Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals
Bouwman, Aniek C. ; Daetwyler, Hans D. ; Chamberlain, Amanda J. ; Ponce, Carla Hurtado ; Sargolzaei, Mehdi ; Schenkel, Flavio S. ; Sahana, Goutam ; Govignon-Gion, Armelle ; Boitard, Simon ; Dolezal, Marlies ; Pausch, Hubert ; Brøndum, Rasmus F. ; Bowman, Phil J. ; Thomsen, Bo ; Guldbrandtsen, Bernt ; Lund, Mogens S. ; Servin, Bertrand ; Garrick, Dorian J. ; Reecy, James ; Vilkki, Johanna ; Bagnato, Alessandro ; Wang, Min ; Hoff, Jesse L. ; Schnabel, Robert D. ; Taylor, Jeremy F. ; Vinkhuyzen, Anna A.E. ; Panitz, Frank ; Bendixen, Christian ; Holm, Lars Erik ; Gredler, Birgit ; Hozé, Chris ; Boussaha, Mekki ; Sanchez, Marie Pierre ; Rocha, Dominique ; Capitan, Aurelien ; Tribout, Thierry ; Barbat, Anne ; Croiseau, Pascal ; Drögemüller, Cord ; Jagannathan, Vidhya ; Vander Jagt, Christy ; Crowley, John J. ; Bieber, Anna ; Purfield, Deirdre C. ; Berry, Donagh P. ; Emmerling, Reiner ; Götz, Kay Uwe ; Frischknecht, Mirjam ; Russ, Ingolf ; Sölkner, Johann ; Tassell, Curtis P. van; Fries, Ruedi ; Stothard, Paul ; Veerkamp, Roel F. ; Boichard, Didier ; Goddard, Mike E. ; Hayes, Ben J. - \ 2018
Nature Genetics 50 (2018). - ISSN 1061-4036 - p. 362 - 367.
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 × 10−8) 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 ChIP–seq 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.
Genetic and nongenetic factors contributing to differences in αS-casein phosphorylation isoforms and other major milk proteins
Fang, Z.H. ; Bovenhuis, H. ; Delacroix-Buchet, A. ; Miranda, G. ; Boichard, D. ; Visker, M.H.P.W. ; Martin, P. - \ 2017
Journal of Dairy Science 100 (2017)7. - ISSN 0022-0302 - p. 5564 - 5577.
Casein haplotype - French Montbéliarde - Genetic variant - Lactation stage

Relative concentrations of αS-casein (αS-CN) phosphorylation isoforms vary considerably among milk of individual cows. We aimed to explore to what extent genetic and other factors contribute to the variation in relative concentrations of αS-CN phosphorylation isoforms and the phosphorylation degree of αS-CN defined as the proportion of isoforms with higher degrees of phosphorylation. We also investigated the associations of genetic variants of milk proteins and casein haplotypes with relative concentrations of αS-CN phosphorylation isoforms and with the phosphorylation degree of αS-CN in French Montbéliarde cattle from the cheese production area of Franche-Comté. Detailed milk protein composition was determined by liquid chromatography coupled with electrospray ionization mass spectrometry from 531 test-day morning milk samples. Parity, lactation stage, and genetic variation of cows contributed to the phenotypic variation in relative concentrations of individual αS-CN phosphorylation isoforms and in the phosphorylation degree of αS-CN. As lactation progressed, we observed a significant increase for relative concentrations of αS-CN isoforms with higher degrees of phosphorylation (αS1-CN-9P, αS2-CN-13P, and αS2-CN-14P) as well as for the phosphorylation degree of both αS1-CN and αS2-CN. Furthermore, the β-CN I variant was associated with a greater proportion of isoforms with lower degrees of phosphorylation (αS1-CN-8P, αS2-CN-10P, and αS2-CN-11P); the β-CN B variant was associated with a greater proportion of isoforms with higher degrees of phosphorylation (αS1-CN-9P, αS2-CN-12P to αS2-CN-14P). The heritability estimates were low to moderate for relative concentrations of αS2-CN phosphorylation isoforms (0.07 to 0.32), high for relative concentrations of αS1-CN-8P (0.84) and αS1-CN-9P (0.56), and moderate for phosphorylation degrees of αS1-CN (0.37) and αS2-CN (0.23). Future studies investigating relations between the phosphorylation degree of αS-CN and technological properties of milk will be beneficial for the dairy industry.

Challenge session: "New legal landscape guiding access and benefit-sharing of animal genetic resources"
Martyniuk, E. ; Kozaowska, Alicja ; Tixier-Boichard, M. ; Venneman, Jan ; Hoffmann, I. ; Baumung, R. ; Visser, L. ; Hiemstra, S.J. - \ 2016
Rome : European Association for Animal Production (EAAP) - 9 p.
GO-FAANG meeting : a Gathering On Functional Annotation of Animal Genomes
Tuggle, Christopher K. ; Giuffra, Elisabetta ; White, Stephen N. ; Clarke, Laura ; Zhou, Huaijun ; Ross, Pablo J. ; Acloque, Hervé ; Reecy, James M. ; Archibald, Alan ; Bellone, Rebecca R. ; Boichard, Michèle ; Chamberlain, Amanda ; Cheng, Hans ; Crooijmans, Richard P.M.A. ; Delany, Mary E. ; Finno, Carrie J. ; Groenen, Martien A.M. ; Hayes, Ben ; Lunney, Joan K. ; Petersen, Jessica L. ; Plastow, Graham S. ; Schmidt, Carl J. ; Song, Jiuzhou ; Watson, Mick - \ 2016
Animal Genetics 47 (2016)5. - ISSN 0268-9146 - p. 528 - 533.
data coordination centre (DCC) - data sharing - Genomics - metanalysis

The Functional Annotation of Animal Genomes (FAANG) Consortium recently held a Gathering On FAANG (GO-FAANG) Workshop in Washington, DC on October 7–8, 2015. This consortium is a grass-roots organization formed to advance the annotation of newly assembled genomes of domesticated and non-model organisms ( The workshop gathered together from around the world a group of 100+ genome scientists, administrators, representatives of funding agencies and commodity groups to discuss the latest advancements of the consortium, new perspectives, next steps and implementation plans. The workshop was streamed live and recorded, and all talks, along with speaker slide presentations, are available at In this report, we describe the major activities and outcomes of this meeting. We also provide updates on ongoing efforts to implement discussions and decisions taken at GO-FAANG to guide future FAANG activities. In summary, reference datasets are being established under pilot projects; plans for tissue sets, morphological classification and methods of sample collection for different tissues were organized; and core assays and data and meta-data analysis standards were established.

Heritability of body surface temperature in hens estimated by infrared thermography at normal or hot temperatures and genetic correlations with egg and feather quality
Loyau, T. ; Zerjal, T. ; Rodenburg, T.B. ; Fablet, J. ; Tixier-Boichard, M. ; Pinard-van der Laan, M.H. ; Mignon-Grasteau, S. - \ 2016
Animal 10 (2016)10. - ISSN 1751-7311 - p. 1594 - 1601.
adaptation - egg quality - genotype–environment interaction - heat stress - laying hens

Exposure of laying hens to chronic heat stress results in loss of egg production. It should be possible to improve hen resilience to chronic heat stress by genetic selection but measuring their sensitivity through internal temperature is time consuming and is not very precise. In this study we used infrared thermography to measure the hen’s capacity to dissipate heat, in a commercial line of laying hens subjected to cycles of neutral (N, 19.6°C) or high (H, 28.4°C) ambient temperatures. Mean body temperatures (BT) were estimated from 9355 infrared images of wing, comb and shank taken from 1200 hens. Genetic parameters were estimated separately for N and H temperatures. Correlations between BT and plumage condition were also investigated. Wing temperature had low heritability (0.00 to 0.09), consistent with the fact that wing temperature mainly reflects the environmental temperature and is not a zone of heat dissipation. The heritability of comb temperature was higher, from 0.15 to 0.19 in N and H conditions, respectively. Finally, the shank temperature provided the highest heritability estimates, with values of 0.20 to 0.22 in H and N conditions, respectively. Taken together, these results show that heat dissipation is partly under genetic control. Interestingly, the genetic correlation between plumage condition and shank and comb temperatures indicated that birds with poor condition plumage also had the possibility to dissipate heat through featherless areas. Genetic correlations of temperature measurements with egg quality showed that temperatures were correlated with egg width and weight, yolk brightness and yellowness and Haugh units only under H conditions. In contrast, shell colour was correlated with leg temperature only at thermo-neutrality.

Meta-analysis of GWAS of bovine stature with >50,000 animals imputed to whole-genome sequence
Bouwman, A.C. ; Pausch, H. ; Govignon-Gion, A. ; Hoze, C. ; Sanchez, M.P. ; Boussaha, M. ; Boichard, D.A. ; Sahana, G. ; Brondum, R.F. ; Guldbrandtsen, B. ; Lund, M. ; Vilkki, J. ; Sargolzaei, M. ; Schenkel, F.S. ; Taylor, J. ; Hoff, J.L. ; Schnabel, R.D. ; Veerkamp, R.F. ; Goddard, M.E. ; Hayes, B.J. - \ 2015
Extensive meta analysis of GWAS in humans has identified 697 significant SNP, however these SNP explain
only 20% the total genetic variation. In order to compare the genetic architecture of stature in humans to
stature in cattle, we performed a large meta-analysis using imputed sequence data. The 1000 Bull Genomes
project provided a multi-breed reference population of 1,147 sequenced animals to impute SNP-chip
genotypes up to whole genome sequence for 15 populations. The populations from Australia, Canada,
Denmark, Finland, France, Germany, the Netherlands, and the USA represented the Angus, Fleckvieh,
Holstein, Jersey, Montbeliarde, Normande, and Nordic Red Dairy Cattle breeds. Genome-wide association
studies were performed on stature phenotypes for each of the populations. Individual GWAS studies revealed
many QTL regions and several regions harboured good candidate genes, e.g. PLAG1, IGF2. Results from
these GWAS studies were combined in a meta-analysis to increase the power for QTL detection and to
refine QTL regions exploiting the different patterns of LD among the breeds. Results of this meta-analysis
will be validated in an independent population to determine how much of the variation in stature can be
explained by the significant SNP
Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project : open letter
Archibald, A.L. ; Bottema, C.D. ; Brauning, R. ; Burgess, S.C. ; Burt, D.W. ; Casas, E. ; Cheng, H.H. ; Clarke, L. ; Couldrey, C. ; Dalrymple, B.P. ; Elsik, C.G. ; Foissac, S. ; Giuffra, E. ; Groenen, M.A.M. ; Hayes, B.J. ; Huang, L.S. ; Khatib, H. ; Kijas, J.W. ; Kim, H. ; Lunney, J.K. ; McCarthy, F.M. ; McEwan, J. ; Moore, S. ; Nanduri, B. ; Notredame, C. ; Palti, Y. ; Plastow, G.S. ; Reecy, J.M. ; Rohrer, G. ; Sarropoulou, E. ; Schmidt, C.J. ; Silverstein, J. ; Tellam, R.L. ; Tixier-Boichard, M. ; Tosser-klopp, G. ; Tuggle, C.K. ; Vilkki, J. ; White, S.N. ; Zhao, S. ; Zhou, H. - \ 2015
Genome Biology 16 (2015). - ISSN 1474-7596 - 6 p.
We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species.
Robustness to chronic heat stress in laying hens: a meta-analysis
Mignon-Grasteau, S. ; Moreri, U. ; Narcy, A. ; Rousseau, X. ; Rodenburg, T.B. ; Tixier-Boichard, M. ; Zerjal, T. - \ 2015
Poultry Science 94 (2015)4. - ISSN 0032-5791 - p. 586 - 600.
high ambient-temperatures - egg quality - naked neck - vitamin-c - performance - dwarf - gene - supplementation - management - nutrition
Chronic heat is a major stress factor in laying hens and many studies on the effect of heat stress have been published. It remains difficult, however, to draw general conclusions about the effect of chronic heat stress on performance and its relationship with genetic and environmental factors, as these studies have been done under varying experimental conditions and using various experimental designs. A meta-analysis enabled us to make a quantitative review of the results from 131 published papers. The relative effects of four factors (genotype, age, group size, and amplitude of temperature variation) and their interactions with temperature were analyzed for 13 traits. After pre-correcting the data for a random study effect, the best model for each trait was selected in a stepwise procedure based on its residual sum of squares. Shell strength, daily feed intake, egg mass, and hen-day egg production were found to be more sensitive to heat stress than the other traits as they dropped by 9.0 to 22.6% between thermo-neutrality (15 to 20°C) and heat stress (30 to 35°C) while yolk and albumen proportions or Haugh units showed nearly no variation with temperature (
A European strategy for animal gene banks
Tixier-Boichard, M. ; Hiemstra, S.J. - \ 2015
Pan European Networks (2015). - 1 p.
Bos taurus strain:dairy beef (cattle): 1000 Bull Genomes Run 2, Bovine Whole Genome Sequence
Bouwman, A.C. ; Daetwyler, H.D. ; Chamberlain, Amanda J. ; Ponce, Carla Hurtado ; Sargolzaei, Mehdi ; Schenkel, Flavio S. ; Sahana, Goutam ; Govignon-Gion, Armelle ; Boitard, Simon ; Dolezal, Marlies ; Pausch, Hubert ; Brøndum, Rasmus F. ; Bowman, Phil J. ; Thomsen, Bo ; Guldbrandtsen, Bernt ; Lund, Mogens S. ; Servin, Bertrand ; Garrick, Dorian J. ; Reecy, James M. ; Vilkki, Johanna ; Bagnato, Alessandro ; Wang, Min ; Hoff, Jesse L. ; Schnabel, Robert D. ; Taylor, Jeremy F. ; Vinkhuyzen, Anna A.E. ; Panitz, Frank ; Bendixen, Christian ; Holm, Lars-Erik ; Gredler, Birgit ; Hozé, Chris ; Boussaha, Mekki ; Sanchez, Marie Pierre ; Rocha, Dominique ; Capitan, Aurelien ; Tribout, Thierry ; Barbat, Anne ; Croiseau, Pascal ; Drögemüller, Cord ; Jagannathan, Vidhya ; Vander Jagt, Christy ; Crowley, John J. ; Bieber, Anna ; Purfield, Deirdre C. ; Berry, Donagh P. ; Emmerling, Reiner ; Götz, Kay Uwe ; Frischknecht, Mirjam ; Russ, Ingolf ; Sölkner, Johann ; Tassell, Curtis P. van; Fries, Ruedi ; Stothard, Paul ; Veerkamp, R.F. ; Boichard, Didier ; Goddard, Mike E. ; Hayes, Ben J. - \ 2014
Bos taurus - PRJNA238491
Whole genome sequence data (BAM format) of 234 bovine individuals aligned to UMD3.1. The aim of the study was to identify genetic variants (SNPs and indels) for downstream analysis such as imputation, GWAS, and detection of lethal recessives. Additional sequences for later 1000 bull genomes runs can be found at partners individual projects including PRJEB9343, PRJNA176557, PRJEB18113, PRNJA343262, PRJNA324822, PRJNA324270, PRJNA277147, PRJEB5462.
Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle
Daetwyler, H.D. ; Capitan, A. ; Pausch, H. ; Stothard, P. ; Binsbergen, R. van; Brondum, R.F. ; Liao, X. ; Djari, A. ; Rodriguez, S.C. ; Grohs, C. ; Esquerré, D. ; Bouchez, O. ; Rossignol, M.N. ; Klopp, C. ; Rocha, D. ; Fritz, S. ; Eggen, A. ; Bowman, P.J. ; Coote, D. ; Chamberlain, A.J. ; Anderson, C.L. ; Tassel, C.P. ; Hulsegge, B. ; Goddard, M.E. ; Guldbrandsten, B. ; Lund, M.S. ; Veerkamp, R.F. ; Boichard, D.A. ; Fries, R. ; Hayes, B.J. - \ 2014
Nature Genetics 46 (2014). - ISSN 1061-4036 - p. 858 - 865.
boophilus-microplus resistance - mitotic chromosomes - genotype imputation - holstein calves - dairy-cattle - milk-yield - bos-taurus - condensin - mutations - gene
The 1000 bull genomes project supports the goal of accelerating the rates of genetic gain in domestic cattle while at the same time considering animal health and welfare by providing the annotated sequence variants and genotypes of key ancestor bulls. In the first phase of the 1000 bull genomes project, we sequenced the whole genomes of 234 cattle to an average of 8.3-fold coverage. This sequencing includes data for 129 individuals from the global Holstein-Friesian population, 43 individuals from the Fleckvieh breed and 15 individuals from the Jersey breed. We identified a total of 28.3 million variants, with an average of 1.44 heterozygous sites per kilobase for each individual. We demonstrate the use of this database in identifying a recessive mutation underlying embryonic death and a dominant mutation underlying lethal chrondrodysplasia. We also performed genome-wide association studies for milk production and curly coat, using imputed sequence variants, and identified variants associated with these traits in cattle.
Robustness to chronic heat stress in laying hens: a meta-analysis
Moreri, U. ; Zerjal, T. ; Rodenburg, T.B. ; Narcy, A. ; Rousseau, X. ; Tixier-Boichard, M. ; Mignon-Grasteau, S. - \ 2013
In: Proceedings of the 8th European Poultry Genetics Symposium, Venice, Italy, 25 - 29 September, 2013. - Venice, Italy : World's Poultry Science Association (WPSA) - p. 58 - 58.
Heat represents a major stress factor in laying hens, but it is difficult to compare published studies, done under very different conditions. A meta-analysis enabled us to make a quantitative review of the results from 100 published papers. Relative effects of four factors (genotype, age, group size and amplitude of temperature variation) were analyzed on feed intake, egg production, egg weight, egg mass and FCR. The GLMselect procedure in SAS was used to select the best model for each trait and to estimate the main effects and their interactions. Daily feed intake, egg mass and hen-day egg production were more sensitive to heat stress as they varied from -16.2% to -19.8% between 20 and 35°C while egg weight and FCR showed less variation (-3.8 to -6.4% between 20 and 35°C). Interactions were most often significant, which reinforces the interest of meta-analysis to summarize literature data. This study highlighted that the impacts of heat stress in laying hens depends on the genotype, age and the amplitude of temperature
1000 Bull Genomes - Toward genomic Selectionf from whole genome sequence Data in Dairy and Beef Cattle
Hayes, B. ; Daetwyler, H.D. ; Fries, R. ; Guldbrandtsen, B. ; Mogens Sando Lund, M. ; Didier A. Boichard, D.A. ; Stothard, P. ; Veerkamp, R.F. ; Hulsegge, B. ; Rocha, D. ; Tassell, C. ; Mullaart, E. ; Gredler, B. ; Druet, T. ; Bagnato, A. ; Goddard, M.E. ; Chamberlain, H.L. - \ 2013
Genomic prediction of breeding values is now used as the basis for selection of dairy cattle, and in some cases beef cattle, in a number of countries. When genomic prediction was introduced most of the information was to thought to be derived from linkage disequilibrium between markers and causative variants. It has become clear that much of the predictive power, based on 50,000 DNA markers, in fact derives from prediction of the effect of large chromosome segments that segregate within fairly closely related animals. This has lead to problems with across breed prediction, rapid decay of predictive power over generations and insufficient accuracy in some situations. Using full genome sequence data in genomic prediction should overcome these problems. If linkage disequilibrium between SNP on standard arrays and causative mutations affecting the quantitative trait is incomplete, accuracy of prediction should be improved as a result of including the actual causative mutations affecting the trait of interest in the data set. Secondly, persistence of accuracy of genomic predictions across generations will be improved with full sequence data, as the genomic predictions no longer depend on associations between SNP and causative mutations which currently erode quite rapidly with recombination. Thirdly, if genomic predictions are made across breeds, using full sequence data is likely to be particularly advantageous, as there is no longer a need to rely on marker- associations which may not persist across breeds. However, the cost of sequencing is such that the very large numbers of animals required for genomic prediction will not be sequenced An alternative strategy is to sequence key ancestors of the population, then impute the genotypes for the sequence variants into much larger reference sets with phenotypes and SNP panel genotypes. The 1000 Bull Genomes Project aims at building such a resource of sequenced key ancestor bulls for the bovine research community. The most recent run of the project included 238 full genome sequences of 130 Holstein, 43 Fleckvieh, 48 Angus and 15 Jersey bulls, sequenced at an average of 10.5 fold coverage. There were 25.2 million filtered sequence variants detected in the sequences, including 23.5 million SNP and 1.7 million insertion-deletions. Agreement of sequence genotypes to genotypes from an 800K SNP array in the sequenced Holstein bulls, where there was most data, was excellent at 98.8%. This increased to 99.7% when the genotypes were imputed based on all sequences. Concordance was slightly lower in other breeds. This project will provide an excellent opportunity to identify the most important causative variants, leading to greater understanding of biology underlying quantitative traits. Examples are given of genomic predictions for fertility, health and production traits using imputed sequence data.
Toward genomic prediction from genome sequence data and the 1000 bull genomes project
Hayes, B. ; Anderson, C.L. ; Daetwyler, H.D. ; Fries, R. ; Guldbrandtsen, B. ; Lund, M. ; Boichard, D.A. ; Stothard, P. ; Veerkamp, R.F. ; Hulsegge, B. ; Rocha, D. ; Tassell, C. ; Coote, D. ; Goddard, M.E. ; The 1000 Bull Genomes Consortium, - \ 2012
In: 4th International Conference of Quantative Genetics. - - p. 55 - 55.
A century of poultry genetics
Tixier-Boichard, M. ; Leenstra, F.R. ; Flock, D. ; Hocking, A.D. ; Weigend, S. - \ 2012
Worlds Poultry Science Journal 68 (2012)2. - ISSN 0043-9339 - p. 307 - 321.
major histocompatibility complex - chicken genome - nucleolar organizer - molecular-cloning - linked factors - linkage map - egg-white - rfp-y - diversity - selection
The 20th Century saw an astonishing advance in our understanding of genetics and the scientific basis of the genetic improvement of farm animals. The application of genetic principles to chickens in the 1950s and 1960s led to a rapid change in the productivity and efficiency of laying hens and broiler chickens, turkeys and ducks. Subsequently, the application of increasingly powerful computers and sophisticated mathematical algorithms has increased the range of traits that could be successfully incorporated into breeding programs. Random sample tests of the performance of laying hens enjoyed a period of popularity and more recently the few remaining tests included husbandry systems in addition to strain evaluation. Characterisation of avian blood groups has led to the identification of the B21 haplotype that confers resistance to Marek's disease and to selection for this locus in commercial lines. The decade following the millennium saw the publication of the genome sequence of the chicken and the identification of millions of single nucleotide polymorphisms that, coupled with technological advances, made the application of whole genome selection practical in poultry. In parallel, the molecular basis for some Mendelian traits described a century ago is now being deciphered. Similar technologies have been applied to study genetic diversity in chickens and have provided insights into the evolution and domestication of chicken breeds. Finally, in this review, the recent development of the European Poultry Genetics Symposia coordinated by Working Group 3 ‘Genetics and Breeding’ that was based on combining the British Poultry Breeders Round Table and AVIAGEN from West and Eastern Europe, is discussed
1000 Bull Genomes Consortium Project
Hayes, B.J. ; Fries, R. ; Lund, M.S. ; Boichard, D.A. ; Stothard, P. ; Veerkamp, R.F. ; Tassell, C. ; Anderson, C.L. ; Hulsegge, B. ; Guldbrandtsen, B. ; Rocha, D. ; Hinirichs, D. ; Bagnato, A. ; Georges, M. ; Spelman, R.J. ; Reecy, J.M. ; Archibald, A.L. ; Goddard, M.E. ; Gredler, B. - \ 2012
In: Plant and Animal Genome XX Conference, San Diego, CA, USA, 14-18 January 2012. -
Genomic selection, where selection decisions are based on estimates of breeding value from genome wide-marker effects, has enormous potential to improve genetic gain in dairy and beef cattle. Although successful in dairy cattle, some major challenges remain 1) only a proportion of the genetic variance is captured, particularly for some traits 2) marker effects are rarely consistent across breeds, 3) accuracy of genomic predictions decays rapidly over time. Using full genome sequences rather than DNA markers in genomic selection could address these challenges. However, sequencing all individuals in the very large resource populations required to estimate the typically small effects of mutations on target traits would be prohibitively expensive. An alternative is to sequence key ancestors contributing most of the genetic material of the current population, and to use this reference for imputation of sequence from SNP chip data. The reference set must still be large, in order to capture for example, rare variants which are likely to explain some of the variation in our target traits. Recognising the need for a comprehensive “reference set” of key ancestors by many groups undertaking cattle research and cattle breeding programs, we have initiated the 1000 bull genomes project. The project will assemble whole genome sequences of cattle from institutions around the world, to provide an extended data base for imputation of genetic variants. This will enable the bovine genomics community to impute full genome sequence from SNP genotypes, and then use this data for genomic selection, and rapid discovery of causal mutations. Some preliminary results from the variant detection pipeline will be reported.
Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools
Hillel, J. ; Groenen, M.A.M. ; Tixier-Boichard, M. ; Korol, A.B. ; David, L. ; Kirzhner, V.M. ; Burke, T. ; Barre-Dirie, A. ; Crooijmans, R.P.M.A. ; Elo, K. ; Fieldman, M.W. ; Freidlin, P.J. ; Maki-Tanila, A. ; Oortwijn, M.E.P. - \ 2003
Genetics, Selection, Evolution 35 (2003)5. - ISSN 0999-193X - p. 533 - 557.
genetic-distance - linkage map - markers - origin - breeds - lines - heterozygosity - fingerprints - diversity - samples
In a project on the biodiversity of chickens funded by the European Commission (EC), eight laboratories collaborated to assess the genetic variation within and between 52 populations from a wide range of chicken types. Twenty-two di-nucleotide microsatellite markers were used to genotype DNA pools of 50 birds from each population. The polymorphism measures for the average, the least polymorphic population ( inbred C line) and the most polymorphic population (Gallus gallus spadiceus) were, respectively, as follows: number of alleles per locus, per population: 3.5, 1.3 and 5.2; average gene diversity across markers: 0.47, 0.05 and 0.64; and proportion of polymorphic markers: 0.91, 0.25 and 1.0. These were in good agreement with the breeding history of the populations. For instance, unselected populations were found to be more polymorphic than selected breeds such as layers. Thus DNA pools are effective in the preliminary assessment of genetic variation of populations and markers. Mean genetic distance indicates the extent to which a given population shares its genetic diversity with that of the whole tested gene pool and is a useful criterion for conservation of diversity. The distribution of population-specific (private) alleles and the amount of genetic variation shared among populations supports the hypothesis that the red jungle fowl is the main progenitor of the domesticated chicken.
Empirical Evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds
Rosenberg, N.A. ; Burke, T. ; Elo, K. ; Feldman, M.W. ; Friedlin, P.J. ; Groenen, M.A.M. ; Hillel, J. ; Maki-Tanila, A. ; Tixier-Boichard, M. ; Vignal, A. ; Wimmers, K. - \ 2001
Genetics 159 (2001). - ISSN 0016-6731 - p. 699 - 713.
We tested the utility of genetic cluster analysis in ascertaining population structure of a large data set for which population structure was previously known. Each of 600 individuals representing 20 distinct chicken breeds was genotyped for 27 microsatellite loci, and individual multilocus genotypes were used to infer genetic clusters. Individuals from each breed were inferred to belong mostly to the same cluster. The clustering success rate, measuring the fraction of individuals that were properly inferred to belong to their correct breeds, was consistently ∼98ÐWhen markers of highest expected heterozygosity were used, genotypes that included at least 8-10 highly variable markers from among the 27 markers genotyped also achieved >95␌lustering success. When 12-15 highly variable markers and only 15-20 of the 30 individuals per breed were used, clustering success was at least 90ÐWe suggest that in species for which population structure is of interest, databases of multilocus genotypes at highly variable markers should be compiled. These genotypes could then be used as training samples for genetic cluster analysis and to facilitate assignments of individuals of unknown origin to populations. The clustering algorithm has potential applications in defining the within-species genetic units that are useful in problems of conservation.
Assessment of biodiversity in a wide range of chicken breeds by genotyping DNA pools for microsatellite loci
Weigend, S. ; Hillel, J. ; Groenen, M.A.M. ; Tixier-Boichard, M. ; Korol, A. ; Kirzner, V. ; Freidlin, P. ; Crooijmans, R.P.M.A. ; Vignal, A. ; Wimmers, K. ; Ponsuksili, S. ; Thomson, P.A. ; Burke, T. ; Maki-Tanila, A. ; Elo, K. ; Barredirie, A. ; Zhivotovsky, L.A. ; Fledman, M.W. - \ 2000
In: book of Abstracts : 27th International Conference on Animal Genetics, 22-26 July, Minneapolis, Minnesota, USA - p. 83 - 83.
Estimation of SNP frequencies in European chicken populations
Vignal, A. ; Monbrun, C. ; Thompson, P. ; Barre-Dirie, A. ; Burke, T. ; Groenen, M.A.M. ; Hillel, M. ; Mäki-Tanila, A. ; Tixier-Boichard, M. ; Wimmers, K. ; Weigend, S. - \ 2000
In: Book of Abstracts : 27th International conference on Animal Genetics, 22-26 July, Minneapolis, Minnesota, USA - p. 71 - 71.
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