Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data
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[1] C. Winckler,et al. Production level, fertility, health traits, and longevity in local and commercial dairy breeds under organic production conditions in Austria, Switzerland, Poland, and Sweden. , 2019, Journal of dairy science.
[2] Mathieu Gautier,et al. RZooRoH: An R package to characterize individual genomic autozygosity and identify homozygous‐by‐descent segments , 2019, Methods in Ecology and Evolution.
[3] Robin Wellmann,et al. Optimum contribution selection for animal breeding and conservation: the R package optiSel , 2019, BMC Bioinformatics.
[4] R. Schnabel,et al. A Multi-Breed Reference Panel and Additional Rare Variation Maximizes Imputation Accuracy in Cattle , 2019, bioRxiv.
[5] T. Marquès-Bonet,et al. Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas , 2019, Current Biology.
[6] T. Günther,et al. The presence and impact of reference bias on population genomic studies of prehistoric human populations , 2018, bioRxiv.
[7] Michel Georges,et al. Harnessing genomic information for livestock improvement , 2018, Nature Reviews Genetics.
[8] Anushya Muruganujan,et al. PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools , 2018, Nucleic Acids Res..
[9] James M. Reecy,et al. Building a livestock genetic and genomic information knowledgebase through integrative developments of Animal QTLdb and CorrDB , 2018, Nucleic Acids Res..
[10] C. Wurmser,et al. Accurate sequence variant genotyping in cattle using variation-aware genome graphs , 2018, Genetics Selection Evolution.
[11] F. Herzog,et al. Swiss alpine summer farming: current status and future development under climate change , 2018 .
[12] M. Groenen,et al. Deleterious alleles in the context of domestication, inbreeding, and selection , 2018, Evolutionary applications.
[13] I. Ammosov,et al. Whole-Genome Sequencing of Three Native Cattle Breeds Originating From the Northernmost Cattle Farming Regions , 2018, bioRxiv.
[14] C. Drögemüller,et al. [Fanconi-Bickel-Syndrom: a novel genetic disease in Original Braunvieh]. , 2018, Schweizer Archiv fur Tierheilkunde.
[15] Huanming Yang,et al. Genetic Architecture and Selection of Chinese Cattle Revealed by Whole Genome Resequencing , 2018, Molecular biology and evolution.
[16] D. A. Magee,et al. Genomic Characterisation of the Indigenous Irish Kerry Cattle Breed , 2018, Front. Genet..
[17] R. Veerkamp,et al. Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals , 2018, Nature Genetics.
[18] Peter K. Joshi,et al. Runs of homozygosity: windows into population history and trait architecture , 2018, Nature Reviews Genetics.
[19] Mathieu Gautier,et al. Age-based partitioning of individual genomic inbreeding levels in Belgian Blue cattle , 2017, Genetics Selection Evolution.
[20] B. Gredler,et al. Population structure and genomic inbreeding in nine Swiss dairy cattle populations , 2017, Genetics Selection Evolution.
[21] G. Brem,et al. Detection of two non-synonymous SNPs in SLC45A2 on BTA20 as candidate causal mutations for oculocutaneous albinism in Braunvieh cattle , 2017, Genetics Selection Evolution.
[22] Kari Stefansson,et al. Graphtyper enables population-scale genotyping using pangenome graphs , 2017, Nature Genetics.
[23] Gregor Gorjanc,et al. A method for allocating low-coverage sequencing resources by targeting haplotypes rather than individuals , 2017, Genetics Selection Evolution.
[24] M. Goddard,et al. Meta-analysis of sequence-based association studies across three cattle breeds reveals 25 QTL for fat and protein percentages in milk at nucleotide resolution , 2017, bioRxiv.
[25] D. Cohen,et al. Publisher's Note , 2017, Neuroscience & Biobehavioral Reviews.
[26] O. Hanotte,et al. The genome landscape of indigenous African cattle , 2017, Genome Biology.
[27] C. Drögemüller,et al. A frameshift mutation in MOCOS is associated with familial renal syndrome (xanthinuria) in Tyrolean Grey cattle , 2016, BMC Veterinary Research.
[28] M. Georges,et al. NGS-based reverse genetic screen for common embryonic lethal mutations compromising fertility in livestock , 2016, Genome research.
[29] M. Gautier,et al. rehh 2.0: a reimplementation of the R package rehh to detect positive selection from haplotype structure , 2016, bioRxiv.
[30] K. Ropka-Molik,et al. Identification of genome-wide selection signatures in the Limousin beef cattle breed. , 2016, Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie.
[31] F. Menzi,et al. Genetic diversity analyses reveal first insights into breed-specific selection signatures within Swiss goat breeds. , 2016, Animal genetics.
[32] C. Drögemüller,et al. A nonsense mutation in the COL7A1 gene causes epidermolysis bullosa in Vorderwald cattle , 2016, BMC Genetics.
[33] Shane A. McCarthy,et al. Reference-based phasing using the Haplotype Reference Consortium panel , 2016, Nature Genetics.
[34] P M VanRaden,et al. Reducing animal sequencing redundancy by preferentially selecting animals with low-frequency haplotypes. , 2016, Journal of dairy science.
[35] Paul M. VanRaden,et al. Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection , 2016, Proceedings of the National Academy of Sciences.
[36] B. Servin,et al. Uncovering Adaptation from Sequence Data: Lessons from Genome Resequencing of Four Cattle Breeds , 2016, Genetics.
[37] F. Cunningham,et al. The Ensembl Variant Effect Predictor , 2016, Genome Biology.
[38] J. Burgstaller,et al. Clinical and biochemical signs in Fleckvieh cattle with genetically confirmed Fanconi-Bickel syndrome (cattle homozygous for Fleckvieh haplotype 2). , 2016, Berliner und Munchener tierarztliche Wochenschrift.
[39] Yali Xue,et al. BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data , 2016, Bioinform..
[40] A. Schnieke,et al. A frameshift mutation in GON4L is associated with proportionate dwarfism in Fleckvieh cattle , 2016, Genetics Selection Evolution.
[41] C. Bendixen,et al. Deep sequencing of Danish Holstein dairy cattle for variant detection and insight into potential loss-of-function variants in protein coding genes , 2015, BMC Genomics.
[42] P. Ng,et al. SIFT missense predictions for genomes , 2015, Nature Protocols.
[43] J. Cole. A simple strategy for managing many recessive disorders in a dairy cattle breeding program , 2015, Genetics Selection Evolution.
[44] T. Andrews,et al. Comparison of predicted and actual consequences of missense mutations , 2015, Proceedings of the National Academy of Sciences.
[45] F. Zhao,et al. Detection of selection signatures in dairy and beef cattle using high-density genomic information , 2015, Genetics Selection Evolution.
[46] Michael DeGiorgio,et al. SweepFinder2: increased sensitivity, robustness and flexibility , 2015, Bioinform..
[47] B. Gutiérrez-Gil,et al. An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds , 2015, Front. Genet..
[48] I. Randhawa,et al. Composite Selection Signals for Complex Traits Exemplified Through Bovine Stature Using Multibreed Cohorts of European and African Bos taurus , 2015, G3: Genes, Genomes, Genetics.
[49] R. Nielsen,et al. Detecting recent selective sweeps while controlling for mutation rate and background selection , 2015, bioRxiv.
[50] A. Schnieke,et al. Homozygous haplotype deficiency reveals deleterious mutations compromising reproductive and rearing success in cattle , 2015, BMC Genomics.
[51] R. Gibbs,et al. Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. , 2015, Human molecular genetics.
[52] Peter H. Sudmant,et al. Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding , 2015, Science.
[53] Steven G. Schroeder,et al. Genomic signatures reveal new evidences for selection of important traits in domestic cattle. , 2015, Molecular biology and evolution.
[54] A. Stella,et al. Challenges and opportunities in genetic improvement of local livestock breeds , 2015, Front. Genet..
[55] C. Jurt,et al. Transhumance Farming in Swiss Mountains: Adaptation to a Changing Environment , 2015 .
[56] M. Boussaha,et al. Identification of the putative ancestral allele of bovine single-nucleotide polymorphisms. , 2014, Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie.
[57] D. Moran,et al. Genetic resources and genomics for adaptation of livestock to climate change , 2014, Front. Genet..
[58] B. Guldbrandtsen,et al. Runs of homozygosity and distribution of functional variants in the cattle genome , 2014, BMC Genomics.
[59] R. Veerkamp,et al. Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle , 2014, Nature Genetics.
[60] R. Nielsen,et al. Classic Selective Sweeps Revealed by Massive Sequencing in Cattle , 2014, PLoS genetics.
[61] H. Schwarzenbacher,et al. A Nonsense Mutation in TMEM95 Encoding a Nondescript Transmembrane Protein Causes Idiopathic Male Subfertility in Cattle , 2014, PLoS genetics.
[62] B. Guldbrandtsen,et al. A 660-Kb Deletion with Antagonistic Effects on Fertility and Milk Production Segregates at High Frequency in Nordic Red Cattle: Additional Evidence for the Common Occurrence of Balancing Selection in Livestock , 2014, PLoS genetics.
[63] F. Nicholas,et al. Mutation discovery for Mendelian traits in non-laboratory animals: a review of achievements up to 2012 , 2013, Animal genetics.
[64] M. Förster,et al. A genome-wide scan for signatures of differential artificial selection in ten cattle breeds , 2013, BMC Genomics.
[65] S. Tishkoff,et al. SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it , 2013, BioEssays : news and reviews in molecular, cellular and developmental biology.
[66] T. Wieland,et al. Assessment of the genomic variation in a cattle population by re-sequencing of key animals at low to medium coverage , 2013, BMC Genomics.
[67] C. V. Van Tassell,et al. Detecting Loci under Recent Positive Selection in Dairy and Beef Cattle by Combining Different Genome-Wide Scan Methods , 2013, PloS one.
[68] Heng Li. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.
[69] Christopher R. Gignoux,et al. Limited Evidence for Classic Selective Sweeps in African Populations , 2012, Genetics.
[70] M. Groenen,et al. Regions of Homozygosity in the Porcine Genome: Consequence of Demography and the Recombination Landscape , 2012, PLoS genetics.
[71] D. Bradley,et al. Runs of homozygosity and population history in cattle , 2012, BMC Genetics.
[72] Richard M Myers,et al. Genomic patterns of homozygosity in worldwide human populations. , 2012, American journal of human genetics.
[73] B. Charlesworth. The Role of Background Selection in Shaping Patterns of Molecular Evolution and Variation: Evidence from Variability on the Drosophila X Chromosome , 2012, Genetics.
[74] M. Lyons,et al. Low-Pass Genome-Wide Sequencing and Variant Inference Using Identity-by-Descent in an Isolated Human Population , 2012, Genetics.
[75] M. Lathrop,et al. Serial translocation by means of circular intermediates underlies colour sidedness in cattle , 2012, Nature.
[76] Tom Druet,et al. Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature , 2011, Nature Genetics.
[77] K. Flisikowski,et al. Genome-Wide Association Study Identifies Two Major Loci Affecting Calving Ease and Growth-Related Traits in Cattle , 2011, Genetics.
[78] Harry Campbell,et al. Genomic Runs of Homozygosity Record Population History and Consanguinity , 2010, PloS one.
[79] R. Nielsen,et al. Ascertainment biases in SNP chips affect measures of population divergence. , 2010, Molecular biology and evolution.
[80] N. Klopp,et al. Dissection of Genetic Factors Modulating Fetal Growth in Cattle Indicates a Substantial Role of the Non-SMC Condensin I Complex, Subunit G (NCAPG) Gene , 2009, Genetics.
[81] P. Taberlet,et al. Genetic diversity of European cattle breeds highlights the conservation value of traditional unselected breeds with high effective population size , 2009, Molecular ecology.
[82] Timothy P. L. Smith,et al. Development and Characterization of a High Density SNP Genotyping Assay for Cattle , 2009, PloS one.
[83] David R. Kelley,et al. A whole-genome assembly of the domestic cow, Bos taurus , 2009, Genome Biology.
[84] Igor Rudan,et al. Runs of homozygosity in European populations. , 2008, American journal of human genetics.
[85] B. Browning,et al. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. , 2007, American journal of human genetics.
[86] 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.
[87] Shameek Biswas,et al. Genomic insights into positive selection. , 2006, Trends in genetics : TIG.
[88] Pardis C Sabeti,et al. Positive Natural Selection in the Human Lineage , 2006, Science.
[89] Xiaoquan Wen,et al. Correction: A Map of Recent Positive Selection in the Human Genome , 2006, PLoS Biology.
[90] J. Pritchard,et al. A Map of Recent Positive Selection in the Human Genome , 2006, PLoS biology.
[91] C. Hagger. Estimates of genetic diversity in the brown cattle population of Switzerland obtained from pedigree information. , 2005, Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie.
[92] R. Nielsen. Molecular signatures of natural selection. , 2005, Annual review of genetics.
[93] Carlos Bustamante,et al. Genomic scans for selective sweeps using SNP data. , 2005, Genome research.
[94] J. Weller,et al. Identification of a missense mutation in the bovine ABCG2 gene with a major effect on the QTL on chromosome 6 affecting milk yield and composition in Holstein cattle. , 2005, Genome research.
[95] A. C. Sørensen,et al. Inbreeding in Danish dairy cattle breeds. , 2005, Journal of dairy science.
[96] Michel Georges,et al. Molecular dissection of a quantitative trait locus: a phenylalanine-to-tyrosine substitution in the transmembrane domain of the bovine growth hormone receptor is associated with a major effect on milk yield and composition. , 2002, Genetics.
[97] R. Fries,et al. Association of a lysine-232/alanine polymorphism in a bovine gene encoding acyl-CoA:diacylglycerol acyltransferase (DGAT1) with variation at a quantitative trait locus for milk fat content , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[98] Michel Georges,et al. Positional candidate cloning of a QTL in dairy cattle: identification of a missense mutation in the bovine DGAT1 gene with major effect on milk yield and composition. , 2002, Nature Reviews Genetics.
[99] R. Santer,et al. Mutations in GLUT2, the gene for the liver-type glucose transporter, in patients with Fanconi-Bickel syndrome , 1997, Nature Genetics.
[100] G. Stranzinger,et al. Red coat color in Holstein cattle is associated with a deletion in the MSHR gene , 1996, Mammalian Genome.
[101] M. Nei,et al. Mathematical model for studying genetic variation in terms of restriction endonucleases. , 1979, Proceedings of the National Academy of Sciences of the United States of America.
[102] F. Nicholas,et al. Online Mendelian Inheritance in Animals (OMIA): inclusion of a hyperlinked table of likely causal variants for inherited disorders and traits , 2018 .
[103] B. Scherf,et al. The Second Report on the State of the World's Animal Genetic Resources for Food and Agriculture , 2015 .
[104] Sequence analysis Advance Access publication June 7, 2011 The variant call format and VCFtools , 2010 .
[105] M. Goddard,et al. Genomic selection based on dense genotypes inferred from sparse genotypes. , 2009 .
[106] S. Henikoff,et al. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm , 2009, Nature Protocols.
[107] I. Martín-Burriel,et al. Marker-assisted conservation of European cattle breeds: An evaluation. , 2006, Animal genetics.
[108] C. Lottaz,et al. BIOINFORMATICS APPLICATIONS NOTE , 2001 .