A5049703762- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Reproductive Physiology in Livestock
- Effects of Environmental Stressors on Livestock
- Genetic Associations and Epidemiology
- Milk Quality and Mastitis in Dairy Cows
- Meat and Animal Product Quality
- Sperm and Testicular Function
- Genetics and Plant Breeding
- Spectroscopy and Chemometric Analyses
- Wheat and Barley Genetics and Pathology
- Gene expression and cancer classification
- Animal Genetics and Reproduction
- Animal Behavior and Welfare Studies
- Odor and Emission Control Technologies
- Ruminant Nutrition and Digestive Physiology
- Reproductive Biology and Fertility
- Animal Nutrition and Physiology
- Molecular Biology Techniques and Applications
- Agriculture Sustainability and Environmental Impact
- Evolution and Genetic Dynamics
- Cancer-related molecular mechanisms research
- CRISPR and Genetic Engineering
- Agriculture and Biological Studies
Roslin Institute
2016-2018
University of Edinburgh
2016-2018
University of Padua
2010-2013
This paper describes AlphaSim, a software package for simulating plant and animal breeding programs. AlphaSim enables the simulation of multiple aspects programs with high degree flexibility. simulates in series steps: (i) simulate haplotype sequences pedigree; (ii) drop haplotypes into base generation pedigree select single-nucleotide polymorphism (SNP) quantitative trait nucleotide (QTN); (iii) assign QTN effects, calculate genetic values, phenotypes; (iv) burn-in generations; (v) perform...
Genomic selection has great potential to increase the efficiency of plant breeding, but its implementation is hindered by high costs collecting necessary data. In this study we evaluated accurate within‐family imputation for enabling cost‐effective genomic selection. We have simulated a breeding program with inbred parents and their segregating progeny distributed among families, which some were used as training set prediction set. Parents genotyped at density (20,000 markers), while or low...
Inherent sources of error and bias that affect the quality sequence data include index hopping towards reference allele. The impact these artefacts is likely greater for low-coverage than high-coverage because has scant information many standard tools processing were designed data. With proliferation cost-effective sequencing, there a need to understand errors on resulting genotype calls from sequencing. We used dataset 26 pigs sequenced both at 2× with multiplexing 30× without show allele...
In this work, we performed simulations to explore the potential of manipulating recombination rates increase response selection in livestock breeding programs. We carried out ten replicates several scenarios that followed a common overall structure but differed average rate along genome (expressed as length chromosome Morgan), genetic architecture trait under selection, and intensity truncation proportion males selected). Recombination were defined by simulating nine different lengths: 0.10,...
Physical and color characteristics of chicken meat were investigated on 193 animals by directly applying a fiberoptic probe to the breast muscle using visible-near-infrared (NIR) spectral range from 350 1,800 nm. Data pH was recorded 48 h postmortem (pH); lightness (L*), redness (a*), yellowness (b*) postmortem; thawing cooking losses shear force after freezing. Partial least squares regressions performed untreated data, raw absorbance data (log(1/R)), multiplicative scatter correction plus...
Abstract In this work, we performed simulations to develop and test a strategy for exploiting surrogate sire technology in animal breeding programs. Surrogate allows the creation of males that lack their own germline cells, but have transplanted spermatogonial stem cells from donor males. With technology, single elite male could give rise huge numbers progeny, potentially as much all production animals particular time period. One hundred replicates various scenarios were performed. Scenarios...
This paper describes a method, called AlphaSeqOpt, for the allocation of sequencing resources in livestock populations with existing phased genomic data to maximise ability phase and impute sequenced haplotypes into whole population. We present two algorithms. The first selects focal individuals that collectively represent maximum possible portion haplotype diversity second allocates fixed budget among families enable phasing their at sequence level. tested performance algorithms simulated...
This study uses simulation to explore and quantify the potential effect of shifting recombination hotspots on genetic gain in livestock breeding programs.We simulated three scenarios that differed locations quantitative trait nucleotides (QTN) genome. In scenario 1, QTN were randomly distributed along chromosomes was restricted occur within specific genomic regions (i.e. hotspots). other two scenarios, both located regions, but whether occurred outside (scenario 2) or inside 3) hotspots. We...
Direct measurements of methane (CH4) from individual animals are difficult and expensive. Predictions based on proxies for CH4 a viable alternative. Most prediction models multiple linear regressions (MLR) predictor variables that not routinely available in commercial farms, such as dry matter intake (DMI) diet composition. The use machine learning (ML) algorithms to predict emissions across-country heterogeneous data sets has been reported. objectives were compare performances ML ensemble...
<h2>ABSTRACT</h2> Dairy bull fertility is traditionally evaluated using semen production and quality traits; however, these attributes explain only part of the differences observed in among bulls. Alternatively, can be directly cow field data. The main objective this study was to investigate Italian Brown Swiss dairy cattle population confirmed pregnancy records. data set included a total 397,926 breeding records from 1,228 bulls 129,858 lactating cows between first fifth lactation 2000...
The aim of this study was to investigate factors influencing the number daughters Holstein bulls during progeny testing using data provided by Italian Friesian Cattle Breeders Association. hypothesis is that there are no differences among artificial insemination studs (AIS) on distribution bulls. For each bull and beginning from 21 months age, over period calculated. Data were available 1973 born between 1986 2004, tested in Italy with at least 4 paternal half-sibs. On average, exited...
Abstract Background Inherent sources of error and bias that affect the quality sequence data include index hopping towards reference allele. The impact these artefacts is likely greater for low-coverage than high-coverage because has scant information standard tools processing were designed data. With proliferation cost-effective sequencing there a need to understand errors on resulting genotype calls. Results We used dataset 26 pigs sequenced both at 2x with multiplexing 30x without show...