Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits

Genome-wide scan reveals genomic regions and candidate genes underlying direct and maternal effects of preweaning calf mortality in Nellore cattle

(2021) N.A. Marín-Garzón et al.   GENOMICS

Genomic scans for selection signatures revealed candidate genes for adaptation and production traits in a variety of cattle breeds

(2021) K.A. Saravanan et al.   GENOMICS

Genome-Wide Runs of Homozygosity Revealed Selection Signatures in Bos indicus

(2020) S. P. Dixit et al.   Frontiers in Genetics

Genetic dissection of reproductive performance of dairy cows under heat stress

(2020) A. Sigdel et al.   ANIMAL GENETICS

Differentially expressed genes identified through RNA‐seq with extreme values of principal components for beef fatty acid in Nelore cattle

(2020) Bianca Ferreira Olivieri et al.   JOURNAL OF ANIMAL BREEDING AND GENETICS

Effects of heat stress on ovarian development and the expression of HSP genes in mice

(2020) Mingyan Bei et al.   JOURNAL OF THERMAL BIOLOGY

A Gene-Set Enrichment and Protein–Protein Interaction Network-Based GWAS with Regulatory SNPs Identifies Candidate Genes and Pathways Associated with Carcass Traits in Hanwoo Cattle

(2020) Krishnamoorthy Srikanth et al.   Genes

Genome-Wide Transcriptome and Metabolome Analyses Provide Novel Insights and Suggest a Sex-Specific Response to Heat Stress in Pigs

(2020) Krishnamoorthy Srikanth et al.   Genes

De novo assembly of the cattle reference genome with single-molecule sequencing

(2020) Benjamin D Rosen et al.   GigaScience

Whole-genome sequencing provides new insights into genetic mechanisms of tropical adaptation in Nellore (Bos primigenius indicus)

(2020) Gerardo Alves Fernandes Júnior et al.   Scientific Reports

Autophagy is a pro-survival adaptive response to heat shock in bovine cumulus-oocyte complexes

(2020) Lais B. Latorraca et al.   Scientific Reports

Runs of homozygosity islands in Italian cosmopolitan and autochthonous pig breeds identify selection signatures in the porcine genome

(2020) Giuseppina Schiavo et al.   Livestock Science

Growth retardation-responsive analysis of mRNAs and long noncoding RNAs in the liver tissue of Leiqiong cattle

(2020) Lingxuan Kong et al.   Scientific Reports

Insights into Genetic Diversity, Runs of Homozygosity and Heterozygosity-Rich Regions in Maremmana Semi-Feral Cattle Using Pedigree and Genomic Data

(2020) Filippo Biscarini et al.   Animals

Transcriptome assisted label free proteomics of hepatic tissue in response to both dietary restriction and compensatory growth in cattle

(2020) Yvonne Mullins et al.   Journal of Proteomics

Integrative Analysis of Transcriptome and GWAS Data to Identify the Hub Genes Associated With Milk Yield Trait in Buffalo

(2019) Tingxian Deng et al.   Frontiers in Genetics

Whole-genome sequencing identifies potential candidate genes for reproductive traits in pigs

(2019) Xinjian Li et al.   GENOMICS

Selection signatures in four German warmblood horse breeds: Tracing breeding history in the modern sport horse

(2019) Wietje Nolte et al.   PLoS One

Genome-wide association for milk production traits and somatic cell score in different lactation stages of Ayrshire, Holstein, and Jersey dairy cattle

(2019) H.R. Oliveira et al.   JOURNAL OF DAIRY SCIENCE

Genome Analysis Reveals Genetic Admixture and Signature of Selection for Productivity and Environmental Traits in Iraqi Cattle

(2019) Akil Alshawi et al.   Frontiers in Genetics

Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes in Three Pig Breeds

(2019) Xie et al.   Animals

Selection signatures in candidate genes and QTL for reproductive traits in Nellore heifers

(2019) Donicer E. Montes et al.   ANIMAL REPRODUCTION SCIENCE

Signatures of selection in the genome of Swedish warmblood horses selected for sport performance

(2019) Michela Ablondi et al.   BMC GENOMICS

Genomic Patterns of Homozygosity in Chinese Local Cattle

(2019) Lingyang Xu et al.   Scientific Reports

Genome-Wide Runs of Homozygosity, Effective Population Size, and Detection of Positive Selection Signatures in Six Chinese Goat Breeds

(2019) Islam et al.   Genes

Identification of candidate genes affecting chronic subclinical mastitis in Norwegian Red cattle: combining genome‐wide association study, topologically associated domains and pathway enrichment analysis

(2019) E. Kirsanova et al.   ANIMAL GENETICS

Influence of common health disorders on the length of productive life and stayability in German Holstein cows

(2019) T. Shabalina et al.   JOURNAL OF DAIRY SCIENCE

Transcriptomic analysis on the promoter regions discover gene networks involving mastitis in cattle

(2019) Abdolvahab Ebrahimpour Gorji et al.   MICROBIAL PATHOGENESIS

Genome-wide identification of runs of homozygosity islands and associated genes in local dairy cattle breeds

(2018) S. Mastrangelo et al.   Animal

Assessing runs of Homozygosity: a comparison of SNP Array and whole genome sequence low coverage data

(2018) Francisco C. Ceballos et al.   BMC GENOMICS

Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle

(2018) Elisa Peripolli et al.   BMC GENOMICS

Runs of homozygosity: windows into population history and trait architecture

(2018) Francisco C. Ceballos et al.   NATURE REVIEWS GENETICS

Haplotype-based genome-wide association study identifies loci and candidate genes for milk yield in Holsteins

(2018) Zhenliang Chen et al.   PLoS One

Association between the expression of miR-26 and goat milk fatty acids

(2018) Hui Wang et al.   REPRODUCTION IN DOMESTIC ANIMALS

Genome-Wide Characterization of Selection Signatures and Runs of Homozygosity in Ugandan Goat Breeds

(2018) Robert B. Onzima et al.   Frontiers in Genetics

Distribution of runs of homozygosity in Chinese and Western pig breeds evaluated by reduced-representation sequencing data

(2018) Zhe Zhang et al.   ANIMAL GENETICS

Genome-wide association study of Mycobacterium avium subspecies Paratuberculosis infection in Chinese Holstein

(2018) Yahui Gao et al.   BMC GENOMICS

Toward a better understanding of folate metabolism in health and disease

(2018) Yuxiang Zheng et al.   JOURNAL OF EXPERIMENTAL MEDICINE

A genomic map of climate adaptation in Mediterranean cattle breeds

(2018) Laurence Flori et al.   MOLECULAR ECOLOGY

Fine-Scale Resolution of Runs of Homozygosity Reveal Patterns of Inbreeding and Substantial Overlap with Recessive Disease Genotypes in Domestic Dogs

(2018) Aaron J. Sams et al.   G3-Genes Genomes Genetics

Identification of artificial selection signatures in Caracu breed lines selected for milk production and meat production

(2017) Bárbara Machado Campos et al.   Livestock Science

Genome-wide Association Studies for Female Fertility Traits in Chinese and Nordic Holsteins

(2017) Aoxing Liu et al.   Scientific Reports

Genetic Architecture and Candidate Genes Identified for Follicle Number in Chicken

(2017) Manman Shen et al.   Scientific Reports

The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds

(2017) Deirdre C. Purfield et al.   PLoS One

Use of single nucleotide polymorphisms in candidate genes associated with daughter pregnancy rate for prediction of genetic merit for reproduction in Holstein cows

(2016) M. S. Ortega et al.   ANIMAL GENETICS

Runs of homozygosity: current knowledge and applications in livestock

(2016) E. Peripolli et al.   ANIMAL GENETICS

A recurrent mitochondrial p.Trp22ArgNDUFB3variant causes a distinctive facial appearance, short stature and a mild biochemical and clinical phenotype

(2016) Charlotte L Alston et al.   JOURNAL OF MEDICAL GENETICS

Comparative analysis of SNP candidates in disparate milk yielding river buffaloes using targeted sequencing

(2016) Ramesh Menon et al.   PeerJ

Runs of homozygosity and distribution of functional variants in the cattle genome

(2015) Qianqian Zhang et al.   BMC GENOMICS

Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses

(2015) Julia Metzger et al.   BMC GENOMICS

Short Communication Genome-wide association with residual body weight gain in Bos indicus cattle

(2015) M.H.A. Santana et al.   GENETICS AND MOLECULAR RESEARCH

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Relationship between Runs of Homozygosity and Inbreeding in Jersey Cattle under Selection

(2015) Eui-Soo Kim et al.   PLoS One

Signatures of positive selection in East African Shorthorn Zebu: A genome-wide single nucleotide polymorphism analysis

(2015) Hussain Bahbahani et al.   Scientific Reports

Genome-wide detection of selective signatures in Simmental cattle

(2014) Huizhong Fan et al.   JOURNAL OF APPLIED GENETICS

Mapping signatures of positive selection in the genome of livestock

(2014) Saber Qanbari et al.   Livestock Science

A New Genotype Imputation Method with Tolerance to High Missing Rate and Rare Variants

(2014) Yumei Yang et al.   PLoS One

Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data

(2013) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Discovery of single nucleotide polymorphisms in candidate genes associated with fertility and production traits in Holstein cattle

(2013) Sarah D Cochran et al.   BMC GENETICS

Genome wide association studies for body conformation traits in the Chinese Holstein cattle population

(2013) Xiaoping Wu et al.   BMC GENOMICS

Beef cattle body temperature during climatic stress: a genome-wide association study

(2013) Jeremy T. Howard et al.   INTERNATIONAL JOURNAL OF BIOMETEOROLOGY

Genotyping by Genome Reducing and Sequencing for Outbred Animals

(2013) Qiang Chen et al.   PLoS One

Genome-wide Association Study Identifies Candidate Genes for Male Fertility Traits in Humans

(2012) Gülüm Kosova et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genomic Patterns of Homozygosity in Worldwide Human Populations

(2012) Trevor J. Pemberton et al.   AMERICAN JOURNAL OF HUMAN GENETICS

rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure

(2012) Mathieu Gautier et al.   BIOINFORMATICS

The UCSC genome browser and associated tools

(2012) R. M. Kuhn et al.   BRIEFINGS IN BIOINFORMATICS

Detecting Selective Sweeps from Pooled Next-Generation Sequencing Samples

(2012) S. Boitard et al.   MOLECULAR BIOLOGY AND EVOLUTION

Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era

(2012) Zhi-Liang Hu et al.   NUCLEIC ACIDS RESEARCH

Chinese Holstein Cattle Shows a Genetic Contribution from Native Asian Cattle Breeds: A Study of Shared Haplotypes and Demographic History

(2011) Miro Ferreri et al.   ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES

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

(2011) Saber Qanbari et al.   BMC GENOMICS

Exome-wide DNA capture and next generation sequencing in domestic and wild species

(2011) Ted Cosart et al.   BMC GENOMICS

Short communication: Genetic effects of heat stress on days open for Thai Holstein crossbreds

(2011) W. Boonkum et al.   JOURNAL OF DAIRY SCIENCE

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Population differentiation as a test for selective sweeps

(2010) H. Chen et al.   GENOME RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH