A5075702907- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Cancer-related molecular mechanisms research
- Epigenetics and DNA Methylation
- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- Genetics and Plant Breeding
- Chromosomal and Genetic Variations
- Animal Nutrition and Physiology
- Sperm and Testicular Function
- Plant Molecular Biology Research
- Animal Genetics and Reproduction
- Molecular Biology Techniques and Applications
- Cancer-related gene regulation
- Neurological diseases and metabolism
- Mycobacterium research and diagnosis
- Wheat and Barley Genetics and Pathology
- Animal Behavior and Welfare Studies
- RNA modifications and cancer
- Prion Diseases and Protein Misfolding
- Trace Elements in Health
- Ruminant Nutrition and Digestive Physiology
- Nutrition, Genetics, and Disease
- Skin Protection and Aging
- Neuroscience of respiration and sleep
University of Alaska Fairbanks
2025
University of Vermont
2015-2024
University of Missouri
2008-2024
Institute of Animal Sciences
2009-2010
University of Alberta
2006-2010
Texas A&M University
2003-2009
Mitchell Institute
2004
Major advances in selection progress for cattle have been made following the introduction of genomic tools over past 10-12 years. These depend upon Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety deficiencies inaccuracies. We present new cattle, ARS-UCD1.2, based on same animal as original to facilitate transfer interpretation results obtained from earlier version, but applying combination modern de novo assembly increase...
The domestication and development of cattle has considerably impacted human societies, but the histories breeds have been poorly understood especially for African, Asian, American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate population structure 134 domesticated bovid Regardless analytical method or sample subset, three major groups Asian indicine, Eurasian taurine, African taurine were consistently observed....
Abstract Background Bovine whole genome linkage disequilibrium maps were constructed for eight breeds of cattle. These data provide fundamental information concerning bovine organization which will allow the design studies to associate genetic variation with economically important traits and also provides background extent long range in Results Linkage was assessed using r 2 among all pairs syntenic markers within cattle from Bos taurus indicus subspecies. included Angus, Charolais, Dutch...
The Pecorans (higher ruminants) are believed to have rapidly speciated in the Mid-Eocene, resulting five distinct extant families: Antilocapridae, Giraffidae, Moschidae, Cervidae, and Bovidae. Due rapid radiation, Pecoran phylogeny has proven difficult resolve, 11 of 15 possible rooted phylogenies describing ancestral relationships among Bovidae each been argued as representations true phylogeny. Here we demonstrate that a genome-wide single nucleotide polymorphism (SNP) genotyping platform...
To gain insight into the number of loci large effect that underlie variation in cattle, a quantitative trait locus (QTL) scan for 14 economically important traits was performed two commercial Angus populations using 390 microsatellites, 11 single nucleotide polymorphisms (SNPs) and one duplication loci. The first population comprised 1769 registered bulls born between 1955 2003, with Expected Progeny Differences computed by American Association. second 38 half-sib families containing 1622...
Abstract Background Genomic selection is a recently developed technology that beginning to revolutionize animal breeding. The objective of this study was estimate marker effects derive prediction equations for direct genomic values 16 routinely recorded traits American Angus beef cattle and quantify corresponding accuracies prediction. Methods Deregressed estimated breeding were used as observations in weighted analysis 3570 sires genotyped using the Illumina BovineSNP50 BeadChip. These...
Abstract Dramatic improvements in measuring genetic variation across agriculturally relevant populations (genomics) must be matched by identifying and trait such many environments (phenomics). Identifying the most critical opportunities challenges genome to phenome (G2P) research is focus of this paper. Previously (Genome Biol, 23(1):1–11, 2022), we laid out how Agricultural Genome Phenome Initiative (AG2PI) will coordinate activities with USA federal government agencies expand...
A second-generation 5000 rad radiation hybrid (RH) map of the cattle genome was constructed primarily using ESTs that were targeted to gaps in existing cattle–human comparative map, as well sparsely populated intervals. total 870 markers added, bringing number mapped on RH panel 1913. Of these, 1463 have significant BLASTN hits (E < e –5 ) against human sequence. created sequence coordinates paired orthologs. One-hundred and ninety-five conserved segments (defined by two or more genes)...
Abstract Background Analyses of population structure and breed diversity have provided insight into the origin evolution cattle. Previously, these studies used a low density microsatellite markers, however, with large number single nucleotide polymorphism markers that are now available, it is possible to perform genome wide genetic analyses in In this study, we high-density panel SNP examine among eight cattle breeds sampled from Bos indicus taurus . Results Two thousand six hundred forty...
Estimated breeding values for average daily feed intake (AFI; kg/day), residual (RFI; kg/day) and gain (ADG; were generated using a mixed linear model incorporating genomic relationships 698 Angus steers genotyped with the Illumina BovineSNP50 assay. Association analyses of estimated (EBVs) performed 41,028 single nucleotide polymorphisms (SNPs), permutation analysis was used to empirically establish genome-wide significance threshold (P < 0.05) each trait. SNPs significantly associated...
Genetic markers can be used to identify and verify the origin of individuals. Motivation for inference ancestry ranges from conservation genetics forensic analysis. High density assays featuring Single Nucleotide Polymorphism (SNP) exploited create a reduced panel containing most informative these purposes. The objectives this study were evaluate methods marker selection determine minimum number BovineSNP50 BeadChip required individuals in European cattle breeds. Delta, Wright's FST, Weir &...
The purpose of this study was to identify loci associated with Mycobacterium avium subspecies paratuberculosis (Map) infection status in US Holsteins using the Illumina BovineSNP50 BeadChip whole genome single nucleotide polymorphism (SNP) assay. Two hundred forty-five cows from dairies New York, Pennsylvania and Vermont enrolled longitudinal herd studies between January 1999 November 2007 were assessed for presence Map both faecal tissue samples. An animal considered infected if any sample...
Abstract Background The domestication and subsequent selection by humans to create breeds biological types of cattle undoubtedly altered the patterning variation within their genomes. Strong fix advantageous large-effect mutations underlying domesticability, breed characteristics or productivity created selective sweeps in which was lost chromosomal region flanking selected allele. Selective have now been identified genomes many animal species including humans, dogs, horses, chickens. Here,...
Acute lymphoblastic leukemia (ALL) is the most common cancer diagnosed in children under age of 15. In addition to genetic aberrations, epigenetic modifications such as DNA methylation are altered and impact gene expression. To identify alterations ALL, genome-wide profiles were generated using methylated CpG island recovery assay followed by next-generation sequencing. More than 25,000 differentially regions (DMR) observed ALL patients with ∼90% present within intronic or intergenic...
Cattle are important agriculturally and relevant as a model organism. Previously described genetic radiation hybrid (RH) maps of the bovine genome have been used to identify genomic regions genes affecting specific traits. Application these influential polymorphisms will be enhanced by integration with each other bacterial artificial chromosome (BAC) libraries. The BAC libraries clone essential for clone-by-clone/whole-genome shotgun sequencing approach taken project. A map was constructed...
Congenital malformations resulting in late abortions and stillbirths affect the economic wellbeing of producers welfare cattle breeding programs. An extremely high incidence "half-sized" calves normal karyotype uninflated lungs was diagnosed progeny Finnish Ayrshire (Bos taurus) bull - YN51. No other visible anatomical abnormalities were apparent stillborn calves. We herein describe positional identification a 110 kb microdeletion maternally imprinted PEG3 domain that results loss paternal...
Summary We performed a genome‐wide association study for W arner– B ratzler shear force ( WBSF ), measure of meat tenderness, by genotyping 3360 animals from five breeds with 54 790 ovine SNP 50 and 96 putative single‐nucleotide polymorphisms s) within μ‐calpain [ HUGO nomenclature calpain 1, (mu/I) large subunit ; CAPN 1 ] calpastatin CAST ). Within‐ across‐breed analyses estimated allele substitution effects ASEs ) genomic best linear unbiased prediction GBLUP variance components...
Molecular estimates of breeding value are expected to increase selection response due improvements in the accuracy and a reduction generation interval, particularly for traits that difficult or expensive record measured late life. Several statistical methods incorporating molecular data into estimation have been proposed, however, most studies utilized simulated which generated linkage disequilibrium may not represent targeted livestock population. A genomic relationship matrix was developed...
To identify the genetic cause of isolated canine ectopia lentis, a well-characterized veterinary disease commonly referred to as primary lens luxation (PLL) and compare with newly described human Weill-Marchesani syndrome (WMS)-like similar etiology.Genomewide association analysis fine mapping by homozygosity were used chromosomal segment harboring PLL locus. The resequencing regional candidate gene was discover mutation in splice donor site predicted exon skipping. Exon skipping confirmed...
Abstract Insecticide use is pervasive as a selective force in modern agroecosystems. Insect herbivores exposed to these insecticides have been able rapidly evolve resistance them, but how they are do so poorly understood. One possible largely unexplored explanation that exposure sublethal doses of may alter epigenetic patterns heritable. For instance, mechanisms, such DNA methylation modifies gene expression without changing the underlying genetic code, facilitate emergence resistant...
Johne's disease, caused by Mycobacterium avium subspecies paratuberculosis (Map), is a fatal disease in cattle. The objective of this study was to identify loci associated with tolerance cows infected Map. Tolerance defined as cow's fitness at given level Map infection intensity. Fitness measured faecal cultures, and intensity culturing four gut tissues. quantitative phenotype numerical indexes cultures peak (peak tolerance, PT) average (average AT) tissue from 245 Holstein cows. categorical...