Impact of strong selection for the PrP major gene on genetic variability of four French sheep breeds (Open Access publication)

Effective selection on the PrP gene has been implemented since October 2001 in all French sheep breeds. After four years, the ARR "resistant" allele frequency increased by about 35% in young males. The aim of this study was to evaluate the impact of this strong selection on genetic variability. It is focussed on four French sheep breeds and based on the comparison of two groups of 94 animals within each breed: the first group of animals was born before the selection began, and the second, 3–4 years later. Genetic variability was assessed using genealogical and molecular data (29 microsatellite markers). The expected loss of genetic variability on the PrP gene was confirmed. Moreover, among the five markers located in the PrP region, only the three closest ones were affected. The evolution of the number of alleles, heterozygote deficiency within population, expected heterozygosity and the Reynolds distances agreed with the criteria from pedigree and pointed out that neutral genetic variability was not much affected. This trend depended on breed, i.e. on their initial states (population size, PrP frequencies) and on the selection strategies for improving scrapie resistance while carrying out selection for production traits

Le phénotypage de précision : des projets qui trouvent des applications grâce à des collaborations réussies

National audienc

Analyse de la longévité fonctionnelle dans les races ovines laitières françaises

International audienceDuring the past few decades, selection objectives have strongly evolved in the French dairy sheep sector to include functional and health traits in addition to production traits. To face new challenges ofsustainability, actors of breeding organizations for small ruminants are now considering selecting traits for robustness. As part of the CASDAR RUSTIC project, a genetic analysis of functional longevity was carried out, considering this trait reflects the ability of ewes to delay their culling for other criteria than production level. Among several indicators of functional longevity, we have chosen to study the Length of Productive Life, which is the number of days between the first lambing of the ewe and its culling. We have therefore implemented a survival analysis using the Survival Kit developed by V. Ducrocq. Only rams with at least 20 uncensored daughters were selected for this study. The heritability obtained ranged from 0.06 and 0.17: these values are of the same order of magnitude as in cattle. Estimated breeding values (EBV) were also calculated and validated by comparing the survival curves of extreme rams on the longevity index. An analysis showed the accuracy of EBV is very dependent on the number of girls whose careers are uncensored and that 30 to 40 daughters uncensored are necessary to reach an accuracy of 0.7. These first results are encouraging, however, this study should be continued, especially to study genetic correlations with the other characters in selection and to integrate functional longevity in selection objectives.Au cours des dernières décennies, les objectifs de sélection ont fortement évolué dans les filières ovines laitières françaises pour intégrer des caractères fonctionnels et de santé en plus des caractères deproduction. Pour répondre aux enjeux de durabilité, les acteurs des schémas de sélection des petits ruminants envisagent désormais de sélectionner des caractères de robustesse. Dans le cadre du projet CASDAR RUSTIC, une analyse génétique de la longévité fonctionnelle, qui traduit la capacité des animaux à retarder leur réforme pour des critères autres que le seul niveau de production, a été réalisée. Parmi plusieurs critères de longévité fonctionnelle, nous avons choisi d’étudier la Durée de Vie Productive qui est le nombre de jour entre la première mise-bas de la brebis et sa date de sortie. Nous avons pour cela mis en œuvre une analyse de survie en utilisant le Kit de Survie développé par V. Ducrocq. Seuls les béliers ayant au moins 20 filles non censurées ont été retenus pour cette étude. Les héritabilités obtenues sont du même ordre de grandeur qu’en bovins et se situent entre 0,06 et 0,17. Des index ont également été calculés puis validés en comparant les courbes de survies de béliers extrêmes sur l’index longévité. Une analyse des CD a montré que la précision des index est très dépendante du nombre de filles dont la carrière est complète et qu’il en faut au moins 30 à 40 pour atteindre un CD de 0,7. Ces premiers résultats sont assez encourageants mais nécessitent d’être encore approfondis, notamment du point de vue de la précision et des corrélations génétiques avec les autres caractères en sélection. Il s’agira ensuite de s’interroger sur la méthodologie à suivre pour intégrer ce caractère dans les objectifs de sélection dans le cadre des évaluations génomiques en routine

Analyse de la longévité fonctionnelle dans les races ovines laitières françaises

International audienceDuring the past few decades, selection objectives have strongly evolved in the French dairy sheep sector to include functional and health traits in addition to production traits. To face new challenges ofsustainability, actors of breeding organizations for small ruminants are now considering selecting traits for robustness. As part of the CASDAR RUSTIC project, a genetic analysis of functional longevity was carried out, considering this trait reflects the ability of ewes to delay their culling for other criteria than production level. Among several indicators of functional longevity, we have chosen to study the Length of Productive Life, which is the number of days between the first lambing of the ewe and its culling. We have therefore implemented a survival analysis using the Survival Kit developed by V. Ducrocq. Only rams with at least 20 uncensored daughters were selected for this study. The heritability obtained ranged from 0.06 and 0.17: these values are of the same order of magnitude as in cattle. Estimated breeding values (EBV) were also calculated and validated by comparing the survival curves of extreme rams on the longevity index. An analysis showed the accuracy of EBV is very dependent on the number of girls whose careers are uncensored and that 30 to 40 daughters uncensored are necessary to reach an accuracy of 0.7. These first results are encouraging, however, this study should be continued, especially to study genetic correlations with the other characters in selection and to integrate functional longevity in selection objectives.Au cours des dernières décennies, les objectifs de sélection ont fortement évolué dans les filières ovines laitières françaises pour intégrer des caractères fonctionnels et de santé en plus des caractères deproduction. Pour répondre aux enjeux de durabilité, les acteurs des schémas de sélection des petits ruminants envisagent désormais de sélectionner des caractères de robustesse. Dans le cadre du projet CASDAR RUSTIC, une analyse génétique de la longévité fonctionnelle, qui traduit la capacité des animaux à retarder leur réforme pour des critères autres que le seul niveau de production, a été réalisée. Parmi plusieurs critères de longévité fonctionnelle, nous avons choisi d’étudier la Durée de Vie Productive qui est le nombre de jour entre la première mise-bas de la brebis et sa date de sortie. Nous avons pour cela mis en œuvre une analyse de survie en utilisant le Kit de Survie développé par V. Ducrocq. Seuls les béliers ayant au moins 20 filles non censurées ont été retenus pour cette étude. Les héritabilités obtenues sont du même ordre de grandeur qu’en bovins et se situent entre 0,06 et 0,17. Des index ont également été calculés puis validés en comparant les courbes de survies de béliers extrêmes sur l’index longévité. Une analyse des CD a montré que la précision des index est très dépendante du nombre de filles dont la carrière est complète et qu’il en faut au moins 30 à 40 pour atteindre un CD de 0,7. Ces premiers résultats sont assez encourageants mais nécessitent d’être encore approfondis, notamment du point de vue de la précision et des corrélations génétiques avec les autres caractères en sélection. Il s’agira ensuite de s’interroger sur la méthodologie à suivre pour intégrer ce caractère dans les objectifs de sélection dans le cadre des évaluations génomiques en routine

Caractérisation des systèmes de production ovins et caprins laitiers en France: 1ère étape vers une étude d'interaction génétique x environnement

National audienc

A fast indirect method to compute functions of genomic relationships concerning genotyped and ungenotyped individuals, for diversity management

Pedigree-based management of genetic diversity in populations, e.g., using optimal contributions, involves computation of the Ax type yielding elements (relationships) or functions (usually averages) of relationship matrices. For pedigree-based relationships A, a very efficient method exists. When all the individuals of interest are genotyped, genomic management can be addressed using the genomic relationship matrix G; however, to date, the computational problem of efficiently computing Gx has not been well studied. When some individuals of interest are not genotyped, genomic management should consider the relationship matrix H that combines genotyped and ungenotyped individuals; however, direct computation of Hx is computationally very demanding, because construction of a possibly huge matrix is required. Our work presents efficient ways of computing Gx and Hx, with applications on real data from dairy sheep and dairy goat breeding schemes. For genomic relationships, an efficient indirect computation with quadratic instead of cubic cost is x = Z (Z'x) / k, where Z is a matrix relating animals to genotypes. For the relationship matrix H, we propose an indirect method based on the difference between vectors Hx - Ax, which involves computation of Ax and of products such as Gw and A(22)(-1) w, where w is a working vector derived from x. The latter computation is the most demanding but can be done using sparse Cholesky decompositions of matrix A(-1), which allows handling very large genomic and pedigree data files. Studies based on simulations reported in the literature show that the trends of average relationships in H and A differ as genomic selection proceeds. When selection is based on genomic relationships but management is based on pedigree data, the true genetic diversity is overestimated. However, our tests on real data from sheep and goat obtained before genomic selection started do not show this. We present efficient methods to compute elements and statistics of the genomic relationships G and of matrix H that combines ungenotyped and genotyped individuals. These methods should be useful to monitor and handle genomic diversity

Genome-wide association mapping for type and mammary health traits in French dairy goats identifies a pleiotropic region on chromosome 19 in the Saanen breed

Type traits and mammary health traits are important to dairy ruminant breeding because they influence animal health, milking ability, and longevity, as well as the economic sustainability of farms. The availability of the genomic sequence and a single nucleotide polymorphism chip in goats has opened up new fields of investigation to better understand the genes and mechanisms that underlie such complex traits and to be able to select them. Our objective was to perform a genome-wide association study in dairy goats for 11 type traits and somatic cell count (SCC) as proxies for mastitis resistance. A genome-wide association study was implemented using a daughter design composed of 1,941 Alpine and Saanen goats sired by 20 artificial insemination bucks, genotyped with the Illumina Goat-SNP50 BeadChip (Illumina Inc., San Diego, CA). This association study was based on both linkage analyses and linkage disequilibrium using QTLmap software (http://dga7.jouy.inra.fr/gtImap/) interval mapping was performed with the likelihood ratio test using linear regr e ssions. Breeds were analyzed together and separately. The study highlighted 37 chromosome-wide significant quantitative trait loci (QTL) with linkage analyses and 222 genome-wide significant QTL for linkage disequilibrium, for type and SCC traits in dairy goats. Genomic control of those traits was mostly polygenic and breed-specific, suggesting that within-breed selection would be favored for those traits. Of note, Capra hircus autosome (CHI) 19 appeared to be highly enriched in single nucleotide polymorphisms associated with type and SCC, with 2 highly significant regions in the Saanen breed. One region (33-42 Mb) was significantly associated with SCC and includes candidate genes associated with response to intramammary infec tions (RARA, STAT3, STAT5A, and STAT5B). Another region of the CHI 19 (24.5-27 Mb) exhibited an adverse pleiotropic effect on milk production (milk, fat yield, and protein yield) and udder traits (udder floor position and rear udder attachment) that agreed with the negative genetic correlations that exist between those 2 groups of traits. These QTL were not found in the Alpine breed. In Alpine, the 2 mast significant regions were associated with chest depth on CHI 6 (45.8-46.0 Mb) and CHI 8 (80.7-81.1 Mb). These results will be helpful for goat selection in the future and could lead to identification of causal mutations

L’amélioration génétique des animaux : une action collective au service des éleveurs et des filières

L’amélioration génétique des animaux : une action collective au service des éleveurs et des filières. Carrefour International Ovin-Capri