A genome-wide scan for candidate lethal variants in Thoroughbred horses

[1]  E. Hill,et al.  Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population , 2020, Scientific Reports.

[2]  Narmada Thanki,et al.  CDD/SPARCLE: the conserved domain database in 2020 , 2019, Nucleic Acids Res..

[3]  S. Mikko,et al.  Signatures of selection in the genome of Swedish warmblood horses selected for sport performance , 2019, BMC Genomics.

[4]  L. Orlando,et al.  Origin and Evolution of Deleterious Mutations in Horses , 2019, Genes.

[5]  S. K. Beeson,et al.  Exploration of fine-scale recombination rate variation in the domestic horse , 2019, Genome research.

[6]  H. Innan,et al.  Genome-wide SNP analysis of Japanese Thoroughbred racehorses , 2019, PloS one.

[7]  M. MacDonald,et al.  Full sequence of mutant huntingtin 3′-untranslated region and modulation of its gene regulatory activity by endogenous microRNA , 2019, Journal of Human Genetics.

[8]  Arne Ludwig,et al.  Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series , 2019, Cell.

[9]  M. Groenen,et al.  Loss of function mutations in essential genes cause embryonic lethality in pigs , 2019, PLoS genetics.

[10]  G. Plastow,et al.  Putative Loci Causing Early Embryonic Mortality in Duroc Swine , 2018, Front. Genet..

[11]  C. Drögemüller,et al.  Comprehensive characterization of horse genome variation by whole-genome sequencing of 88 horses. , 2018, Animal genetics.

[12]  M. Groenen,et al.  Deleterious alleles in the context of domestication, inbreeding, and selection , 2018, Evolutionary applications.

[13]  G. Lindgren,et al.  A genome-wide association study for harness racing success in the Norwegian-Swedish coldblooded trotter reveals genes for learning and energy metabolism , 2018, BMC Genetics.

[14]  E. Z. Zhang,et al.  Genetic characterization of inbred lines from Shaan A and B groups for identifying loci associated with maize grain yield , 2018, BMC Genetics.

[15]  S. Allen,et al.  Dynamic changes in gene expression and signalling during trophoblast development in the horse , 2018, Reproduction.

[16]  M. L. Idda,et al.  Genetic variants in mRNA untranslated regions , 2018, Wiley interdisciplinary reviews. RNA.

[17]  S. Ho,et al.  Founder-specific inbreeding depression affects racing performance in Thoroughbred horses , 2018, Scientific Reports.

[18]  M. Noor,et al.  Are Lethal Alleles Too Abundant in Humans? , 2017, Trends in genetics : TIG.

[19]  M. Groenen,et al.  A systematic survey to identify lethal recessive variation in highly managed pig populations , 2017, BMC Genomics.

[20]  R. Schnabel,et al.  Candidate lethal haplotypes and causal mutations in Angus cattle , 2017, BMC Genomics.

[21]  D. Boichard,et al.  Rapid Discovery of De Novo Deleterious Mutations in Cattle Enhances the Value of Livestock as Model Species , 2017, Scientific Reports.

[22]  Arne Ludwig,et al.  Ancient genomic changes associated with domestication of the horse , 2017, Science.

[23]  M. Mallicote,et al.  Genomewide association study reveals a risk locus for equine metabolic syndrome in the Arabian horse. , 2017, Journal of animal science.

[24]  E. Casas,et al.  A Review of Selected Genes with Known Effects on Performance and Health of Cattle , 2016, Front. Vet. Sci..

[25]  L. Orlando,et al.  The Evolutionary Origin and Genetic Makeup of Domestic Horses , 2016, Genetics.

[26]  M. Georges,et al.  NGS-based reverse genetic screen for common embryonic lethal mutations compromising fertility in livestock , 2016, Genome research.

[27]  Steve D. M. Brown,et al.  High-throughput discovery of novel developmental phenotypes , 2017 .

[28]  M. Husemann,et al.  Effective population size in ecology and evolution , 2016, Heredity.

[29]  S. Piertney,et al.  Evidence of the phenotypic expression of a lethal recessive allele under inbreeding in a wild population of conservation concern. , 2016, The Journal of animal ecology.

[30]  S. Mikko,et al.  Using an Inbred Horse Breed in a High Density Genome-Wide Scan for Genetic Risk Factors of Insect Bite Hypersensitivity (IBH) , 2016, PloS one.

[31]  A. Makrigiannis,et al.  Ly49 knockdown in mice results in aberrant uterine crypt formation and impaired blastocyst implantation. , 2016, Placenta.

[32]  T. Marquès-Bonet,et al.  Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs , 2015, Proceedings of the National Academy of Sciences.

[33]  R. Davoli,et al.  Two Mutations in the Caprine MTHFR 3'UTR Regulated by MicroRNAs Are Associated with Milk Production Traits , 2015, PloS one.

[34]  S. Fan,et al.  Association of maternal KIR and fetal HLA-C genes with the risk of preeclampsia in the Chinese Han population. , 2015, Placenta.

[35]  J. Woolliams,et al.  Genetic contributions and their optimization. , 2015, Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie.

[36]  H. Stefánsson,et al.  Identification of a large set of rare complete human knockouts , 2015, Nature Genetics.

[37]  Leif Andersson,et al.  Prehistoric genomes reveal the genetic foundation and cost of horse domestication , 2014, Proceedings of the National Academy of Sciences.

[38]  J. Petersen,et al.  Haplotype diversity in the equine myostatin gene with focus on variants associated with race distance propensity and muscle fiber type proportions. , 2014, Animal genetics.

[39]  J. Sölkner,et al.  Inbreeding and runs of homozygosity: A possible solution to an old problem , 2014 .

[40]  M. Stephens,et al.  An Estimate of the Average Number of Recessive Lethal Mutations Carried by Humans , 2014, Genetics.

[41]  A. Makrigiannis,et al.  Ly49 receptors activate angiogenic mouse DBA+ uterine natural killer cells , 2014, Cellular and Molecular Immunology.

[42]  J. Weidhaas,et al.  A germline mutation in the BRCA1 3’UTR predicts Stage IV breast cancer , 2014, BMC Cancer.

[43]  A. Makrigiannis,et al.  Ly49 Receptors: Innate and Adaptive Immune Paradigms , 2014, Front. Immunol..

[44]  Ira M. Hall,et al.  SAMBLASTER: fast duplicate marking and structural variant read extraction , 2014, Bioinform..

[45]  J. Petersen,et al.  The American Quarter Horse: population structure and relationship to the thoroughbred. , 2014, The Journal of heredity.

[46]  J. Roser,et al.  RNA-Seq Transcriptome Profiling of Equine Inner Cell Mass and Trophectoderm1 , 2014, Biology of reproduction.

[47]  T. Spencer.  Early pregnancy: Concepts, challenges, and potential solutions , 2013 .

[48]  Damian Smedley,et al.  Genome-wide Generation and Systematic Phenotyping of Knockout Mice Reveals New Roles for Many Genes , 2013, Cell.

[49]  P. Horin,et al.  Natural Killer Cell Receptor Genes in the Family Equidae: Not only Ly49 , 2013, PloS one.

[50]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[51]  E. Beltranena,et al.  Swine convert co-products from food and biofuel industries into animal protein for food , 2013 .

[52]  E. G. Cothran,et al.  Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data , 2013, PloS one.

[53]  Steven G. Schroeder,et al.  Identification of a Nonsense Mutation in CWC15 Associated with Decreased Reproductive Efficiency in Jersey Cattle , 2013, PloS one.

[54]  E. G. Cothran,et al.  Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds , 2013, PLoS genetics.

[55]  A. García-Dorado.  Understanding and Predicting the Fitness Decline of Shrunk Populations: Inbreeding, Purging, Mutation, and Standard Selection , 2012, Genetics.

[56]  P. VanRaden,et al.  Harmful recessive effects on fertility detected by absence of homozygous haplotypes. , 2011, Journal of dairy science.

[57]  K. Nishida,et al.  Mechanisms and consequences of alternative polyadenylation. , 2011, Molecules and Cells.

[58]  C. Aurich.  Reproductive cycles of horses. , 2011, Animal reproduction science.

[59]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[60]  J. Woolliams,et al.  Linkage disequilibrium and historical effective population size in the Thoroughbred horse. , 2010, Animal genetics.

[61]  E. Hill,et al.  Targets of selection in the Thoroughbred genome contain exercise-relevant gene SNPs associated with elite racecourse performance. , 2010, Animal genetics.

[62]  M. Carrington,et al.  Maternal activating KIRs protect against human reproductive failure mediated by fetal HLA-C2. , 2010, The Journal of clinical investigation.

[63]  D. Antczak,et al.  Maternal Immune Responses to Trophoblast: The Contribution of the Horse to Pregnancy Immunology , 2010, American journal of reproductive immunology.

[64]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[65]  W. Allen,et al.  A review of implantation and early placentation in the mare. , 2009, Placenta.

[66]  Davis J. McCarthy,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[67]  D. Charlesworth,et al.  The genetics of inbreeding depression , 2009, Nature Reviews Genetics.

[68]  N. Orr,et al.  A Genome Scan for Positive Selection in Thoroughbred Horses , 2009, PloS one.

[69]  M. Webster,et al.  The legacy of domestication: accumulation of deleterious mutations in the dog genome. , 2008, Molecular biology and evolution.

[70]  M. Carrington,et al.  Association of maternal killer-cell immunoglobulin-like receptors and parental HLA-C genotypes with recurrent miscarriage. , 2008, Human reproduction.

[71]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[72]  P. Taylor,et al.  Ly49B Is Expressed on Multiple Subpopulations of Myeloid Cells1 , 2006, The Journal of Immunology.

[73]  Florian Caiment,et al.  A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep , 2006, Nature Genetics.

[74]  J. Trowsdale,et al.  Comparative Genomics of Natural Killer Cell Receptor Gene Clusters , 2005, PLoS genetics.

[75]  Steven Henikoff,et al.  SIFT: predicting amino acid changes that affect protein function , 2003, Nucleic Acids Res..

[76]  D. Antczak,et al.  Control of Expression of Major Histocompatibility Complex Genes in Horse Trophoblast1 , 2002, Biology of reproduction.

[77]  L. Keller,et al.  Inbreeding effects in wild populations. , 2002 .

[78]  D. Bradley,et al.  Microsatellite diversity, pedigree relatedness and the contributions of founder lineages to thoroughbred horses. , 2001, Animal genetics.

[79]  D. Antczak,et al.  Paternal and maternal major histocompatibility complex class I antigens are expressed co-dominantly by equine trophoblast. , 1994, Placenta.

[80]  J. Crow,et al.  Mutation rate and dominance of genes affecting viability in Drosophila melanogaster. , 1972, Genetics.

[81]  S. Wright.  Evolution in mendelian populations , 1931 .

[82]  W. Allen,et al.  Half a century of equine reproduction research and application: A veterinary tour de force , 2018, Equine veterinary journal.

[83]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[84]  Claude-Alain H. Roten,et al.  Fast and accurate short read alignment with Burrows–Wheeler transform , 2009, Bioinform..