A5078907613- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Genetics and Plant Breeding
- Cancer-related molecular mechanisms research
- Effects of Environmental Stressors on Livestock
- Genetic diversity and population structure
- Ruminant Nutrition and Digestive Physiology
- Reproductive Physiology in Livestock
- Molecular Biology Techniques and Applications
- Diverse Educational Innovations Studies
- Economics of Agriculture and Food Markets
- Wheat and Barley Genetics and Pathology
- Genomics and Phylogenetic Studies
- Animal Behavior and Welfare Studies
- Meat and Animal Product Quality
- Cleft Lip and Palate Research
- Protein Hydrolysis and Bioactive Peptides
- Supply Chain and Inventory Management
- Livestock Management and Performance Improvement
- Agricultural Economics and Policy
- Animal Genetics and Reproduction
- Animal Nutrition and Physiology
- Forensic and Genetic Research
- Food Supply Chain Traceability
- Environmental DNA in Biodiversity Studies
University of Tennessee at Knoxville
2020-2025
University of Missouri
2019-2024
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 These depend upon Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety deficiencies inaccuracies.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...
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...
Genotypic information produced from single nucleotide polymorphism (SNP) arrays has routinely been used to identify genomic regions associated with complex traits in beef and dairy cattle. Herein, we assembled a dataset consisting of 15,815 Red Angus cattle distributed across the continental U.S. union set 836,118 imputed SNPs conduct genome-wide association analyses (GWAA) for growth using univariate linear mixed models (LMM); including birth weight, weaning yearling weight. Genomic...
Abstract Background During the last decade, use of common-variant array-based single nucleotide polymorphism (SNP) genotyping in beef and dairy industries has produced an astounding amount medium-to-low density genomic data. Although low-density assays work well context prediction, they are less useful for detecting mapping causal variants effects rare not captured. The objective this project was to maximize accuracies genotype imputation from medium- marker set obtained by combining two...
Single nucleotide polymorphism (SNP) arrays have facilitated discovery of genetic markers associated with complex traits in domestic cattle; thereby enabling modern breeding and selection programs. Genome-wide association analyses (GWAA) for growth were conducted on 10,837 geographically diverse U.S. Gelbvieh cattle using a union set 856,527 imputed SNPs. Birth weight (BW), weaning (WW), yearling (YW) analyzed GEMMA EMMAX (via genotypes). Genotype-by-environment (GxE) interactions also...
Selection on complex traits can rapidly drive evolution, especially in stressful environments. This polygenic selection does not leave intense sweep signatures the genome, rather many loci experience small allele frequency shifts, resulting large cumulative phenotypic changes. Directional and local adaptation are changing populations; but, identifying underlying or environmental has been difficult. We use genomic data tens of thousands cattle from three populations, distributed over time...
Understanding genotype-by-environment interactions (G × E) is crucial to understand environmental adaptation in mammals and improve the sustainability of agricultural production. Here, we present an extensive study investigating interaction genome-wide SNP markers with a vast assortment variables searching for SNPs controlling phenotypic variance (vQTL) using large beef cattle dataset. We showed that G E contribute 10.1%, 3.8%, 2.8% birth weight, weaning yearling respectively. association...
Abstract Background Genetic and genomic selection programs require large numbers of phenotypes observed for animals in shared environments. Direct measurements like meat quality, methane emission, disease susceptibility are difficult expensive to measure at scale but critically important livestock production. Our work leans on our understanding the “Central Dogma” molecular genetics leverage intermediates as cheaply-measured proxies organism-level phenotypes. The rapidly declining cost...
Directional selection alters the genome via hard sweeps, soft and polygenic selection. However, mapping is difficult because it does not leave clear signatures on like a selective sweep. In populations with temporally stratified genotypes, Generation Proxy Selection Mapping (GPSM) method identifies variants associated generation number (or appropriate proxy) thus undergoing directional allele frequency changes. Here, we use GPSM two large datasets of beef cattle to detect associations...
Feral populations, those which successfully persist outside of cultivation or husbandry, provide unique opportunities to study the genomic impacts domestication and local adaptation. We argue that by leveraging resources designed for domestic counterparts, powerful phylogenetic population data collection analyses can be disentangle complex demographic processes. Surveys feral populations in a wide range organisms from animals plants reflects growing interest feralization (see Glossary)...
The Caribbean is a genetically diverse region with heterogeneous admixture compositions influenced by local island ecologies, migrations, colonial conflicts, and demographic histories. Commonwealth of Dominica mountainous in the Lesser Antilles historically known to harbor communities unique patterns migration, mixture, isolation. This community-based population genetic study adds biological evidence inform post-colonial narrative histories Dominican horticultural village. High density...
The ability of livestock to reproduce efficiently is critical the sustainability animal agriculture. Antral follicle count (AFC) and reproductive tract scores (RTS) can be used estimate fertility in beef heifers, but genetic mechanisms influencing variation these measures are not well understood. Two genome-wide association studies (GWAS) were conducted identify significant loci associated with traits. In total, 293 crossbred heifers genotyped on Bovine GGP 50K chip genotypes imputed 836,121...
The GeneMax (GMX) Advantage test, developed by Zoetis, uses approximately 50,000 single nucleotide polymorphisms (SNP) to predict the genomic potential of a commercial Angus heifer. Genetic predictions are provided for Calving Ease Maternal, Weaning Weight, Heifer Pregnancy, Milk, Mature Dry Matter Intake, Carcass Marbling, Yield, and three economic selection indices. Test results can inform culling decisions made beef cattle producers. To measure accuracy trait predictions, data from...
Abstract Selection on complex traits can rapidly drive evolution, especially in stressful environments. This polygenic selection does not leave intense sweep signatures the genome, rather many loci experience small allele frequency shifts, resulting large cumulative phenotypic changes. Directional and local adaptation are actively changing populations; but, identifying underlying or environmental has been difficult. We use genomic data tens of thousands cattle from three populations,...
Abstract Background Understanding the genetic basis of genotype-by-environment interactions (GxE) is crucial to understand environmental adaptation in mammals and improve sustainability agricultural production. In addition, GxE information could also be useful predict vulnerability populations climate change. Results Here, we present an extensive study investigating interaction genome-wide SNP markers with a vast assortment variables searching for SNPs controlling phenotypic variance (vQTL)...
Abstract The Neosho madtom (Noturus placidus) is a small catfish, generally less than 3 inches in length, unique to the Neosho-Spring River system within Arkansas Basin. It was federally listed as threatened 1990, largely due habitat loss. For conservation efforts, we generated whole-genome sequence data from 10 individuals originating geographically separated populations evaluate genetic diversity and population structure. A genome de novo assembled, size content were assessed. Single...
Abstract Background The use of array-based SNP genotyping in the beef and dairy industries has produced an astounding amount medium-to-low density genomic data last decade. While low-density assays work exceptionally well context prediction, they are less useful mapping causal variant discovery. This project focuses on maximizing imputation accuracies to marker set two high-density research assays, Illumina Bovine HD, GGP-F250 which contains a large proportion rare potentially functional...
Abstract We estimate a hedonic pricing model to determine producers’ value for bull expected progeny differences (EPDs), genomic-enhanced EPDs, and phenotypic traits. Birth weight EPD, ribeye area sale weight, age, frame score, other factors had statistically significant impact on prices. GE-EPDs were not associated with change in the sales prices expect weaned calf birth EPDs. Including provides unique contribution. The results from this work will inform educational programming purchasers...
Abstract Feed efficiency is an important factor for improving the sustainability and economic value of beef production. Although feed moderately heritable, it a complex trait affected by numerous factors such as diet, rumen microbiome, energy metabolism. Recent work has examined molecular control cattle divergent in efficiency; however, limited focused on transcriptomic regulation variation efficiency, specifically, genes contributing to muscle growth The hypothesis this study was that with...
Abstract Background Genetic and genomic selection programs require large numbers of phenotypes observed for animals in shared environments. Direct measurements like meat quality, methane emission, disease susceptibility are difficult expensive to measure at scale but critically important livestock production. Our work leans on our understanding the “Central Dogma” molecular genetics leverage intermediates as cheaply-measured proxies organism-level phenotypes. The rapidly declining cost...
Abstract Animals with greater feed efficiency use fewer resources to produce skeletal muscle, the primary product in beef production. As muscle represents approximately 50% of BW cattle, efficient utilization is interconnected growth. However, little known about molecular pathways interconnecting these two components The overall objective study was determine relationships between and growth at level cattle. specific this identify genes that are associated variation ADG, as an index We...
Abstract The bull buying behavior of Iowa cattle producers was assessed using an online simulated auction. Participants (n = 45) were asked a series questions to determine the type they wished bid on and purchase price for bull. Questions included breeding objective producer whether would be bred heifers. identify breed interested in purchasing, traits that most important their objective, maximum amount willing pay. Once buyer information complete, responses randomly redistributed other...
Abstract Inefficiencies in reproduction are the largest drivers of loss United States beef production. Nearly all reproductive traits at least modestly heritable, making genetic selection and improvement possible over long term. Cow-centric present unique challenges, as they not expressed male animals will be observed until later productive life a female, if all. This makes cow-centric fertility ideal candidates for with Expected Progeny Differences (EPDs). We used commercially generated...