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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Whole-genome resequencing of wild and domestic sheep identifies genes associated with morphological and agronomic traits
Xin Li,Ji Yang,Ji Yang,Min Shen,Xing-Long Xie,Guangjian Liu,Ya-Xi Xu,Ya-Xi Xu,Feng-Hua Lv,Feng-Hua Lv,Hua Yang,Yong-Lin Yang,Liu Changbin,Ping Zhou,Peng-Cheng Wan,Zhang Yunsheng,Lei Gao,Yang Jingquan,Pi Wenhui,Yan-Ling Ren,Zhi-Qiang Shen,Feng Wang,Juan Deng,Juan Deng,Song-Song Xu,Hosein Salehian-Dehkordi,EEr Hehua,Ali Esmailizadeh,Mostafa Dehghani-Qanatqestani,Ondřej Štěpánek,C. Weimann,Georg Erhardt,Agraw Amane,Agraw Amane,Joram M. Mwacharo,Jian-Lin Han,Jian-Lin Han,Olivier Hanotte,Olivier Hanotte,Olivier Hanotte,Johannes A. Lenstra,Juha Kantanen,David W. Coltman,James Kijas,Michael William Bruford,Kathiravan Periasamy,Xinhua Wang,Meng-Hua Li,Meng-Hua Li +48 more
TL;DR: Deep resequencing of 248 wild and domestic sheep is presented, with associated data and analysis that provides insights into the demographic history of sheep and a valuable genomic resource for future genetic studies and improved genome-assisted breeding of Sheep and other domestic animals.
Journal ArticleDOI
Genomic prediction using imputed whole-genome sequence data in Holstein Friesian cattle.
Rianne van Binsbergen,Mario P. L. Calus,Marco C. A. M. Bink,Fred A. van Eeuwijk,Chris Schrooten,Roel F. Veerkamp +5 more
TL;DR: Compared to BovineHD genotype data, using imputed sequence data for genomic prediction produced no advantage and a training set with a larger number of individuals that are distantly related to each other and genomic prediction models that incorporate biological information on the SNPs or that apply stricter SNP pre-selection should be considered.
Journal ArticleDOI
Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent.
Marta Pereira Verdugo,Victoria E. Mullin,Victoria E. Mullin,Amelie Scheu,Amelie Scheu,Valeria Mattiangeli,Kevin G. Daly,Pierpaolo Maisano Delser,Pierpaolo Maisano Delser,Andrew J. Hare,Joachim Burger,Matthew J. Collins,Matthew J. Collins,Ron Kehati,Paula Wapnish Hesse,Deirdre Fulton,Eberhard Sauer,Fatemeh Azadeh Mohaseb,Fatemeh Azadeh Mohaseb,Hossein Davoudi,Hossein Davoudi,Roya Khazaeli,Johanna Lhuillier,Claude Rapin,Saeed Ebrahimi,Mutalib Khasanov,S. M. Farhad Vahidi,David E. MacHugh,Okan Ertugrul,Chaido Koukouli-Chrysanthaki,Adamantios Sampson,George Kazantzis,Ioannis Kontopoulos,Jelena Bulatović,Ivana Stojanović,Abdesalam Mikdad,Norbert Benecke,Jörg Linstädter,Mikhail V. Sablin,Robin Bendrey,Robin Bendrey,Lionel Gourichon,Benjamin S. Arbuckle,Marjan Mashkour,Marjan Mashkour,David Orton,Liora Kolska Horwitz,Matthew D. Teasdale,Matthew D. Teasdale,Daniel G. Bradley +49 more
TL;DR: Genome-wide analysis of 67 ancient Near Eastern cattle remains reveals regional variation that has since been obscured by admixture in modern populations, and mitochondrial DNA stasis supports that this introgression was male-driven, suggesting that selection of arid-adapted zebu bulls enhanced herd survival.
Journal ArticleDOI
Taming the Past: Ancient DNA and the Study of Animal Domestication
TL;DR: It is shown how the understanding of the genetic basis of animal domestication and the origins and dispersal of livestock and companion animals during the Upper Paleolithic and Neolithic periods is being rapidly transformed through new scientific knowledge generated with paleogenomic methods.
Journal ArticleDOI
Sequence-based Association Analysis Reveals an MGST1 eQTL with Pleiotropic Effects on Bovine Milk Composition.
Mathew D Littlejohn,Mathew D Littlejohn,Kathryn Tiplady,Tania Fink,Klaus Lehnert,Thomas Lopdell,Thomas Johnson,Christine Couldrey,M. Keehan,Richard G. Sherlock,Chad Harland,Andrew D Scott,Russell G. Snell,Stephen R. Davis,Richard J. Spelman +14 more
TL;DR: Genome sequence-based imputation and association mapping in a population of 64,244 taurine cattle reveals a cluster of 17 non-coding variants spanning MGST1 that are highly associated with milk fat percentage, and a range of other milk composition traits, and implicate MG ST1, a gene with no obvious mechanistic relationship to milk composition regulation, as causally involved in these processes.
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
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Journal ArticleDOI
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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.