Journal ArticleDOI
Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle
Hans D. Daetwyler,Aurélien Capitan,Hubert Pausch,Paul Stothard,Rianne van Binsbergen,R.F. Brøndum,Xiaoping Liao,Anis Djari,Sabrina Rodriguez,Cécile Grohs,Diane Esquerre,Olivier Bouchez,Marie-Noelle Rossignol,Christophe Klopp,Dominique Rocha,Sébastien Fritz,André Eggen,Phil J. Bowman,David Coote,Amanda J. Chamberlain,Charlotte Anderson,Curt P VanTassell,Ina Hulsegge,Michael E. Goddard,Bernt Guldbrandtsen,M.S. Lund,Roel F. Veerkamp,Didier Boichard,Ruedi Fries,Ben J. Hayes +29 more
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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.Abstract:
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.read more
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Journal ArticleDOI
Genome-wide association studies for additive and dominance effects for body composition traits in commercial crossbred Piétrain pigs.
M. Heidaritabar,Marco C. A. M. Bink,Elda Dervishi,Patrick Charagu,A. E. Huisman,Graham Plastow +5 more
TL;DR: In this article , the additive and dominance effects of the most significant variant in the quantitative trait loci (QTL) regions were estimated for a commercial crossbred Piétrain pigs using both 50'K array and sequence genotypes.
Journal ArticleDOI
Mating allocations in Holstein combining genomic information and linear programming optimization at the herd level.
Christian Bengtsson,H. Stålhammar,Jørn Rind Thomasen,W.F. Fikse,Erling Strandberg,Susanne Eriksson +5 more
TL;DR: In this article , the authors used linear programming to optimize economic scores within each herd, considering genetic level, genetic relationship, semen cost, the economic impact of genetic defects, polledness, and β-casein.
Posted ContentDOI
Genomic prediction including SNP-specific variance predictors
TL;DR: In this paper, the authors proposed a general model for genomic selection using a link function approach within the hierarchical generalized linear model framework (hglm) that can include external information on the markers.
Journal ArticleDOI
Mutation of the MYH3 gene causes recessive cleft palate in Limousine cattle
Anne Vaiman,Sébastien Fritz,Christian Beauvallet,Mekki Boussaha,Cécile Grohs,Nathalie Daniel-Carlier,Anne Relun,Didier Boichard,Jean-Luc Vilotte,Amandine Duchesne +9 more
TL;DR: In this paper , a new form of hereditary cleft palate in Limousine cattle was identified, which is a common malformation in mammals with environmental or hereditary aetiologies.
References
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Journal ArticleDOI
The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
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TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Book ChapterDOI
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Journal ArticleDOI
A method and server for predicting damaging missense mutations.
Ivan Adzhubei,Steffen Schmidt,Leonid Peshkin,Vasily Ramensky,Anna Gerasimova,Peer Bork,Alexey S. Kondrashov,Shamil R. Sunyaev +7 more
TL;DR: A new method and the corresponding software tool, PolyPhen-2, which is different from the early tool polyPhen1 in the set of predictive features, alignment pipeline, and the method of classification is presented and performance, as presented by its receiver operating characteristic curves, was consistently superior.
Journal ArticleDOI
Database resources of the National Center for Biotechnology Information
David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.