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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TLDR
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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Posted ContentDOI
Accuracy of whole-genome sequence imputation using hybrid peeling in large pedigreed livestock populations
Roger Ros-Freixedes,Andrew Whalen,Ching-Yi Chen,Gregor Gorjanc,William O Herring,Alan J. Mileham,John M. Hickey +6 more
TL;DR: The coupling of an appropriate sequencing strategy and imputation method, such as described and validated here, is a powerful strategy for generating whole-genome sequence data in large pedigreed populations with high accuracy.
Posted ContentDOI
Whole Genome Detection of Sequence and Structural Polymorphism in Six Diverse Horses
Mohammed Al Abri,Mohammed Al Abri,Heather M. Holl,Sara E. Kalla,Nathan B. Sutter,Samantha A. Brooks +5 more
TL;DR: The genome re-sequencing and variant detection analysis for six horses belonging to geographically and physiologically diverse breeds revealed putatively functional variants including genes associated with size variation like ANKRD1 and HMGA1 in the very large Percheron and the ZFAT gene in the American Miniature horse.
Posted ContentDOI
Deciphering the wisent demographic and adaptive histories from individual whole-genome sequences
Mathieu Gautier,Katayoun Moazami-Goudarzi,Hubert Levéziel,Hugues Parinello,Cécile Grohs,Stéphanie Rialle,Rafał Kowalczyk,Laurence Flori +7 more
TL;DR: It is found that the wisent demography remained more fluctuating during the Pleistocene, in agreement with a scenario in which wisents responded to successive glaciations by habitat fragmentation rather than southward and eastward migration as for the bovine ancestors.
Journal ArticleDOI
The impact of genomic and traditional selection on the contribution of mutational variance to long-term selection response and genetic variance
Herman A. Mulder,Sang Hong Lee,Sang Hong Lee,Sam Clark,Ben J. Hayes,Julius H. J. van der Werf +5 more
TL;DR: It is advocated that more sustainable genomic selection strategies are required to optimize long-term selection response and to maintain genetic diversity.
Journal ArticleDOI
Genomic Selection. I: Latest Trends and Possible Ways of Development
TL;DR: Genomic selection is one of the most promising and safest methods for improving the genetic qualities of farm animals and plants as discussed by the authors, and it can play a key role in this process.
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.
Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
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
Primer3 on the WWW for general users and for biologist programmers.
Steve Rozen,Helen Skaletsky +1 more
TL;DR: This chapter assumes acquaintance with the principles and practice of PCR, as outlined in, for example, refs.
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.