A5020004415- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Genetics and Plant Breeding
- Animal Behavior and Welfare Studies
- Effects of Environmental Stressors on Livestock
- Reproductive Physiology in Livestock
- Animal Genetics and Reproduction
- Ruminant Nutrition and Digestive Physiology
- Cancer-related molecular mechanisms research
- Animal Nutrition and Physiology
- Epigenetics and DNA Methylation
- Microbial infections and disease research
- Meat and Animal Product Quality
- Genetic diversity and population structure
- Agricultural Economics and Policy
- Molecular Biology Techniques and Applications
- Reproductive Biology and Fertility
- Genetics and Neurodevelopmental Disorders
- Aquaculture disease management and microbiota
- Plant and fungal interactions
- Dietary Effects on Health
- Birth, Development, and Health
- Gut microbiota and health
- Milk Quality and Mastitis in Dairy Cows
- Agricultural Innovations and Practices
University of Nebraska–Lincoln
2016-2025
Drexel University
2023
University of Dayton
2023
Universidade de São Paulo
2020
Empresa de Pesquisa Agropecuária do Rio Grande do Norte
2020
Brazilian Agricultural Research Corporation
2020
Universidade Federal de Viçosa
2020
Roman L. Hruska U.S. Meat Animal Research Center
2017
ProMedica Toledo Hospital
2011
University of Georgia
2005-2009
Single nucleotide polymorphism (SNP) arrays for domestic cattle have catalyzed the identification of genetic markers associated with complex traits inclusion in modern breeding and selection programs. Using actual imputed Illumina 778K genotypes 3887 U.S. beef from 3 populations (Angus, Hereford, SimAngus), we performed genome-wide association analyses feed efficiency growth including average daily gain (ADG), dry matter intake (DMI), mid-test metabolic weight (MMWT), residual (RFI),...
The importance of the rumen microbiota on nutrient cycling to animal is well recognized; however, our understanding influence microbiome composition feed efficiency limited. microbiomes two large cohorts (125 heifers and 122 steers) were characterized identify specific bacterial members (operational taxonomic units [OTUs]) associated with traits (ADFI, ADG, G:F) in beef cattle. heifer steer fed a forage-based diet concentrate-based diet, respectively. A sample was obtained from each via...
Major challenges for illuminating the genetic basis of phenotypic evolution are to identify causative mutations, quantify their functional effects, trace origins as new or preexisting variants, and assess manner in which segregating variation is transduced into species differences. Here, we report an experimental analysis hemoglobin (Hb) function within among Peromyscus mice that native different elevations. A multilocus survey sequence duplicated HBA HBB genes maniculatus revealed...
The identification of genetic markers associated with complex traits that are expensive to record such as feed intake or efficiency would allow these be included in selection programs. To identify large-effect QTL, we performed a series genome-wide association studies and functional analyses using 50 K 770 SNP genotypes scored 5,133 animals from 4 independent beef cattle populations (Cycle VII, Angus, Hereford Simmental × Angus) phenotypes for average daily gain, dry matter intake, metabolic...
In light of recent host-microbial association studies, a consensus is evolving that species composition the gastrointestinal microbiota polygenic trait governed by interactions between host genetic factors and environment. Here, we investigated effect in shaping bacterial rumen performing genome-wide study. Using common set 61,974 single-nucleotide polymorphisms found cattle genomes (n = 586) corresponding community composition, identified operational taxonomic units (OTUs), Families Phyla...
Although the efficacy of genomic predictors based on within-breed training looks promising, it is necessary to develop and evaluate across-breed for technology be fully applied in beef industry. The efficacies trained one breed utilized predict genetic merit differing breeds simulation studies have been reported, as using data from multiple purebreds. However, comparable cattle field not reported. Molecular breeding values weaning yearling weight were derived evaluated a database containing...
Heterosis, assumed proportional to expected breed heterozygosity, was calculated for 6834 individuals with birth, weaning and yearling weight records from Cycle VII advanced generations of the U.S. Meat Animal Research Center (USMARC) Germplasm Evaluation (GPE) project. Breeds represented in these data included: Angus, Hereford, Red Charolais, Gelbvieh, Simmental, Limousin Composite MARC III. Heterosis further estimated by proportions British × (B B), Continental C) (C crosses breed-specific...
Traditional selection for sow reproductive longevity is ineffective due to low heritability and late expression of the trait. Incorporation DNA markers into programs potentially a more practical approach improving lifetime productivity. Using resource population crossbred gilts, we explored pleiotropic sources variation that influence age at puberty longevity. Of traits recorded before breeding, only significantly affected probability females would produce first parity litter. The genetic...
Despite the health concerns and nutritional importance of fatty acids, there is a relative paucity studies in literature that report genetic or genomic parameters, especially case sheep populations. To investigate architecture acid composition sheep, we conducted genome-wide association (GWAS) estimated heritabilities for profile Longissimus dorsi muscle 216 male sheep. Genomic heritability estimates content ranged from 0.25 to 0.46, indicating substantial variation exists evaluated traits....
Cattle are an attractive animal model of fertility in women due to their high degree similarity relative follicle selection, embryo cleavage, blastocyst formation, and gestation length. To facilitate future studies the epigenetic underpinnings aging effects female reproductive axis, several DNA methylation-based biomarkers (epigenetic clocks) for bovine oocytes presented. One such clock was germane only oocytes, while a dual-tissue highly predictive age both blood. Dual species clocks that...
Animal traits develop through the expression and action of numerous regulatory realizator genes that comprise a gene network (GRN). For each GRN, its underlying patterns are controlled by cis -regulatory elements (CREs) bind activating repressing transcription factors. These interactions drive cell-type developmental stage-specific transcriptional activation or repression. Most GRNs remain incompletely mapped, major barrier to this daunting task is CRE identification. Here, we used an in...
Steers ( = 480; 22% with black hides and 78% red hides) were used to study the effects of shade feeding zilpaterol hydrochloride (ZH) on performance, carcass quality, heat stress, mobility, body temperature (BT). A randomized block design a 2 × factorial treatment arrangement was 4 replicates per treatment. Factors included housing type (open or shaded pens) ZH (0 8.33 mg/kg DM) last 21 d feed 3-d withdrawal. Cattle blocked by BW into heavy light randomly assigned pen within each block....
The primary reason livers are condemned is due to abscesses, which visible lesions detected on the liver during routine harvest of animal. Condemned deemed not fit for human consumption, and result in over $15M lost income U.S. beef industry each year. Liver scoring a 4-level measurement abscess severity: 0 (no abscesses), A- (mild: 1-2 small A (moderate: 2-4 active abscesses) A+ (severe: 1 or more large, abscesses). We quantified degree known sources variation, including genomic differences...
Abstract Four methods were proposed for adding additional criteria to identify informative sequence variations (HISV) from Bos Taurus imputed low-pass genomic data genetic prediction. All selected variants an original set of ~ 60 million. First, HISV encoding protein cavity sites, 3D structures provided by ALPHA Fold 2 analyzed using the Fpocket application forming residues and TBLASTN mapped them in genome UCD 2.0. Second, parsed KGML files representing biological pathways (Bos) Homosapien...
Abstract To identify highly informative features among ~60 million imputed sequence variants in Bos Taurus a deep learning model based on the attention mechanism, that can learn contextual association between tokens (nucleotides) from given input sequence, was developed. Training occurred with multiple 9 nucleotide fragments of non-variant regions. The same size an observed variant at center were used to test calculate probability occurrence reported center. Those predicted lowest...
Abstract A crossbred beef cattle population (n=2,212) was used to assess the impact of variants identified from imputed low-pass sequence (LPS) on robustness predictions across breed types for traits birth weight (BWT) and post-weaning gain (PWG). Variants were selected based functional partitioned into four groups (Low, Modifier, Moderate, High) later re-partitioned consequence mutation (i.e., missense untranslated region variants, etc.) six (G1-G6). Each subset construct a genomic...
Abstract In the beef industry, average daily dry matter intake (ADDMI) and gain (ADG) are economically relevant traits. Both ADDMI ADG influenced by host genomics rumen microbiomic composition. Therefore, these data can be used to predict future performance of animals for better management decisions. This study 417 steers 300 heifers with phenotypic, genomic, data. There were four diet groups, two (high concentrate) forage). Two methods creating microbial (co) variance matrices tested, Van...
Abstract Background Infectious Bovine Keratoconjunctivitis (IBK), commonly known as pinkeye, is one of the most significant diseases beef cattle. As such, IBK costs US industry at least 150 million annually. However, strategies to prevent are limited, with cases resulting in treatment antibiotics once disease has developed. Longitudinal studies evaluating establishment ocular microbiota may identify critical risk periods for outbreaks or changes that predispose animals IBK. Results In an...
Abstract Infectious bovine keratoconjunctivitis (IBK), commonly known as pinkeye, is a disease that infects the ocular surface and surrounding tissue which concern to animal health welfare well producer economics. Vaccinations have been shown variable efficacy, while limited genetics studies using either ulcer scores or binary phenotypes suggested direct genetic selection for resistance would be slow. Therefore, an investigation into host component of microbiome was conducted. Animals were...
Metagenomic sequencing is the process of extracting all genomic information from a given sample. Most metagenomic studies remove any host reads as matter course. However, can be used basis for genotype imputation to obtain whole sequences. The accuracy these imputed genotypic calls bovine ocular sample was determined by comparing results those commercial array. Overall, proved have high concordance with array (average 83% and correlation 0.81 no filtering). Accuracy increased filters read...
Birth weight (BWT) and calving difficulty (CD) were recorded on 4,579 first-parity females from the Germplasm Evaluation Program at U.S. Meat Animal Research Center (USMARC). Both traits analyzed using a bivariate animal model with direct maternal effects. Calving was transformed USMARC scores to corresponding -scores standard normal distribution based incidence rate of scores. Breed fraction covariates included estimate breed differences. Heritability estimates (SE) for BWT direct, CD...