A5045309070- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Genetics and Plant Breeding
- Wheat and Barley Genetics and Pathology
- Animal Nutrition and Physiology
- Evolution and Genetic Dynamics
- Genetic Associations and Epidemiology
- Animal Behavior and Welfare Studies
- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- Animal Genetics and Reproduction
- Plant and animal studies
- Insect and Pesticide Research
- Insect and Arachnid Ecology and Behavior
- CRISPR and Genetic Engineering
- Effects of Environmental Stressors on Livestock
- Gene expression and cancer classification
- Rabbits: Nutrition, Reproduction, Health
- Cancer-related molecular mechanisms research
- Reproductive Physiology in Livestock
- Ruminant Nutrition and Digestive Physiology
- Meat and Animal Product Quality
- Livestock Management and Performance Improvement
- Milk Quality and Mastitis in Dairy Cows
- Agriculture and Biological Studies
Roslin Institute
2016-2025
University of Edinburgh
2016-2025
Edinburgh College
2024
ORCID
2024
University of Ljubljana
2013-2023
New South Wales Department of Primary Industries
2022
GTx (United States)
2021
Bayer (United States)
2021
Bayer (Germany)
2021
Commonwealth Scientific and Industrial Research Organisation
2014
Abstract Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and usually only way of obtaining ground-truth data to evaluate inferences. Because this, large number specialized programs have been developed, each filling particular niche, but with largely overlapping functionality substantial duplication effort. Here, we introduce msprime version 1.0, which efficiently implements ancestry mutation simulations based on...
ABSTRACT Genomic selection offers great potential for increasing the rate of genetic improvement in plant breeding programs. This research used simulation to evaluate effectiveness different strategies genotyping and phenotyping enable genomic early generation individuals (e.g., F 2 ) programs involving biparental or similar backcross top cross) populations. By using phenotypes that were previously collected other populations, decisions could be made without waiting pertain directly...
We propose a strategy for implementing genomic selection in plant breeding programs developing inbred lines that reorganizes traditional into two distinct components. These components are: (i) population improvement component to develop improved germplasm through rapid recurrent and (ii) product development identify new varieties or parents hybrids using program designs. Stochastic simulations of entire over 40 yr were used evaluate the effectiveness this relative conventional without three...
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...
Abstract This paper introduces AlphaSimR, an R package for stochastic simulations of plant and animal breeding programs. AlphaSimR is a highly flexible software able to simulate wide range programs diploid autopolyploid species. ideal testing the overall strategy detailed design utilizes scripting approach building that particularly well suited modeling complex programs, such as commercial The primary benefit this it frees users from preset program designs allows them model nearly any...
Key message Optimal cross selection increases long-term genetic gain of two-part programs with rapid recurrent genomic selection. It achieves this by optimising efficiency converting diversity into through reducing the loss and drop prediction accuracy cycling. This study evaluates optimal to balance maintenance in plant breeding The program reorganises a conventional population improvement component increase mean value germplasm product development standard methods develop new lines. Rapid...
Abstract As a result of recombination, adjacent nucleotides can have different paths genetic inheritance and therefore the genealogical trees for sample DNA sequences vary along genome. The structure capturing details these intricately interwoven is referred to as an ancestral recombination graph (ARG). Classical formalisms focused on mapping coalescence events nodes in ARG. However, this approach out step with some modern developments, which do not represent terms or explicitly infer them....
Genome editing (GE) is a method that enables specific nucleotides in the genome of an individual to be changed. To date, use GE livestock has focussed on simple traits are controlled by few quantitative trait (QTN) with large effects. The aim this study was evaluate potential improve many QTN, referred here as promotion alleles (PAGE). Multiple scenarios were simulated test alternative PAGE strategies for trait. They differed (i) number edits per sire (0 100), (ii) generation 500), and (iii)...
Next-generation sequencing techniques, such as genotyping-by-sequencing (GBS), provide alternatives to single nucleotide polymorphism (SNP) arrays. The aim of this work was evaluate the potential GBS compared SNP array genotyping for genomic selection in livestock populations. value quantified by simulation analyses which three parameters were varied: (i) genome-wide sequence read depth (x) per individual from 0.01x 20x or using genotyping; (ii) number genotyped markers 3000 300 000; and...
The limited genetic diversity of elite maize germplasms raises concerns about the potential to breed for new challenges. Initiatives have been formed over years identify and utilize useful from landraces overcome this issue. aim study was evaluate proposed designs initiate a pre-breeding program within Seeds Discovery (SeeD) initiative with emphasis on harnessing polygenic variation using genomic selection. We evaluated these stochastic simulation provide decision support effect several...
Genomic selection offers several routes for increasing the genetic gain or efficiency of plant breeding programmes. In various species livestock, there is empirical evidence increased rates from use genomic to target different aspects breeder's equation. Accurate predictions value are central this, and design training sets in turn achieving sufficient levels accuracy. summary, small numbers close relatives very large distant expected enable with higher To quantify effect some properties on...
Abstract Background In the Neolithic, domestic sheep migrated into Europe and subsequently spread in westerly northwesterly directions. Reconstruction of these migrations subsequent genetic events requires a more detailed characterization current phylogeographic differentiation. Results We collected 50 K single nucleotide polymorphism (SNP) profiles Balkan that are currently found near major Neolithic point entry Europe, combined data with published genotypes from southwest-Asian,...
Early simulations indicated that whole-genome sequence data (WGS) could improve the accuracy of genomic predictions within and across breeds. However, empirical results have been ambiguous so far. Large datasets capture most diversity in a population must be assembled allele substitution effects are estimated with high accuracy. The objectives this study were to use large pig dataset from seven intensely selected lines assess benefits using WGS for prediction compared commercial marker...
For genomic selection in clonally propagated crops with diploid (-like) meiotic behavior to be effective, crossing parents should selected based on predicted cross-performance unless dominance is negligible. (GS) clonal breeding programs Genomic prediction of enables efficient exploitation the additive and value simultaneously. Here, we compared different GS strategies for behavior, using strawberry as an example. We used stochastic simulation evaluate six combinations three two parent...
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic datasets remains major obstacle. Today, more realistic are possible thanks to large increases quantity quality available genetic data, sophistication inference simulation software. However, implementing these still requires substantial time specialized knowledge. These challenges especially pronounced simulating genomes...
Reliability is an important parameter in breeding. It measures the precision of estimated breeding values (EBV) and, thus, potential response to selection on those EBV. The EBV commonly measured by relating prediction error variance (PEV) base population additive genetic (base PEV reliability), while for squared correlation between and (BV) candidates (reliability selection). While these two are equivalent unselected populations, they not selected populations. aim this study was quantify...
Genotyping‐by‐sequencing (GBS) is an alternative genotyping method to single‐nucleotide polymorphism (SNP) arrays that has received considerable attention in the plant breeding community. In this study we use simulation quantify potential of low‐coverage GBS and imputation for cost‐effective genomic selection biparental segregating populations. The simulations comprised a range scenarios where SNP array or data were used train model, predict values, both. generated with sequencing coverages...
Over the last two decades, application of genomic selection has been extensively studied in various crop species, and it become a common practice to report prediction accuracies using cross validation. However, obtained from random validation can be strongly inflated due population or family structure, characteristic shared by many breeding populations. An understanding effect structure on accuracy is essential for successful plant programs. The objective this study was make its implications...
In this paper, we simulate deleterious load in an animal breeding program, and compare the efficiency of genome editing selection for decreasing it. Deleterious variants can be identified by bioinformatics screening methods that use sequence conservation biological prior information about protein function. However, once have been identified, how they used breeding? We simulated a closed population is subject to both natural against artificial quantitative trait representing goal. was...
Abstract Background Backfat thickness is an important carcass composition trait for pork production and commonly included in swine breeding programmes. In this paper, we report the results of a large genome-wide association study backfat using data from eight lines diverse genetic backgrounds. Methods Data comprised 275,590 pigs with backgrounds (breeds Large White, Landrace, Pietrain, Hampshire, Duroc, synthetic lines) genotyped imputed 71,324 single-nucleotide polymorphisms (SNPs). For...
Abstract Key message The integration of known and latent environmental covariates within a single-stage genomic selection approach provides breeders with an informative practical framework to utilise genotype by environment interaction for prediction into current future environments. This paper develops which integrates special factor analytic framework. linear mixed model Smith et al. (2001) is effective method analysing multi-environment trial (MET) datasets, but has limited practicality...
Rice ( Oryza sativa L.) has two main subspecies, indica and japonica , which coexist in many regions but are often treated separately during breeding. Combining both subspecies quantitative genetic analyses could enhance improvement, however, this requires appropriately modelling their history. The ancestral recombination graph (ARG) is an effective population genetics tool that comprehensively succinctly represents a species' This study evaluated the use of ARG, encoded as tree sequence, to...
Crossbreeding is successfully implemented worldwide to improve animal productivity and adaptability. However, recurrent failures of crossbreeding programmes in African countries imply the need design effective strategies for predominant smallholder production systems. A comprehensive simulation procedure mimicked body weight (BWL) tick count (TCL) incidence a local taurine cattle breed an exotic indicine beef (BWE TCE, respectively). The two breeds were crossed produce F1 rotational animals....
An approach is described for simulating data sequence, genotype, and phenotype to study genomic selection genome-wide association studies (GWAS). The simulation method, implemented in a software package called AlphaDrop, can be used simulate phenotypes with flexibility terms of the historical population structure, recent pedigree distribution quantitative trait loci effects, sequence single nucleotide polymorphism-phased alleles genotypes. Ten replicates representative scenario livestock...