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
Integrating genome-wide association and expression quantitative trait loci (eQTL) analyses identifies genes affecting fertility in cattle and suggests a common set of genes regulating fertility in mammals
TL;DR: The authors used genome-wide association (GWAS) summary statistics for heifer puberty (pubertal or not at 600 days) from 27,707 cattle; multi-trait GWAS signals from 2,119 cattle for four fertility traits, including days to calving, age at first calving and heifer pregnancy status, and foetus age in weeks; and expression quantitative trait locus (eQTL) for whole blood from 489 cattle.
Journal ArticleDOI
Optimizing Sequencing Resources in Genotyped Livestock Populations Using Linear Programming.
TL;DR: In this paper, the authors present two applications of linear programming for the efficient allocation of sequencing resources for genotyped livestock populations such that the entire population can be imputed, maximizing the efficiency of whole genome sequencing budgets.
Journal ArticleDOI
Association Studies and Genomic Prediction for Genetic Improvements in Agriculture
TL;DR: The concepts, theories, methods, applications, and future implications of association studies and predicting unknown genetic value or future phenotypic events using genomics in the area of breeding in agriculture are introduced.
Journal ArticleDOI
Combining genome-wide association study based on low-coverage whole genome sequencing and transcriptome analysis to reveal the key candidate genes affecting meat color in pigs.
TL;DR: In this paper , a genome-wide association study based on low-coverage whole-genome sequencing was performed to decipher the genetic basis of meat color traits, and the results revealed that 10 genes were the potential candidates for regulating meat color.
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.