A5051865915- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Genetics and Plant Breeding
- Fish Ecology and Management Studies
- Wheat and Barley Genetics and Pathology
- Genetic diversity and population structure
- Crop Yield and Soil Fertility
- Genetic Associations and Epidemiology
- Reproductive Physiology in Livestock
- Aquaculture disease management and microbiota
- Aquaculture Nutrition and Growth
- Fish Biology and Ecology Studies
- Marine Bivalve and Aquaculture Studies
- Food composition and properties
- Cancer-related molecular mechanisms research
- Aluminum toxicity and tolerance in plants and animals
- Effects of Environmental Stressors on Livestock
- Manufacturing Process and Optimization
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Evolution and Paleontology Studies
- Advanced Multi-Objective Optimization Algorithms
- Genomics and Phylogenetic Studies
- Identification and Quantification in Food
- Plant nutrient uptake and metabolism
- Viral Infections and Vectors
Commonwealth Scientific and Industrial Research Organisation
2013-2025
Agriculture and Food
2022-2025
Data61
2016-2019
ACT Government
2013-2019
Australian National University
2013
The University of Melbourne
2009-2010
Cooperative Research Centre for Beef Genetic Technologies
2009-2010
University of New England
2009-2010
Wageningen University & Research
2010
QIMR Berghofer Medical Research Institute
2009
Two key findings from genomic selection experiments are 1) the reference population used must be very large to subsequently predict accurate estimated breeding values (GEBV), and 2) prediction equations derived in one breed do not GEBV when applied other breeds. Both a problem for breeds where number of individuals is limited. A multi-breed potential solution, here we investigate accuracies Holstein dairy cattle Jersey single or multi-breed. The were obtained both as function elements...
In genome-wide association studies (GWAS), hundreds of thousands genetic markers (SNPs) are tested for with a trait or phenotype. Reported effects tend to be larger in magnitude than the true these markers, so-called “winner’s curse.” We argue that classical definition unbiasedness is not useful this context and propose use different property estimator we advocate. suggest an integrated approach estimation SNP prediction values, treating as random instead fixed effects. Statistical methods...
Abstract Background Next-generation sequencing technologies provide new opportunities to identify the genetic components responsible for trait variation. However, in species with large polyploid genomes, such as bread wheat, ability rapidly genes underlying quantitative loci (QTL) remains non-trivial. To overcome this, we introduce a novel pipeline that analyses, by RNA-sequencing, multiple near-isogenic lines segregating targeted QTL. Results We use this approach characterize major and...
Summary Genomic selection describes a strategy based on genomic breeding values predicted from dense single nucleotide polymorphism (SNP) data. Multiple methods have been proposed but the critical issue is how to decide whether an SNP should be included in predictive set estimate values. One major disadvantage of traditional Bayes B approach its high computational demands caused by changing dimensionality models. The use stochastic search variable (SSVS) retains same assumptions about...
Identification of alleles towards the selection for improved seedling vigour is a key objective many wheat breeding programmes. A multiparent advanced generation intercross (MAGIC) population developed from four commercial spring cultivars (cvv. Baxter, Chara, Westonia and Yitpi) containing ca. 1000 F(2) -derived, F(6:7) RILs was assessed at two contrasting soil temperatures (12 20 °C) shoot length coleoptile characteristics thickness. Narrow-sense heritabilities were high (h(2) =...
Farmed Atlantic salmon (Salmo salar) is a globally important production species, including in Australia where breeding and selection has been progress since the 1960s. The recent development of SNP genotyping platforms means genome-wide association genomic prediction can now be implemented to speed genetic gain. As precursor, this study collected genotypes at 218 132 SNPs 777 fish from Tasmanian population assess levels diversity, strength linkage disequilibrium (LD) imputation accuracy....
Rhizosheaths comprise soil bound to roots, and in wheat (Triticum aestivum L.) rhizosheath size correlates with root hair length. The aims of this study were determine the effect that a large has on phosphorus (P) acquisition by investigate genetic control grown acid soil.Near-isogenic lines differing evaluated two soils. soils fertilized mineral nutrients included treatments either low or high P. same treated CaCO3 raise pH detoxify Al(3+) Genotypic differences apparent only when was...
Abstract Teleost fish exhibit a remarkable diversity in the control of sex determination, offering opportunity to identify novel differentiation mechanisms and their ecological consequences. Here, we perform GWAS using 4715 46,501 SNP map determination three separate genomic locations Atlantic salmon ( Salmo salar ). To characterize each, whole genome sequencing was performed 30-fold depth coverage 20 representing each identified lineages. polymorphism reveals male carry single copy specific...
A key developmental transformation in the life of all vertebrates is transition to sexual maturity, whereby individuals are capable reproducing for first time. In farming Atlantic salmon, early maturation prior harvest size has serious negative production impacts.We report genome wide association studies (GWAS) using fish measured freshwater or marine environment. Genotypic data from a custom 50 K single nucleotide polymorphism (SNP) array was used identify 13 significantly associated SNP...
Genomic information was included for the first time in prediction of breeding values Atlantic salmon within Australian Salmon Enterprises Tasmania Pty Ltd selective program 2016. The process to realize genomic selection begun 2014 with scheme finalized and fully implemented 2018. high potential family accelerate genetic gain, something not possible using traditional pedigree-based approach, provided impetus implementation. Efficient effective genotyping platforms are essential selection....
Genomic selection describes a strategy based on genomic estimated breeding values (GEBV) predicted from dense genetic markers such as single nucleotide polymorphism (SNP) data. Different Bayesian models have been suggested to derive the prediction equation, with main difference centred around specification of prior distributions.The simulated dataset 13(th) QTL-MAS workshop was analysed using four approaches predict GEBV for animals without phenotypic information. distributions were assumed...
Abstract Identifying the genetic architecture of complex traits requires access to populations with sufficient diversity and recombination. Multiparent Advanced Generation InterCross (MAGIC) are a powerful resource due their balanced population structure, allelic diversity, enhanced However, implementing MAGIC in polyploids such as wheat is challenging, harbors many introgressions, inversions, other factors that interfere linkage mapping. By utilizing comprehensive crossing strategy,...
Summary Mapping of quantitative trait loci (QTLs) underlying variation in traits continues to be a powerful tool genetic study plants and other organisms. Whole genome average interval mapping (WGAIM), mixed model QTL approach using all intervals or markers simultaneously, has been demonstrated outperform composite mapping, common for analysis. However, the advent high-throughput high-dimensional marker platforms provides challenge. To overcome this, dimension reduction technique is proposed...
Multiparent Advanced Generation Inter-Cross (MAGIC) populations are now being utilized to more accurately identify the underlying genetic basis of quantitative traits through trait loci (QTL) analyses and subsequent gene discovery. The expanded diversity present in such amplified number recombination events mean that QTL can be identified at a higher resolution. Most conducted separately for each within single environment. Separate analysis does not take advantage correlation structure found...
Continuous-time Markov processes are often used to model the complex natural phenomenon of sequence evolution. To make process evolution tractable, simplifying assumptions made about properties and underlying process. The validity one such assumption, time-homogeneity, has never been explored. Violations this assumption can be found by identifying non-embeddability. A is non-embeddable if it not embedded in a continuous time-homogeneous In study, non-embeddability was demonstrated exist when...
Two homoeologous QTLs for number of spikelets per spike (SPS) were mapped on chromosomes 7AL and 7BL using two wheat MAGIC populations. Sets lines contrasting the QTL developed which allowed validation fine mapping identification a previously described candidate gene, WHEAT ORTHOLOG OF APO1 (WAPO1). Using transgenic overexpression in both low high SPS line, we provide functional role this gene determining also hexaploid wheat. We show that expression levels positively correlate with multiple...
Abstract Background Identifying the genetic architecture of complex traits requires access to populations with sufficient diversity and recombination. Multi-parent Advanced Generation InterCross (MAGIC) are a powerful resource due their balanced population structure, allelic enhanced However, implementing MAGIC in polyploids such as wheat is not trivial, harbours many introgressions, inversions other factors that interfere linkage mapping. Results By utilising comprehensive crossing...
The simulated dataset of the 13th QTL-MAS workshop was analysed to i) detect QTL and ii) predict breeding values for animals without phenotypic information. Several parameterisations considering all SNP simultaneously were applied using Gibbs sampling.Fourteen detected at different time points. Correlations between estimated high models, except when model used that assumed effects came from one distribution. selected 14 found associated with QTL, gave close unity correlations full...
For dairy producers, a reliable description of lactation curves is valuable tool for management and selection. From breeding production viewpoint, milk yield persistency total are important traits. Understanding the genetic drivers phenotypic variation both these traits could provide means improving in commercial production. It has been shown that Natural Cubic Smoothing Splines (NCSS) can model features with greater flexibility than traditional parametric methods. NCSS were used to sire...