35 research outputs found
The impact of genomic selection on genetic diversity and genetic gain in three French dairy cattle breeds
International audienceAbstractBackgroundIn France, implementation of genomic evaluations in dairy cattle breeds started in 2009 and this has modified the breeding schemes drastically. In this context, the goal of our study was to understand the impact of genomic selection on the genetic diversity of bulls from three French dairy cattle breeds born between 2005 and 2015 (Montbéliarde, Normande and Holstein) and the factors that are involved.MethodsWe compared annual genetic gains, inbreeding rates based on runs of homozygosity (ROH) and pedigree data, and mean ROH length within breeds, before and after the implementation of genomic selection.ResultsGenomic selection induced an increase in mean annual genetic gains of 50, 71 and 33% for Montbéliarde, Normande and Holstein bulls, respectively, and in parallel, the generation intervals were reduced by a factor of 1.7, 1.9 and 2, respectively. We found no significant change in inbreeding rate for the two national breeds, Montbéliarde and Normande, and a significant increase in inbreeding rate for the Holstein international breed, which is now as high as 0.55% per year based on ROH and 0.49% per year based on pedigree data (equivalent to a rate of 1.36 and 1.39% per generation, respectively). The mean ROH length was longer for bulls from the Holstein breed than for those from the other two breeds.ConclusionsWith the implementation of genomic selection, the annual genetic gain increased for bulls from the three major French dairy cattle breeds. At the same time, the annual loss of genetic diversity increased for Holstein bulls, possibly because of the massive use of a few elite bulls in this breed, but not for Montbéliarde and Normande bulls. The increase in mean ROH length in Holstein may reflect the occurrence of recent inbreeding. New strategies in breeding schemes, such as female donor stations and embryo transfer, and recent implementation of genomic evaluations in small regional breeds should be studied carefully in order to ensure the sustainability of breeding schemes in the future
Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences
Background: In recent years, several bovine genome sequencing projects were carried out with the aim of developing genomic tools to improve dairy and beef production efficiency and sustainability.[br/]
Results: In this study, we describe the first French cattle genome variation dataset obtained by sequencing 274 whole genomes representing several major dairy and beef breeds. This dataset contains over 28 million single nucleotide polymorphisms (SNPs) and small insertions and deletions. Comparisons between sequencing results and SNP array genotypes revealed a very high genotype concordance rate, which indicates the good quality of our data.[br/]
Conclusions: To our knowledge, this is the first large-scale catalog of small genomic variations in French dairy and beef cattle. This resource will contribute to the study of gene functions and population structure and also help to improve traits through genotype-guided selection
Genetic determinism of spontaneous masculinisation in XX female rainbow trout: new insights using medium throughput genotyping and whole-genome sequencing
International audienceRainbow trout has a male heterogametic (XY) sex determination system controlled by a major sex-determining gene, sdY. Unexpectedly, a few phenotypically masculinised fish are regularly observed in all-female farmed trout stocks. To better understand the genetic determinism underlying spontaneous maleness in XX-rainbow trout, we recorded the phenotypic sex of 20,210 XX-rainbow trout from a French farm population at 10 and 15 months post-hatching. The overall masculinisation rate was 1.45%. We performed two genome-wide association studies (GWAS) on a subsample of 1139 individuals classified as females, intersex or males using either medium-throughput genotyping (31,811 SNPs) or whole-genome sequencing (WGS, 8.7 million SNPs). The genomic heritability of maleness ranged between 0.48 and 0.62 depending on the method and the number of SNPs used for the estimation. At the 31K SNPs level, we detected four QTL on three chromosomes (Omy1, Omy12 and Omy20). Using WGS information, we narrowed down the positions of the two QTL detected on Omy1 to 96 kb and 347 kb respectively, with the second QTL explaining up to 14% of the total genetic variance of maleness. Within this QTL, we detected three putative candidate genes, fgfa8, cyp17a1 and an uncharacterised protein (LOC110527930), which might be involved in spontaneous maleness of XX-female rainbow trout
Rigoletto
De cada obra s'ha digitalitzat un programa sencer. De la resta s'han digitalitzat les parts que són diferents.Director: José Sabate
Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals
peer-reviewedH.D.D., A.J.C., P.J.B. and B.J.H. would like to acknowledge the Dairy Futures
Cooperative Research Centre for funding. H.P. and R.F. acknowledge funding
from the German Federal Ministry of Education and Research (BMBF) within the
AgroClustEr âSynbreedâSynergistic Plant and Animal Breedingâ (grant 0315527B).
H.P., R.F., R.E. and K.-U.G. acknowledge the Arbeitsgemeinschaft SĂŒddeutscher
RinderzĂŒchter, the Arbeitsgemeinschaft Ăsterreichischer FleckviehzĂŒchter
and ZuchtData EDV Dienstleistungen for providing genotype data. A. Bagnato
acknowledges the European Union (EU) Collaborative Project LowInputBreeds
(grant agreement 222623) for providing Brown Swiss genotypes. Braunvieh Schweiz
is acknowledged for providing Brown Swiss phenotypes. H.P. and R.F. acknowledge
the German Holstein Association (DHV) and the ConfederaciĂłn de Asociaciones
de Frisona Española (CONCAFE) for sharing genotype data. H.P. was financially
supported by a postdoctoral fellowship from the Deutsche Forschungsgemeinschaft
(DFG) (grant PA 2789/1-1). D.B. and D.C.P. acknowledge funding from the
Research Stimulus Fund (11/S/112) and Science Foundation Ireland (14/IA/2576).
M.S. and F.S.S. acknowledge the Canadian Dairy Network (CDN) for providing the
Holstein genotypes. P.S. acknowledges funding from the Genome Canada project
entitled âWhole Genome Selection through Genome Wide Imputation in Beef Cattleâ and acknowledges WestGrid and Compute/Calcul Canada for providing
computing resources. J.F.T. was supported by the National Institute of Food and
Agriculture, US Department of Agriculture, under awards 2013-68004-20364 and
2015-67015-23183. A. Bagnato, F.P., M.D. and J.W. acknowledge EU Collaborative
Project Quantomics (grant 516 agreement 222664) for providing Brown Swiss
and Finnish Ayrshire sequences and genotypes. A.C.B. and R.F.V. acknowledge
funding from the publicâprivate partnership âBreed4Foodâ (code BO-22.04-011-
001-ASG-LR) and EU FP7 IRSES SEQSEL (grant 317697). A.C.B. and R.F.V.
acknowledge CRV (Arnhem, the Netherlands) for providing data on Dutch and
New Zealand Holstein and Jersey bulls.Stature is affected by many polymorphisms of small effect in humans1. In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 Ă 10â8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIPâseq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals
Développement d'évaluations génomiques multiraciales chez les bovins laitiers
Within-breed genomic selection is now implemented in a number of large cattle breeds. However, building reference populations large enough remains a major challenge for smaller breeds. Combining reference populations and implementing a multi-breed approach appears to be an appealing alternative for small breeds.Such an approach requires conserved linkage disequilibrium across breeds to maintain the association between QTL and markers. Therefore, the use of a high density chip is generally needed. Error rates for high density imputation from medium density genotypes, classically used in cattle, were estimated. The mean error rate was below 1% in most dairy cattle breed which implies that a large high density imputed reference populations can be available for genomic selection at low cost. Reference populations from the three major French dairy breeds were imputed to high density and used to develop a multi-breed genomic evaluation.Several alternative genomic selection approaches (within-breed or multi-breed, based on medium or high density genotypes) were compared for breeds with different sizes of reference population. Improvement of genomic prediction accuracy due to the multi-breed evaluation was observed for breeds with 500 animals or less in their reference population. Accuracy of a third alternative using multi-breed evaluation based on medium density genotypes of closely related breeds was investigated. The benefit of multi-breed genomic evaluation was then three times higher in this situation than in the one where populations from major dairy cattle breeds were pooled. It can be noted that in both situations, using within-breed genomic information allowed a significant gain in accuracy compared to pedigree-based evaluations even for a small breed, when all sires of selection candidates belong to the reference population.These results suggest that implementation of genomic selection is feasible in small dairy cattle breeds. However further work is required to determine which optimal strategy can/must be implemented in a given breed.L'efficacitĂ© de la sĂ©lection gĂ©nomique Ă©tant principalement dĂ©pendante de la taille de la population de rĂ©fĂ©rence, seules les principales races laitiĂšres françaises bĂ©nĂ©ficient aujourd'hui d'Ă©valuations gĂ©nomiques. Pour contourner cette contrainte et dĂ©velopper des Ă©valuations gĂ©nomiques pour les races rĂ©gionales, il a Ă©tĂ© proposĂ© de crĂ©er une population de rĂ©fĂ©rence commune entre races.Cependant, utiliser une population de rĂ©fĂ©rence multiraciale nĂ©cessite que le lien entre QTL et marqueurs soit conservĂ© entre races, ce qui implique, sauf cas particulier, l'utilisation d'une puce haute densitĂ©. Les taux d'erreur d'imputation des gĂ©notypes haute densitĂ© Ă partir de gĂ©notypes moyenne densitĂ© (classiquement utilisĂ©s en bovins) ont Ă©tĂ© Ă©tudiĂ©s. La prĂ©cision d'imputation Ă©tant supĂ©rieure Ă 99% dans la majoritĂ© des races laitiĂšres, l'imputation des gĂ©notypes des animaux des populations de rĂ©fĂ©rence des principales races laitiĂšres a Ă©tĂ© rĂ©alisĂ©e. Cette population de rĂ©fĂ©rence « haute densitĂ© » a ensuite Ă©tĂ© utilisĂ©e pour le dĂ©veloppement d'Ă©valuations gĂ©nomiques multiraciales. Plusieurs stratĂ©gies d'Ă©valuations gĂ©nomiques (intra-race ou multi-race, Ă partir de gĂ©notypes moyenne ou haute densitĂ©) ont Ă©tĂ© comparĂ©es pour diffĂ©rentes tailles de populations de rĂ©fĂ©rence. Les Ă©valuations multiraciales basĂ©es sur la puce haute densitĂ© permettent d'amĂ©liorer la prĂ©cision des Ă©valuations gĂ©nomiques dans le cas d'une population de rĂ©fĂ©rence de 500 taureaux ou moins. L'efficacitĂ© d'une troisiĂšme stratĂ©gie utilisant des Ă©valuations gĂ©nomiques multiraciales Ă partir de la puce moyenne densitĂ© pour un groupe de races proches a donc Ă©tĂ© Ă©tudiĂ©e. L'augmentation de la prĂ©cision des Ă©valuations gĂ©nomiques observĂ©e dans ce cas Ă©tait trois fois supĂ©rieure Ă celle qui avait Ă©tĂ© observĂ©e dans le cas des principales races laitiĂšres. Par ailleurs, dans les deux cas Ă©tudiĂ©s ici, la prĂ©cision des Ă©valuations gĂ©nomiques intra-races est relativement Ă©levĂ©e, mĂȘme dans le cas d'une population de rĂ©fĂ©rence rĂ©duite, lorsque les pĂšres des candidats Ă la sĂ©lection sont inclus dans la population de rĂ©fĂ©rence.Les rĂ©sultats obtenus suggĂšrent donc que la mise en place d'Ă©valuations gĂ©nomiques dans les races rĂ©gionales est envisageable. Il faudra toutefois poursuivre les travaux pour dĂ©terminer quelle stratĂ©gie optimale peut/doit ĂȘtre utilisĂ©e dans chacune des races
Multi-breed genomic evaluations in dairy cattle
L'efficacitĂ© de la sĂ©lection gĂ©nomique Ă©tant principalement dĂ©pendante de la taille de la population de rĂ©fĂ©rence, seules les principales races laitiĂšres françaises bĂ©nĂ©ficient aujourd'hui d'Ă©valuations gĂ©nomiques. Pour contourner cette contrainte et dĂ©velopper des Ă©valuations gĂ©nomiques pour les races rĂ©gionales, il a Ă©tĂ© proposĂ© de crĂ©er une population de rĂ©fĂ©rence commune entre races.Cependant, utiliser une population de rĂ©fĂ©rence multiraciale nĂ©cessite que le lien entre QTL et marqueurs soit conservĂ© entre races, ce qui implique, sauf cas particulier, l'utilisation d'une puce haute densitĂ©. Les taux d'erreur d'imputation des gĂ©notypes haute densitĂ© Ă partir de gĂ©notypes moyenne densitĂ© (classiquement utilisĂ©s en bovins) ont Ă©tĂ© Ă©tudiĂ©s. La prĂ©cision d'imputation Ă©tant supĂ©rieure Ă 99% dans la majoritĂ© des races laitiĂšres, l'imputation des gĂ©notypes des animaux des populations de rĂ©fĂ©rence des principales races laitiĂšres a Ă©tĂ© rĂ©alisĂ©e. Cette population de rĂ©fĂ©rence « haute densitĂ© » a ensuite Ă©tĂ© utilisĂ©e pour le dĂ©veloppement d'Ă©valuations gĂ©nomiques multiraciales. Plusieurs stratĂ©gies d'Ă©valuations gĂ©nomiques (intra-race ou multi-race, Ă partir de gĂ©notypes moyenne ou haute densitĂ©) ont Ă©tĂ© comparĂ©es pour diffĂ©rentes tailles de populations de rĂ©fĂ©rence. Les Ă©valuations multiraciales basĂ©es sur la puce haute densitĂ© permettent d'amĂ©liorer la prĂ©cision des Ă©valuations gĂ©nomiques dans le cas d'une population de rĂ©fĂ©rence de 500 taureaux ou moins. L'efficacitĂ© d'une troisiĂšme stratĂ©gie utilisant des Ă©valuations gĂ©nomiques multiraciales Ă partir de la puce moyenne densitĂ© pour un groupe de races proches a donc Ă©tĂ© Ă©tudiĂ©e. L'augmentation de la prĂ©cision des Ă©valuations gĂ©nomiques observĂ©e dans ce cas Ă©tait trois fois supĂ©rieure Ă celle qui avait Ă©tĂ© observĂ©e dans le cas des principales races laitiĂšres. Par ailleurs, dans les deux cas Ă©tudiĂ©s ici, la prĂ©cision des Ă©valuations gĂ©nomiques intra-races est relativement Ă©levĂ©e, mĂȘme dans le cas d'une population de rĂ©fĂ©rence rĂ©duite, lorsque les pĂšres des candidats Ă la sĂ©lection sont inclus dans la population de rĂ©fĂ©rence.Les rĂ©sultats obtenus suggĂšrent donc que la mise en place d'Ă©valuations gĂ©nomiques dans les races rĂ©gionales est envisageable. Il faudra toutefois poursuivre les travaux pour dĂ©terminer quelle stratĂ©gie optimale peut/doit ĂȘtre utilisĂ©e dans chacune des races.Within-breed genomic selection is now implemented in a number of large cattle breeds. However, building reference populations large enough remains a major challenge for smaller breeds. Combining reference populations and implementing a multi-breed approach appears to be an appealing alternative for small breeds.Such an approach requires conserved linkage disequilibrium across breeds to maintain the association between QTL and markers. Therefore, the use of a high density chip is generally needed. Error rates for high density imputation from medium density genotypes, classically used in cattle, were estimated. The mean error rate was below 1% in most dairy cattle breed which implies that a large high density imputed reference populations can be available for genomic selection at low cost. Reference populations from the three major French dairy breeds were imputed to high density and used to develop a multi-breed genomic evaluation.Several alternative genomic selection approaches (within-breed or multi-breed, based on medium or high density genotypes) were compared for breeds with different sizes of reference population. Improvement of genomic prediction accuracy due to the multi-breed evaluation was observed for breeds with 500 animals or less in their reference population. Accuracy of a third alternative using multi-breed evaluation based on medium density genotypes of closely related breeds was investigated. The benefit of multi-breed genomic evaluation was then three times higher in this situation than in the one where populations from major dairy cattle breeds were pooled. It can be noted that in both situations, using within-breed genomic information allowed a significant gain in accuracy compared to pedigree-based evaluations even for a small breed, when all sires of selection candidates belong to the reference population.These results suggest that implementation of genomic selection is feasible in small dairy cattle breeds. However further work is required to determine which optimal strategy can/must be implemented in a given breed
Multi-breed genomic evaluations in dairy cattle
L'efficacitĂ© de la sĂ©lection gĂ©nomique Ă©tant principalement dĂ©pendante de la taille de la population de rĂ©fĂ©rence, seules les principales races laitiĂšres françaises bĂ©nĂ©ficient aujourd'hui d'Ă©valuations gĂ©nomiques. Pour contourner cette contrainte et dĂ©velopper des Ă©valuations gĂ©nomiques pour les races rĂ©gionales, il a Ă©tĂ© proposĂ© de crĂ©er une population de rĂ©fĂ©rence commune entre races.Cependant, utiliser une population de rĂ©fĂ©rence multiraciale nĂ©cessite que le lien entre QTL et marqueurs soit conservĂ© entre races, ce qui implique, sauf cas particulier, l'utilisation d'une puce haute densitĂ©. Les taux d'erreur d'imputation des gĂ©notypes haute densitĂ© Ă partir de gĂ©notypes moyenne densitĂ© (classiquement utilisĂ©s en bovins) ont Ă©tĂ© Ă©tudiĂ©s. La prĂ©cision d'imputation Ă©tant supĂ©rieure Ă 99% dans la majoritĂ© des races laitiĂšres, l'imputation des gĂ©notypes des animaux des populations de rĂ©fĂ©rence des principales races laitiĂšres a Ă©tĂ© rĂ©alisĂ©e. Cette population de rĂ©fĂ©rence « haute densitĂ© » a ensuite Ă©tĂ© utilisĂ©e pour le dĂ©veloppement d'Ă©valuations gĂ©nomiques multiraciales. Plusieurs stratĂ©gies d'Ă©valuations gĂ©nomiques (intra-race ou multi-race, Ă partir de gĂ©notypes moyenne ou haute densitĂ©) ont Ă©tĂ© comparĂ©es pour diffĂ©rentes tailles de populations de rĂ©fĂ©rence. Les Ă©valuations multiraciales basĂ©es sur la puce haute densitĂ© permettent d'amĂ©liorer la prĂ©cision des Ă©valuations gĂ©nomiques dans le cas d'une population de rĂ©fĂ©rence de 500 taureaux ou moins. L'efficacitĂ© d'une troisiĂšme stratĂ©gie utilisant des Ă©valuations gĂ©nomiques multiraciales Ă partir de la puce moyenne densitĂ© pour un groupe de races proches a donc Ă©tĂ© Ă©tudiĂ©e. L'augmentation de la prĂ©cision des Ă©valuations gĂ©nomiques observĂ©e dans ce cas Ă©tait trois fois supĂ©rieure Ă celle qui avait Ă©tĂ© observĂ©e dans le cas des principales races laitiĂšres. Par ailleurs, dans les deux cas Ă©tudiĂ©s ici, la prĂ©cision des Ă©valuations gĂ©nomiques intra-races est relativement Ă©levĂ©e, mĂȘme dans le cas d'une population de rĂ©fĂ©rence rĂ©duite, lorsque les pĂšres des candidats Ă la sĂ©lection sont inclus dans la population de rĂ©fĂ©rence.Les rĂ©sultats obtenus suggĂšrent donc que la mise en place d'Ă©valuations gĂ©nomiques dans les races rĂ©gionales est envisageable. Il faudra toutefois poursuivre les travaux pour dĂ©terminer quelle stratĂ©gie optimale peut/doit ĂȘtre utilisĂ©e dans chacune des races.Within-breed genomic selection is now implemented in a number of large cattle breeds. However, building reference populations large enough remains a major challenge for smaller breeds. Combining reference populations and implementing a multi-breed approach appears to be an appealing alternative for small breeds.Such an approach requires conserved linkage disequilibrium across breeds to maintain the association between QTL and markers. Therefore, the use of a high density chip is generally needed. Error rates for high density imputation from medium density genotypes, classically used in cattle, were estimated. The mean error rate was below 1% in most dairy cattle breed which implies that a large high density imputed reference populations can be available for genomic selection at low cost. Reference populations from the three major French dairy breeds were imputed to high density and used to develop a multi-breed genomic evaluation.Several alternative genomic selection approaches (within-breed or multi-breed, based on medium or high density genotypes) were compared for breeds with different sizes of reference population. Improvement of genomic prediction accuracy due to the multi-breed evaluation was observed for breeds with 500 animals or less in their reference population. Accuracy of a third alternative using multi-breed evaluation based on medium density genotypes of closely related breeds was investigated. The benefit of multi-breed genomic evaluation was then three times higher in this situation than in the one where populations from major dairy cattle breeds were pooled. It can be noted that in both situations, using within-breed genomic information allowed a significant gain in accuracy compared to pedigree-based evaluations even for a small breed, when all sires of selection candidates belong to the reference population.These results suggest that implementation of genomic selection is feasible in small dairy cattle breeds. However further work is required to determine which optimal strategy can/must be implemented in a given breed
Investigating the impact of paternal age, paternal heat stress, and estimation of non-genetic paternal variance on dairy cow phenotype
Abstract Background Linear models that are commonly used to predict breeding values in livestock species consider paternal influence solely as a genetic effect. However, emerging evidence in several species suggests the potential effect of non-genetic semen-mediated paternal effects on offspring phenotype. This study contributes to such research by analyzing the extent of non-genetic paternal effects on the performance of Holstein, MontbĂ©liarde, and Normande dairy cows. Insemination data, including semen Batch Identifier (BI, a combination of bull identification and collection date), was associated with various traits measured in cows born from the insemination. These traits encompassed stature, milk production (milk, fat, and protein yields), udder health (somatic cell score and clinical mastitis), and female fertility (conception rates of heifers and cows). We estimated (1) the effects of age at collection and heat stress during spermatogenesis, and (2) the variance components associated with BI or Weekly aggregated BI (WBI). Results Overall, the non-genetic paternal effect estimates were small and of limited biological importance. However, while heat stress during spermatogenesis did not show significant associations with any of the traits studied in daughters, we observed significant effects of bull age at semen collection on the udder health of daughters. Indeed, cows born from bulls collected after 1500 days of age had higher somatic cell scores compared to those born from bulls collected at a younger age (less than 400 days old) in both Holstein and Normande breeds (+â3% andâ+â5% of the phenotypic mean, respectively). In addition, across all breeds and traits analyzed, the estimates of non-genetic paternal variance were consistently low, representing on average 0.13% and 0.09% of the phenotypic variance for BI and WBI, respectively (ranging from 0 to 0.7%). These estimates did not significantly differ from zero, except for milk production traits (milk, fat, and protein yields) in the Holstein breed and protein yield in the MontbĂ©liarde breed when WBI was considered. Conclusions Our findings indicate that non-genetic paternal information transmitted through semen does not substantially influence the offspring phenotype in dairy cattle breeds for routinely measured traits. This lack of substantial impact may be attributed to limited transmission or minimal exposure of elite bulls to adverse conditions