstrated that simple physico-chemical traits recorded in carcasses and meat were efficient to discriminate rabbits from three different rearing systems using LDA or DTA procedures. These systems could have further implications for future traceability of breeding origin. Copyright © 2007 Society of Chemical Industry

Il est possible de modérer l’accroissement des coefficients de parenté et de consanguinité dans les populations sélectionnées en calculant les taux optimaux d’utilisation des reproducteurs, compte tenu de la diversité génétique existante, et en optimisant ensuite les accouplements. Les potentialités d’une telle approche ont été testées rétrospectivement sur la population Landrace Français en sélection en comparaison aux saillies réellement effectuées au cours d’une période test de 21 semaines. La contrainte majeure a été la conservation du niveau génétique moyen pour l’objectif global de sélection de la population, pour ne pas pénaliser le progrès génétique à court terme. En optimisant l’utilisation des verrats disponibles durant cette période, il aurait été possible de diminuer les coefficients de parenté et de consanguinité d’environ 20 %. Cette diminution aurait pu être portée à environ 30 % si en plus on avait optimisé le renouvellement et les réformes en considérant la variabilité génétique, toujours avec la même contrainte de niveau génétique inchangé par rapport au réel. A partir des résultats de cette dernière optimisation, il est possible de définir pour chaque individu un index synthétique pénalisé qui combine l’index synthétique actuel et une pénalité proportionnelle à sa parenté moyenne avec le reste de la population. Le coefficient de pondération de la parenté a été trouvé très élevé en dépit de la clause de conservation des niveaux génétiques pour l’index synthétique actuel. Ces résultats montrent l’intérêt qu’il y aurait à fournir à l’avenir, au moment de chaque évaluation génétique, les résultats de ces optimisations effectuées en continu, de manière à promouvoir la préservation de la variabilité génétique par les acteurs de la sélection., Tempering the increase of coancestry and inbreeding coefficients in selected populations is made possible through calculation of the optimal contributions allowed for breeding animals, given the current situation with regards to genetic diversity, and furthermore, through optimal distribution of matings. The potential of such an approach was tested by retrospective optimisation on the French Landrace po-pulation in reference to the matings actually carried out during a 21-week test period. The major constraint was that the average overall EBV (Estimated Breeding Value) should be the same as the observed one, in order to not damage short-term genetic gain. Optimising breeding allocations to boars would have led one to decrease coancestry and inbreeding coefficients by about 20 %. This decrease would have even climbed to about 30 %, if replacements and disposals had been optimised after accounting for genetic variability while keeping the same constraint of genetic level identical to the observed one. This last optimisation gave the appropriate information for defining a penalized overall EBV for each individual, combining the current EBV and a penalty proportional to this coancestry with the rest of the population. Weight of coancestry was found to be very high, despite the strong requirement of maintaining the same genetic level for the current overall EBV. These results show the potential value, in the future, of completing each periodical calculation of EBV by optimisations considering genetic variability and of releasing the corresponding information to breeders, in order to enhance maintenance of genetic variability.

Semen production was analysed in two rabbit lines (low, L and high, H) derived by 5 generations of divergent selection for 63-d body weight from a commercial heavy breed. A total of 31 bucks were collected during 18 weeks, once a week, by 2 solicitations at a 15 min interval (giving the 1 st and 2 nd rank ejaculate). Performances were recorded only one week out of two, resulting in 9 collection series. Sexual activity did no t differ between lines. A total of 256 and 226 ejaculates were observed in the L and H lines, respectively. The percent of efficient ejaculates (= fit for insemination) was markedly higher in the L line (66.5% vs. 44.2% in the H line) due to lower potential elimination for presence of urine, or insufficient volume or insufficient mass motility. Considering only the main effect of the lines, the line influenced mass motility, the volume and the concentration of the ejaculates, as well as 4 parameters from a computer assisted sperm motility analysis (path velocity, VAP, track linearity, LIN, track speed, VCL and beat cross frequency, BCF). Mass motility and the volume of the ejaculates were higher in the L line while the semen concentration was higher in the H line. Overall, the total number of sperms and the number of motile sperms per ejaculate were similar in both lines. The interaction between line and rank of the ejaculate on concentration, percent of motile sperms per ejaculate and LIN was a very interesting feature of the results. For example, in the L line, both ejaculates had the same concentration, while in the H line, the 1 st ejaculate was more concentrated than the second one. This pattern was maintained all along the experiment. The L line had highe r values of VAP, LIN and VCL but lower value of BCF. The efficient number of sperms by ejaculate, a synthetic criteria taking into account the number of motile sperms per ejaculate and the ability of the ejaculate for insemination was significantly higher in the L line: 229 vs 170 x10 6 sperms per ejaculate in the H line.

The analysis of nonlinear function-valued characters is very important in genetic studies, especially for growth traits of agricultural and laboratory species. Inference in nonlinear mixed effects models is, however, quite complex and is usually based on likelihood approximations or Bayesian methods. The aim of this paper was to present an efficient stochastic EM procedure, namely the SAEM algorithm, which is much faster to converge than the classical Monte Carlo EM algorithm and Bayesian estimation procedures, does not require specification of prior distributions and is quite robust to the choice of starting values. The key idea is to recycle the simulated values from one iteration to the next in the EM algorithm, which considerably accelerates the convergence. A simulation study is presented which confirms the advantages of this estimation procedure in the case of a genetic analysis. The SAEM algorithm was applied to real data sets on growth measurements in beef cattle and in chickens. The proposed estimation procedure, as the classical Monte Carlo EM algorithm, provides significance tests on the parameters and likelihood based model comparison criteria to compare the nonlinear models with other longitudinal methods.

Results from performance tests and competitions of young horses are used by major European warmblood horse breeding associations for genetic evaluations. The aim of this review was to compare genetic parameters for various tests of young horses to assess their efficiency in selection for dressage and show-jumping. Improved understanding of genetic information across countries is also necessary, as foreign trade with semen is rapidly increasing. The review is based on inquiries to European breed associations and on (17) scientific publications available, which have analysed genetic parameters of young horse data and/or relationships between young and mature horse results in sport. Despite differences in testing methods of young horses, results for major horse populations were in good agreement. Specially designed young horse performance tests, including stallion tests, showed high heritabilities and high genetic correlations with later competition results. We recommend that test results are encouraged to be used across countries for genetic evaluation of imported stallions and semen. Short station tests are generally preferred when selecting stallions for both dressage and jumping traits, whereas competition data may be used when selecting for only one discipline. We also recommend that extensive field testing of young horses is encouraged and should include both genders.

The estimation of genetic correlations between a nonlinear trait such as longevity and linear traits is computationally difficult on large datasets. A two-step approach was proposed and was checked via simulation. First, univariate analyses were performed to get genetic variance estimates and to compute pseudo-records and their associated weights. These pseudo-records were virtual performances free of all environmental effects that can be used in a BLUP animal model, leading to the same breeding values as in the (possibly nonlinear) initial analyses. By combining these pseudo-records in a multiple trait model and fixing the genetic and residual variances to their values computed during the first step, we obtained correlation estimates by AI-REML and approximate MT-BLUP predicted breeding values that blend direct and indirect information on longevity. Mean genetic correlations and reliabilities obtained on simulated data confirmed the suitability of this approach in a wide range of situations. When nonzero residual correlations exist between traits, a sire model gave nearly unbiased estimates of genetic correlations, while the animal model estimates were biased upwards. Finally, when an incorrect genetic trend was simulated to lead to biased pseudo-records, a joint analysis including a time effect could adequately correct for this bias.

A report of the Scientific Committee on Animal Health and Animal Welfare of the European Commission (CEC, 1999.) includes recommendations for setting up monitoring programmes for classical swine fever (CSF) infection in a wild-boar population, based on the assumption that one would detect at least 5% prevalence in a CSF-infected wild-boar population. This assumption, however, is not science based. We propose an alternative method to provide evidence for a wild-boar population being free of CSF and evaluate the efficiency of a surveillance programme that was implemented in Belgium in 1998. In our study, the probability of freedom of CSF-virus was estimated based on 789 samples; these were collected from wild-boars within the surveillance programme (within the three provinces which include 95% of the Belgian wild-boar population) and examined by three diagnostics methods (antibody detection, virus detection and virus RNA detection). A Bayesian framework was used for the estimation, accounting for the diagnostic test characteristics without the assumption of the presence of a gold standard. The median probability of freedom of CSF-virus was estimated at 0.970, with a 95% credibility interval of 0.149–1.000. Independent on the choice of the prior information, the posterior distributions for the probability of freedom of CSF-virus were always skewed close to the upper boundary of 1. This represents a big gain of knowledge since we did not use any prior information for the probability of freedom of CSF-virus and took the uncertainty about the accuracy of the diagnostic methods into account.

Weaning weights from 83 389 Limousin calves born between 1993 and 2002 in France and the Trans-Tasman block (Australia/New Zealand) were analysed to compare different strategies for running an international genetic evaluation for the breed. These records were a subset of the complete data for both countries and comprised a sample of herds that had recorded progeny of sires used across both countries. Genetic and phenotypic parameters for weaning weight were estimated within the countries. The estimates of direct genetic heritabilities were higher in France than in the Trans-Tasman block (0.31 vs. 0.22), while direct-maternal genetic correlations were less negative in the Trans-Tasman block (-0.10) than in France (-0.21). Different strategies for an international evaluation were studied, and the correlations between the estimated breeding values (EBV) of national evaluations and these strategies were derived. The international evaluation strategies were a) an animal model on raw performance data with non unity genetic correlations and heterogeneous residual and genetic variances across countries; b) the same animal model applied to pre-corrected (for fixed effects) performance data; and c) a sire model on de-regressed proofs (MACE). Estimates of the genetic correlations between weaning weight in both countries were 0.86 (0.80) for direct (maternal) genetic effects for the first strategy. Estimation of variance components by MACE appeared to be very sensitive to the sample of bulls and their reliability approximations. Variance component estimates obtained using pre-corrected data were inconsistent with estimates on raw data. However, the EBV predicted using pre-corrected data and parameters estimated from the raw data were similar to those predicted from raw data. Correlations between national and international EBV were always high (> 0.90) for sires, whichever genetic effect (direct or maternal) or international evaluation model was considered. The ranking of the bulls in the top 100 is of primary interest in terms of international genetic evaluation. In this study, some re-ranking of sires was observed for the top 100 bulls between countries and between the three international evaluation models. Thus, the origin of top sires may vary according to the implemented international evaluation strategy.

Functional longevity of dairy cows has been routinely evaluated in France since 1997 using a survival analysis model. Recently, we proposed a genetic trend validation test that could be used before including national data in an international evaluation of bulls on longevity of their daughters. Its application to the French Holstein data revealed a large overestimation of the genetic trend. It was found that the bias is the result of a change in the baseline hazard rate over time. A new proportional hazards model is proposed which accounts for this change. In the new model, the baseline is described as a stratified, piecewise Weibull hazard function within lactation, i.e. a function of the number of days since the most recent calving. Stratification is within year and parity. Different Weibull hazard functions are used over four periods: 0 to 270 days, 271 to 380 days, 381 days to day when dried, dry period until the next calving. The non-genetic effects included in the model were slightly different from the previous one. In particular the interaction effects between the within herd-year class of production and lactation number × stage of lactation on the one hand and year-season were accounted for. The estimated genetic variance was smaller than with the old model. The new genetic trend is almost flat. An illustration of the efficiency of selection on the estimated breeding values for longevity is presented.

National audience; The percentage of French trotters born in 2003 with Standardbred genes was 75 %. The mean value of the proportion of standardbred genes of these horses was 16 % and so the average proportion of Standardbred genes in the whole population of French trotters was 12 %.The reason was mainly the use of the 1/2 American stallion Florestan and its offspring (33 %). The influence of the American stallion Workaholic and its offspring was only 17 %. This cross breeding was very different from the cross of the Holstein breed in Black and Whitedairy cattle during the 1980’s. There was no back cross with the American population but with the French population and the percentage of Standardbred genes was maintained by the superior use of stallions with American genes (31 offspring per year versus 13). The introduction of Standardbred genes has been achieved and the percentage of genes was stable due to mating between crossed horses. The high percentage of French trotters with Standardbred genes contrasted with the small number of American founders: 13 ancestors were sufficient to explain 99 % of the Standardbred genes! The effect of Standardbred genes on race performance was favourable and linear. The effect was greater for the annual earning per start at 3 years (11 % of phenotypic deviation for 10 % of American genes) than for total cumulated life earning at 5 years of age (7 % of phenotypic deviation). In any case this effect explained less than 2 % of the variability.; Les 3/4 des Trotteurs Français nés en 2003 ont des gènes étrangers issus des croisements réalisés avec le Standardbred américain depuis 1978. La part de gènes américains de ces chevaux est de 16 %, ce qui donne une proportion de 12 % de gènes américains pour l’ensemble de la population Trotteur Français. La diffusion des gènes américains s’est réalisée principalement par le 1/2 américain Florestan et ses produits (33 %). L’apport du pur américain Workaholic (et ses produits) ne représente que 17 %. C’est une introduction très différente de la holsteinisation de la race bovine Pie Noire car il n’y a pas de retour actuellement sur la race parentale étrangère et le taux de gènes étrangers ne s’est maintenu que par l’utilisation préférentielle des étalons porteurs de gènes étrangers par rapport aux purs français (31 produits annuels contre 13). Maintenant que l’introduction est achevée, le taux de gènes étrangers est stabilisé et généralisé, il perdure par accouplement des animaux croisés. Cette large diffusion contraste avec le faible nombre de fondateurs américains : 13 ancêtres suffisent à expliquer 99 % des gènes américains dans les Trotteurs Français ! L’influence du taux de gènes étrangers sur la performance (indice standardisé à un écart type de 20) est favorable et linéaire. Elle est plus importante sur le gain par départ à l’âge de 3 ans (2,2 points à 3 ans pour 10 % de gènes étrangers) qu’à 5 ans sur le gain total cumulé de la carrière (1,4 points) mais n’explique que 2 % de la variabilité.

Summary Little information is available about gait characteristics and the level of performance in racehorses. The aim of that cross-sectional experiment was to study the relationships between some locomotor variables and the level of performance of trotter racehorses. A total of 104 horses from 3 to 7 years old performed a four-step locomotor test on the track with an accelerometric device: Equimetrix™. The population was divided into two groups on the basis of their official performance index: Index of TRot (ITR). These two groups were: an elite performers group (n=52) and a medium performers group (n=52). Locomotor variables: stride frequency, stance and propulsion durations, stride length, symmetry, regularity, dorsoventral, longitudinal and lateral activities were calculated at four different speeds (8.5, 11, 11.7 m/s and maximal speed). The variables were compared between two performance groups by an analysis of variance. The main results indicated that elite performers presented significantly higher stride frequency, longer stance and propulsion durations at submaximal and maximal speed. In conclusion, biomechanical characteristics of trotter racehorses, such as stride frequency and propulsion duration, might be useful criteria to quantify gait efficiency in trotter racehorses.