Genomic Signatures Reveal New Evidences for Selection of Important Traits in Domestic Cattle

Selection for complex traits leaves little or no classic signatures of selection

(2014) Kathryn E Kemper et al.   BMC GENOMICS

Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins

(2014) Lingyang Xu et al.   BMC GENOMICS

A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattle

(2014) Lingyang Xu et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits

(2014) J.B. Cole et al.   JOURNAL OF DAIRY SCIENCE

Signatures of selection in five Italian cattle breeds detected by a 54K SNP panel

(2014) Giordano Mancini et al.   MOLECULAR BIOLOGY REPORTS

Current perspectives and the future of domestication studies

(2014) G. Larson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Classic Selective Sweeps Revealed by Massive Sequencing in Cattle

(2014) Saber Qanbari et al.   PLoS Genetics

Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle

(2014) Jared E. Decker et al.   PLoS Genetics

RCircos: an R package for Circos 2D track plots

(2013) Hongen Zhang et al.   BMC BIOINFORMATICS

Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine height

(2013) Yuri T Utsunomiya et al.   BMC GENETICS

Study of whole genome linkage disequilibrium in Nellore cattle

(2013) Rafael Espigolan et al.   BMC GENOMICS

Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping

(2013) Laercio R Porto-Neto et al.   BMC GENOMICS

A genome-wide scan for signatures of differential artificial selection in ten cattle breeds

(2013) Sophie Rothammer et al.   BMC GENOMICS

Detecting Signatures of Selection Through Haplotype Differentiation Among Hierarchically Structured Populations

(2013) M. I. Fariello et al.   GENETICS

Derived variants at six genes explain nearly half of size reduction in dog breeds

(2013) M. Rimbault et al.   GENOME RESEARCH

The genomic signature of dog domestication reveals adaptation to a starch-rich diet

(2013) Erik Axelsson et al.   NATURE

Genome-Wide Detection of Selective Signature in Chinese Holstein

(2013) Dunfei Pan et al.   PLoS One

Novel Insights into the Bovine Polled Phenotype and Horn Ontogenesis in Bovidae

(2013) Aurélie Allais-Bonnet et al.   PLoS One

Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds

(2013) Jessica L. Petersen et al.   PLoS Genetics

SNP-based association mapping of the polled gene in divergent cattle breeds

(2012) D. Seichter et al.   ANIMAL GENETICS

Limited Evidence for Classic Selective Sweeps in African Populations

(2012) J. M. Granka et al.   GENETICS

A Quasi-Exclusive European Ancestry in the Senepol Tropical Cattle Breed Highlights the Importance of the slick Locus in Tropical Adaptation

(2012) Laurence Flori et al.   PLoS One

Bovine Polledness – An Autosomal Dominant Trait with Allelic Heterogeneity

(2012) Ivica Medugorac et al.   PLoS One

Identification of a Short Region on Chromosome 6 Affecting Direct Calving Ease in Piedmontese Cattle Breed

(2012) Silvia Bongiorni et al.   PLoS One

A High Resolution Genome-Wide Scan for Significant Selective Sweeps: An Application to Pooled Sequence Data in Laying Chickens

(2012) Saber Qanbari et al.   PLoS One

Whole-genome resequencing of two elite sires for the detection of haplotypes under selection in dairy cattle

(2012) D. M. Larkin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Strong signatures of selection in the domestic pig genome

(2012) C.-J. Rubin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Analysis of the World's Sheep Breeds Reveals High Levels of Historic Mixture and Strong Recent Selection

(2012) James W. Kijas et al.   PLOS BIOLOGY

Patterns of Ancestry, Signatures of Natural Selection, and Genetic Association with Stature in Western African Pygmies

(2012) Joseph P. Jarvis et al.   PLoS Genetics

A High Density SNP Array for the Domestic Horse and Extant Perissodactyla: Utility for Association Mapping, Genetic Diversity, and Phylogeny Studies

(2012) Molly E. McCue et al.   PLoS Genetics

Association, effects and validation of polymorphisms within the NCAPG - LCORL locus located on BTA6 with feed intake, gain, meat and carcass traits in beef cattle

(2011) Amanda K Lindholm-Perry et al.   BMC GENETICS

Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle

(2011) Saber Qanbari et al.   BMC GENOMICS

Polymorphic Regions Affecting Human Height Also Control Stature in Cattle

(2011) J. E. Pryce et al.   GENETICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Genome-Wide Footprints of Pig Domestication and Selection Revealed through Massive Parallel Sequencing of Pooled DNA

(2011) Andreia J. Amaral et al.   PLoS One

Deciphering the genetic basis of animal domestication

(2011) P. Wiener et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Parallel Adaptive Divergence among Geographically Diverse Human Populations

(2011) Jacob A. Tennessen et al.   PLoS Genetics

Inference of Relationships in Population Data Using Identity-by-Descent and Identity-by-State

(2011) Eric L. Stevens et al.   PLoS Genetics

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Identification of Selection Signatures in Cattle Breeds Selected for Dairy Production

(2010) A. Stella et al.   GENETICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Using Population Genomics to Detect Selection in Natural Populations: Key Concepts and Methodological Considerations

(2010)   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Fibroblast-derived HB-EGF promotes Cdx2 expression in esophageal squamous cells

(2010) Farzana B Rahman et al.   LABORATORY INVESTIGATION

Whole-genome resequencing reveals loci under selection during chicken domestication

(2010) Carl-Johan Rubin et al.   NATURE

Tracking footprints of artificial selection in the dog genome

(2010) J. M. Akey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection

(2010) S. R. Grossman et al.   SCIENCE

Vertebrate pigmentation: from underlying genes to adaptive function

(2010) Joanna K. Hubbard et al.   TRENDS IN GENETICS

Genetic Architecture of Complex Traits and Accuracy of Genomic Prediction: Coat Colour, Milk-Fat Percentage, and Type in Holstein Cattle as Contrasting Model Traits

(2010) Ben J. Hayes et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A whole genome Bayesian scan for adaptive genetic divergence in West African cattle

(2009) Mathieu Gautier et al.   BMC GENOMICS

Inhibition of cytokinesis by overexpression of NudCL that is localized to the centrosome and midbody

(2009) Yuqi Cai et al.   CELL RESEARCH

Signals of recent positive selection in a worldwide sample of human populations

(2009) J. K. Pickrell et al.   GENOME RESEARCH

KIT variants in bovine ovarian cells and corpus luteum

(2009) Daniela Koch et al.   GROWTH FACTORS

Genome-wide association study identifies eight loci associated with blood pressure

(2009) Christopher Newton-Cheh et al.   NATURE GENETICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

From evolutionary genetics to human immunology: how selection shapes host defence genes

(2009) Luis B. Barreiro et al.   NATURE REVIEWS GENETICS

Mapping genes for complex traits in domestic animals and their use in breeding programmes

(2009) Michael E. Goddard et al.   NATURE REVIEWS GENETICS

Genome-wide scans for footprints of natural selection

(2009) T. K. Oleksyk et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Genome Scan for Positive Selection in Thoroughbred Horses

(2009) Jingjing Gu et al.   PLoS One

Development and Characterization of a High Density SNP Genotyping Assay for Cattle

(2009) Lakshmi K. Matukumalli et al.   PLoS One

The Genome Response to Artificial Selection: A Case Study in Dairy Cattle

(2009) Laurence Flori et al.   PLoS One

Diversity and evolution of 11 innate immune genes in Bos taurus taurus and Bos taurus indicus cattle

(2009) C. M. Seabury et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Signatures of natural selection are not uniform across genes of innate immune system, but purifying selection is the dominant signature

(2009) S. Mukherjee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coat Variation in the Domestic Dog Is Governed by Variants in Three Genes

(2009) E. Cadieu et al.   SCIENCE

Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds

(2009) et al.   SCIENCE

Contrasting Mode of Evolution at a Coat Color Locus in Wild and Domestic Pigs

(2009) Meiying Fang et al.   PLoS Genetics

The bovine lactation genome: insights into the evolution of mammalian milk

(2009) Danielle G Lemay et al.   GENOME BIOLOGY

A genome map of divergent artificial selection betweenBos taurusdairy cattle andBos taurusbeef cattle

(2008) B. J. Hayes et al.   ANIMAL GENETICS

Positive Selection in the Human Genome: From Genome Scans to Biological Significance

(2008) Joanna L. Kelley et al.   Annual Review of Genomics and Human Genetics

Complete mitochondrial genomes of Bos taurus and Bos indicus provide new insights into intra-species variation, taxonomy and domestication

(2008) S. Hiendleder et al.   CYTOGENETIC AND GENOME RESEARCH

A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sheep

(2008) B. J. Norris et al.   GENOME RESEARCH

Highly effective SNP-based association mapping and management of recessive defects in livestock

(2008) Carole Charlier et al.   NATURE GENETICS

Patterns of Positive Selection in Six Mammalian Genomes

(2008) Carolin Kosiol et al.   PLoS Genetics

genepop’007: a complete re-implementation of the genepop software for Windows and Linux

(2007) FRANÇOIS ROUSSET   Molecular Ecology Resources