Genomes and Genes
Curtis P van Tassell
Affiliation: Agricultural Research Service
- Imputation of microsatellite alleles from dense SNP genotypes for parental verificationMatthew McClure
Bovine Functional Genomics Lab, United States Department of Agriculture, Agriculture Research Service Beltsville, MD, USA
Front Genet 3:140. 2012..This approach may be applicable to additional cattle breeds and other species that wish to migrate from MS- to SNP-based parental verification...
- Effect of sample stratification on dairy GWAS resultsLi Ma
Department of Animal Science, University of Minnesota, St Paul, Minnesota, USA
BMC Genomics 13:536. 2012....
- Whole genome SNP discovery and analysis of genetic diversity in Turkey (Meleagris gallopavo)Muhammad L Aslam
Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708WD Wageningen, The Netherlands
BMC Genomics 13:391. 2012..Genomic selection requires a large number of genetic markers such as e.g. single nucleotide polymorphisms (SNPs) the most abundant source of genetic variation within the genome...
- Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine heightYuri T Utsunomiya
Faculdade de Medicina Veterinaria de Aracatuba, Univ Estadual Paulista, Aracatuba, Sao Paulo, Brazil
BMC Genet 14:52. 2013....
- SNP discovery and allele frequency estimation by deep sequencing of reduced representation librariesCurtis P van Tassell
Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, Maryland 20705, USA
Nat Methods 5:247-52. 2008..67. This approach for simultaneous de novo discovery of high-quality SNPs and population characterization of allele frequencies may be applied to any species with at least a partially sequenced genome...
- An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotationGregory P Harhay
USDA ARS US Meat Animal Research Center, State Spur 18 D, Clay Center, NE 68901, USA
Genome Biol 11:R102. 2010..We present an atlas of RNA abundance for 92 adult, juvenile and fetal cattle tissues and three cattle cell lines...
- A whole-genome assembly of the domestic cow, Bos taurusAleksey V Zimin
Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA
Genome Biol 10:R42. 2009..The genome of the domestic cow, Bos taurus, was sequenced using a mixture of hierarchical and whole-genome shotgun sequencing methods...
- Prevalence of the prion protein gene E211K variant in U.S. cattleMichael P Heaton
USDA, ARS, U, S, Meat Animal Research Center USMARC, State Spur 18D, P O Box 166, Clay Center, NE 68933, USA
BMC Vet Res 4:25. 2008..S. cattle...
- Genomic characteristics of cattle copy number variationsYali Hou
Bovine Functional Genomics Laboratory, ANRI, USDA ARS, Beltsville, Maryland 20705, USA
BMC Genomics 12:127. 2011..In the dairy industry, a large quantity of SNP genotyping results are becoming available and can be used for CNV discovery to understand and accelerate genetic improvement for complex traits...
- Unlocking the bovine genomeRoss L Tellam
CSIRO Livestock Industries, St Lucia, QLD, Australia
BMC Genomics 10:193. 2009....
- High-resolution haplotype block structure in the cattle genomeRafael Villa-Angulo
Department of Bioinformatics and Computational Biology, George Mason University, VA, USA
BMC Genet 10:19. 2009..6 Mb with an average density of approximately one SNP per 4 kb, and characterized the linkage disequilibrium (LD) and haplotype block structure within individual breeds and groups of breeds in relation to their geographic origin and use...
- Discovery and profiling of bovine microRNAs from immune-related and embryonic tissuesLuiz L Coutinho
United States Department of Agriculture, Agricultural Research Center, Beltsville Area Research Center, Beltsville, Maryland 20705, USA
Physiol Genomics 29:35-43. 2007..These results support the premise that species differences in regulation of gene expression by miR occur primarily at the level of expression and processing...
- Effects of increased milking frequency on gene expression in the bovine mammary glandErin E Connor
Bovine Functional Genomics Laboratory, USDA ARS, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
BMC Genomics 9:362. 2008....
- Comparative transcriptome analysis of in vivo- and in vitro-produced porcine blastocysts by small amplified RNA-serial analysis of gene expression (SAR-SAGE)Jeremy R Miles
USDA ARS, Biotechnology and Germplasm Laboratory, Beltsville, Maryland 20705, USA
Mol Reprod Dev 75:976-88. 2008....
- SNP-PHAGE--High throughput SNP discovery pipelineLakshmi K Matukumalli
US Department of Agriculture, ARS, Beltsville Agricultural Research Center, Bovine Functional Genomics Laboratory, Beltsville, MD 20705, USA
BMC Bioinformatics 7:468. 2006..Although these tasks are routinely performed by several groups, an integrated open source SNP discovery pipeline that can be easily adapted by new groups interested in SNP marker development is currently unavailable...
- Copy number variation of individual cattle genomes using next-generation sequencingDerek M Bickhart
USDA ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville, Maryland 20705, USA
Genome Res 22:778-90. 2012..By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome...
- Identification of conserved regulatory elements in mammalian promoter regions: a case study using the PCK1 promoterGeorge E Liu
Bovine Functional Genomics Laboratory, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
Genomics Proteomics Bioinformatics 6:129-43. 2008..Our full set of TFBS predictions is freely available at http://bfgl.anri.barc.usda.gov/tfbsConsSites...
- A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysisIk Young Choi
Soybean Genomics and Improvement Laboratory, USDA, ARS, Beltsville, Maryland 20705, USA
Genetics 176:685-96. 2007....
- Fine mapping of copy number variations on two cattle genome assemblies using high density SNP arrayYali Hou
Bovine Functional Genomics Laboratory, ANRI, USDA ARS, BARC East, Beltsville, MD 20705, USA
BMC Genomics 13:376. 2012..In our previous study using the low density BovineSNP50 array, we reported a copy number variation (CNV) analysis on Btau_4.0 with 521 animals of 21 cattle breeds, yielding 682 CNV regions with a total length of 139.8 megabases...
- Genomic regions showing copy number variations associate with resistance or susceptibility to gastrointestinal nematodes in Angus cattleYali Hou
Bovine Functional Genomics Laboratory, ANRI, USDA ARS, Building 200, Room 124B, BARC East, Beltsville, MD 20705, USA
Funct Integr Genomics 12:81-92. 2012..Network analyses indicated that the PS-specific genes were particularly enriched for inflammatory response, immune cell trafficking, metabolic disease, cell cycle, and cellular organization and movement...
- Identification of estrogen-responsive genes in the parenchyma and fat pad of the bovine mammary gland by microarray analysisRobert W Li
Bovine Functional Genomics Laboratory, United States Department of Agriculture Agricultural Research Service, Beltsville, Maryland 20705, USA
Physiol Genomics 27:42-53. 2006..The distinctive expression patterns regulated by estrogen in parenchyma and fat pad shed light on the need for both tissues to obtain normal mammary development...
- Effect of artificial selection on runs of homozygosity in u.s. Holstein cattleEui Soo Kim
Bovine Functional Genomics Laboratory, USDA ARS, Beltsville, Maryland, United States of America
PLoS ONE 8:e80813. 2013..Many of these selection signatures corresponded to quantitative trait loci for milk, fat, and protein yield previously found in contemporary Holsteins. ..
- Identification of a nonsense mutation in CWC15 associated with decreased reproductive efficiency in Jersey cattleTad S Sonstegard
Bovine Functional Genomics, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, USA
PLoS ONE 8:e54872. 2013..Whole-genome resequencing proved to be a powerful strategy to rapidly identify a previously mapped deleterious mutation in a known carrier of a recessive lethal allele...
- Serial analysis of gene expression during elongation of the peri-implantation porcine trophectoderm (conceptus)Le Ann Blomberg
Biotechnology and Germplasm Laboratory, United States Department of Agriculture Agricultural Research Service, Beltsville, Maryland 20705, USA
Physiol Genomics 20:188-94. 2005..These results validate the utility of SAGE in the pig and establish an initial model linking gene expression profiles at the pathway level with phenotypic progression from ovoid to filamentous stages of conceptus development...
- Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cowsJohn B Cole
Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland, USA
BMC Genomics 12:408. 2011..Here, we report results of a genome-wide analysis of predicted transmitting ability (PTA) of 31 production, health, reproduction and body conformation traits in contemporary Holstein cows...
- Transcriptome profiling of the tubular porcine conceptus identifies the differential regulation of growth and developmentally associated genesLe Ann Blomberg
Biotechnology and Germplasm Laboratory, USDA Agricultural Research Service, Beltsville, MD 20705, USA
Mol Reprod Dev 73:1491-502. 2006..The function(s) of these factors and potential modulation by estrogen clearly needs to be elucidated to understand their physiological role in normal conceptus development...
- A genome-wide survey reveals a deletion polymorphism associated with resistance to gastrointestinal nematodes in Angus cattleLingyang Xu
GEL Bovine Functional Genomics Laboratory, BARC, USDA ARS, Building 306, Room 111, BARC East, Beltsville, MD, 20705, USA
Funct Integr Genomics 14:333-9. 2014..As this CNV co-segregates with linked SNPs and associated genes, we suspect that it could contribute to the detected variations in gene expression and thus differences in host parasite resistance. ..
- Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequencesGeorge E Liu
USDA, ARS, ANRI, Bovine Functional Genomics Laboratory, Beltsville Agricultural Research Center BARC East, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
BMC Genomics 7:140. 2006..Approximately 11 Mb of finished high quality genomic sequences were sampled from cattle, dog and human to estimate genomic divergences and their regional variation among these lineages...
- Application of machine learning in SNP discoveryLakshmi K Matukumalli
Beltsville Agricultural Research Center, Bovine Functional Genomics Laboratory, US Department of Agriculture, ARS, Beltsville, MD 20705, USA
BMC Bioinformatics 7:4. 2006..ML methods have also been successfully applied to other bioinformatics problems in predicting genes, promoters, transcription factor binding sites and protein structures...
- EST-PAGE--managing and analyzing EST dataLakshmi K Matukumalli
US Department of Agriculture, ARS, Beltsville Agricultural Research Center, Bovine Functional Genomics Laboratory, Beltsville, MD 20705, USA
Bioinformatics 20:286-8. 2004....
- Local inflammation as a possible mechanism of resistance to gastrointestinal nematodes in Angus heifersRobert W Li
Bovine Functional Genomics Laboratory, USDA ARS, Beltsville, MD 20705, USA
Vet Parasitol 145:100-7. 2007..These data indicate that resistant animals can better maintain inflammatory responses at the site of infection, suggesting a possible novel mechanism of resistance...
- Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects BH1, HH2, and HH3 reveal a putative causative mutation in SMC2 for HH3Matthew C McClure
United States Department of Agriculture, Agriculture Research Service, Bovine Functional Genomics Laboratory, Beltsville, Maryland, United States of America
PLoS ONE 9:e92769. 2014..The absence of concordant variations for HH2 or BH1 suggests either the underlying causative mutations lie within a non-exomic region or in exome regions not covered by the capture array. ..
- Bovine genomics update: making a cow jump over the moonTad S Sonstegard
USDA, ARS, Bovine Functional Genomics Laboratory, Beltsville Agricultural Research Center BARC East, Beltsville, MD 20705, USA
Genet Res 84:3-9. 2004....
- Expressed sequence tag analysis of Eimeria-stimulated intestinal intraepithelial lymphocytes in chickensWongi Min
Animal Parasitic Diseases Laboratory, Animal and Natural Resources Institute, US Dept of Agriculture, Beltsville, MD 20705, USA
Mol Biotechnol 30:143-50. 2005..This EST library will provide a valuable resource for profiling global gene expression in normal and pathogen-infected chickens and identifying additional unique immune-related genes...
- Serial analysis of gene expression in turkey sperm storage tubules in the presence and absence of resident spermEzhou L Long
Biotechnology and Germplasm Laboratory, Animal and Natural Resources Institute, USDA ARS, Beltsville, Maryland 20705, USA
Biol Reprod 69:469-74. 2003..The bioinformatics and experimental procedures employed to clone turkey avidin and confirm its differential expression represent a useful paradigm for analyzing SAGE tag data from relatively uncharacterized model systems...
- Analysis of bovine mammary gland EST and functional annotation of the Bos taurus gene indexTad S Sonstegard
USDA, ARS, Beltsville Agricultural Research Center, Beltsville, Maryland 20705, USA
Mamm Genome 13:373-9. 2002..These results demonstrate that bovine sequence expression data serve as a resource for characterizing mammalian transcriptomes and identifying those genes potentially unique to ruminants...
- Predicting perchlorate exposure in milk from concentrations in dairy feedClifford P Rice
Environmental Management and Byproduct Utilization Laboratory, USDA, Agricultural Research Service, Beltsville, Maryland 20715, USA
J Agric Food Chem 55:8806-13. 2007..The study suggests that reducing perchlorate concentration in dairy feed may reduce perchlorate concentrations in milk as well as the potential to reduce human exposure to perchlorate in milk...