A5034296455- Genetic Mapping and Diversity in Plants and Animals
- Genetic and phenotypic traits in livestock
- Molecular Biology Techniques and Applications
- Cancer-related molecular mechanisms research
- Meat and Animal Product Quality
- Animal Behavior and Welfare Studies
- Animal Nutrition and Physiology
- Animal Genetics and Reproduction
- Genetics and Plant Breeding
- Muscle Physiology and Disorders
- Growth Hormone and Insulin-like Growth Factors
- RNA Research and Splicing
- Epigenetics and DNA Methylation
- RNA and protein synthesis mechanisms
- Virus-based gene therapy research
- Animal Virus Infections Studies
- MicroRNA in disease regulation
- Herpesvirus Infections and Treatments
- RNA regulation and disease
- RNA modifications and cancer
- Chromosomal and Genetic Variations
- Genomics and Chromatin Dynamics
- CRISPR and Genetic Engineering
- Viral gastroenteritis research and epidemiology
- Gene expression and cancer classification
Michigan State University
2015-2024
Scotland's Rural College
2019
Consejo Nacional de Investigaciones Científicas y Técnicas
2019
University of Buenos Aires
2019
Roman L. Hruska U.S. Meat Animal Research Center
1995-2018
University of Southampton
2018
Erasmus Hospital
2013
Animal Science Research Institute
2003-2011
Michigan United
2011
Iowa State University
1990-1999
Abstract Gene regulatory elements are central drivers of phenotypic variation and thus critical importance towards understanding the genetics complex traits. The Functional Annotation Animal Genomes consortium was formed to collaboratively annotate functional in animal genomes, starting with domesticated animals. Here we present an expansive collection datasets from eight diverse tissues three important agricultural species: chicken ( Gallus gallus ), pig Sus scrofa cattle Bos taurus )....
In 2008, a consortium led by the Agricultural Research Service (ARS) and National Institute for Food Agriculture (NIFA) published "Blueprint USDA Efforts in Animal Genomics 2008-2017," which served as guiding document research funding animal genomics. decade that followed, many of goals set forth blueprint were accomplished. However, several other require further research. addition, new topics not covered original blueprint, are result emerging technologies, exploration. To develop new,...
The functional annotation of livestock genomes is crucial for understanding the molecular mechanisms that underpin complex traits economic importance, adaptive evolution and comparative genomics. Here, we provide most comprehensive catalogue to date regulatory elements in pig (Sus scrofa) by integrating 223 epigenomic transcriptomic data sets, representing 14 biologically important tissues. We systematically describe dynamic epigenetic landscape across tissues functionally annotating 15...
The success of marker assisted selection depends on the amount linkage disequilibrium (LD) across genome. To implement in swine breeding industry, information about extent and degree LD is essential. objective this study to estimate four US breeds pigs (Duroc, Hampshire, Landrace, Yorkshire) subsequently calculate persistence phase among them using a 60 k SNP panel. In addition, we report when only fraction available markers, over distance.Average r2 between adjacent all chromosomes was 0.36...
Numerous long non-coding RNAs (lncRNAs) have been identified and their roles in gene regulation humans, mice, other model organisms studied; however, far less research has focused on lncRNAs farm animal species. While previous studies chickens, cattle, pigs specific developmental stages or differentially expressed under conditions a limited number of tissues, more comprehensive identification these species is needed. The goal the FAANG Consortium (Functional Annotation Animal Genomes) to...
Pigs from the F(2) generation of a Duroc x Pietrain resource population were evaluated to discover QTL affecting carcass composition and meat quality traits. Carcass phenotypes included primal cut weights, skeletal characteristics, backfat thickness, LM area. Meat data pH, temperature, objective subjective color information, marbling firmness scores, drip loss. Additionally, chops analyzed for moisture, protein, fat as well cook yield Warner-Bratzler shear force measurements. Palatability...
Currently, association studies are analysed using statistical mixed models, with marker effects estimated by a linear transformation of genomic breeding values. The variances needed when performing the tests association. However, approaches used to estimate parameters rely on prior variance or constant additive variance. Alternatively, we propose standardized test each effect, which generally differ among other. Random values from model including fixed and covariance matrix linearly...
Abstract Background Although considerable progress has been made towards annotating the noncoding portion of human and mouse genomes, regulatory elements in other species, such as livestock, remain poorly characterized. This lack functional annotation poses a substantial roadblock to agricultural research diminishes value these species model organisms. As active are typically characterized by chromatin accessibility, we implemented Assay for Transposase Accessible Chromatin (ATAC-seq)...
Controversy exists on the effect of obesity bone development during puberty.Our objective was to determine differences in volumetric mineral density (vBMD) and geometry male obese adolescents (ObAs) overlap with changes maturation, muscle mass force development, circulating sex steroids IGF-I. We hypothesized that parameters are more evident at weight-bearing site serum estradiol most prominent.We recruited 51 ObAs (10-19 years) entry a residential weight-loss program healthy age-matched...
Meishan is a pig breed indigenous to China and famous for its high fecundity. The traits of are strongly associated with distinct evolutionary history domestication. However, the genomic evidence linking domestication pigs unique features still poorly understood. goal this study investigate signatures related phenotypic via large-scale sequencing. We found that occurred in Taihu Basin area between Majiabang Liangzhu Cultures, during which 300 protein-coding genes have underwent positive...
Pigs from the F(2) generation of a Duroc x Pietrain resource population were evaluated to discover QTL affecting growth and composition traits. Body weight ultrasound estimates 10th-rib backfat, last-rib LM area serially measured throughout development. Estimates fat-free total lean, body fat, empty protein, lipid, ADG 10 22 wk age calculated, random regression analyses performed estimate individual animal phenotypes representing intercept linear rates increase in these serial A 510 animals...
Childhood obesity is associated with an accelerated skeletal maturation. However, data concerning pubertal development and sex steroid levels in obese adolescents are scarce contrasting. To study steroids relation to sexual maturation serum prostate specific antigen (PSA), as a marker of androgen activity, boys from early late adolescence. Ninety (aged 10–19 y) at the start residential treatment program 90 age-matched controls were studied cross-sectionally. Pubertal status was assessed...
Abstract Genomic selection has the potential to increase genetic progress. Genotype imputation of high-density single-nucleotide polymorphism (SNP) genotypes can improve cost efficiency genomic breeding value (GEBV) prediction for pig breeding. Consequently, objectives this work were to: (1) estimate accuracy evaluation and GEBV three traits in a Yorkshire population (2) quantify loss when imputed under two scenarios: high-cost, high-accuracy scenario which only candidates from low-density...
Abstract Background F 2 resource populations have been used extensively to map QTL segregating between pig breeds. A limitation associated with the use of these for fine mapping is reduced number founding individuals and recombinations haplotypes occurring in population. These limitations, however, become advantageous when attempting impute unobserved genotypes using within family segregation information. trade-off would be re-type high density SNP panels low (tagSNP) followed by imputation....
Nearly 6,000 QTL have been reported for 588 different traits in pigs, more than any other livestock species. However, this effort has translated into only a few confirmed causative variants. A powerful strategy revealing candidate genes involves expression (eQTL) mapping, where the mRNA abundance of set transcripts is used as response variable scan.
A three-generation resource population was constructed by crossing pigs from the Duroc and Pietrain breeds. In this study, 954 F(2) animals were used to identify quantitative trait loci (QTL) affecting carcass meat quality traits. Based on results of first scan analyzed with a line-cross (LC) model using 124 microsatellite markers 510 animals, 9 chromosomes selected for genotyping additional markers. Twenty genotyped 20 in 444 animals. Three different Mendelian models least-squares QTL...
Economically important growth and meat quality traits in pigs are controlled by cascading molecular events occurring during development continuing throughout the conversion of muscle to meat. However, little is known about genes mechanisms involved this process. Evaluating transcriptomic profiles skeletal initial steps leading can identify key regulators polygenic phenotypes. In addition, mapping transcript abundance through genome-wide association analysis using high-density marker...
Summary Differences in gene expression were compared between RNAs from lungs of high (HR) and low (LR) porcine reproductive respiratory syndrome virus (PRRSV) burden pigs using the swine protein–annotated long oligonucleotide microarray, Pigoligoarray. Pathway analyses carried out to determine biological processes, pathways networks that differ LR HR responses. existed for 16 signalling [ P < 0.01/−log ( ‐value) >1.96]. Top canonical included acute phase response signalling, crosstalk...
Genotype imputation is a cost efficient alternative to use of high density genotypes for implementing genomic selection. The objective this study was investigate variables affecting accuracy from low tagSNP (average distance between 100kb 1Mb) sets in swine, selected using LD information, physical location, or genotype imputation. We compared results based on several varying densities and three different methods. In addition, we assessed the effect size composition reference panel haplotypes...
Abstract Background Skeletal muscle growth and development from embryo to adult consists of a series carefully regulated changes in gene expression. Understanding these developmental agriculturally important species is essential the production high quality meat products. For example, consumer demand for lean, inexpensive products has driven turkey industry unprecedented through intensive genetic selection. However, achievements increased body weight mass have been countered by an incidence...