Gregor Gorjanc

Gregor Gorjanc
The University of Edinburgh | UoE · Roslin Institute

Doctor of Philosophy

About

233
Publications
35,155
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2,809
Citations
Citations since 2017
156 Research Items
2365 Citations
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Introduction
I lead the HighlanderLab, which focuses on managing and improving populations using data science, genetics, and breeding. We focus on populations used for food, feed, and fibre production with some spillover into other populations. We are particularly interested in: (i) methods for genetics and breeding, (ii) design and optimisation of breeding programmes, and (iii) analysis of data to unravel biology and to find new ways of improving populations.

Publications

Publications (233)
Preprint
Full-text available
Background The Western honeybee is an economically important species globally, but has been experiencing colony losses that lead to economical damage and decreased genetic variability. This situation is spurring additional interest in honeybee breeding and conservation programs. Stochastic simulators are essential tools for rapid and low-cost testi...
Preprint
Full-text available
Small breeding programs are limited in achieving competitive genetic gain and prone to high rates of inbreeding. Thus, they often import genetic material to increase genetic gain and to limit the loss of genetic variability. However, the benefit of import depends on the strength of genotype by environment interaction. It also also diminishes the re...
Article
Full-text available
Background It is expected that functional, mainly missense and loss-of-function (LOF), and regulatory variants are responsible for most phenotypic differences between breeds and genetic lines of livestock species that have undergone diverse selection histories. However, there is still limited knowledge about the existing missense and LOF variation...
Article
Full-text available
Background By entering the era of mega-scale genomics, we are facing many computational issues with standard genomic evaluation models due to their dense data structure and cubic computational complexity. Several scalable approaches have been proposed to address this challenge, such as the Algorithm for Proven and Young (APY). In APY, genotyped ani...
Article
Full-text available
Tea [Camellia sinensis (L.) O. Kuntze] is mainly grown in low- to middle-income countries (LMIC) and is a global commodity. Breeding programs in these countries face the challenge of increasing genetic gain because the accuracy of selecting superior genotypes is low and resources are limited. Phenotypic selection (PS) is traditionally the primary m...
Preprint
Full-text available
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 data sets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of available genetic data, and to the s...
Article
Full-text available
Rubber tree (Hevea brasiliensis) is the main feedstock for commercial rubber; however, its long vegetative cycle has hindered the development of more productive varieties via breeding programs. With the availability of H. brasiliensis genomic data, several linkage maps with associated quantitative trait loci have been constructed and suggested as a...
Article
Full-text available
Key message The integration of known and latent environmental covariates within a single-stage genomic selection approach provides breeders with an informative and practical framework to utilise genotype by environment interaction for prediction into current and future environments. Abstract This paper develops a single-stage genomic selection app...
Article
Full-text available
Background 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 that capture most of the genomic diversity in a population must be assembled so that allele substitution effects are estimated...
Article
Full-text available
Poaceae, among the most abundant plant families, includes many economically important polyploid species, such as forage grasses and sugarcane (Saccharum spp.). These species have elevated genomic complexities and limited genetic resources, hindering the application of marker-assisted selection strategies. Currently, the most promising approach for...
Conference Paper
Full-text available
African dairy production systems are characterized by small herd size and low genetic connectedness between herds. This situation makes it difficult to accurately estimate environmental and genetic effects. We evaluated how accounting for spatial relationship between neighbouring herds impacts genetic evaluation of 305-days milk yield in South Afri...
Preprint
Full-text available
This paper develops a single-stage genomic selection (GS) approach which incorporates information on multiple traits and multiple environments within a partially separable factor analytic framework. The factor analytic linear mixed model is an effective method for analysing multi-environment trial (MET) datasets, but is yet to be extended to GS for...
Conference Paper
Full-text available
Quantifying the sources of genetic change is essential for optimising breeding programmes. However, breeding programmes are often complex because many breeding groups are subject to different breeding actions. Understanding the contribution of these groups to changes in genetic mean and variance is essential to understanding genetic change in breed...
Conference Paper
Full-text available
Genetic evaluation databases accumulated vast amounts of genomic information that are skyrocketing computational needs for standard genomic evaluation models due to their cubic computational complexity. Several scalable approaches have been proposed, such as the Algorithm for Proven and Young (APY), where genotyped animals are usually randomly part...
Conference Paper
Full-text available
The microbiome composition influences the host response to selection and shapes complex phenotypes. It is a multifactorial complex trait in which the microbial inheritance, the host-genome, and the own microbial interactions influence its variability. The expensive sequence-based techniques limit the availability of empirical data. Thus, other appr...
Conference Paper
Full-text available
A full-scale simulation that can cover all aspects of an ongoing breeding programme is a useful tool to test future breeding decisions. For example, dairy breeding is facing new challenges to include feed efficiency and methane emission traits in their breeding goals. To this end we have simulated a real size breeding programme of the Norwegian Red...
Conference Paper
Full-text available
Studies indicate that mito-genome variation impacts phenotypes in a range of species. In dairy cattle up to 5% of phenotypic variation for milk production has been associated to mito-genome variation. Bearing in mind that milk production is a very energy demanding process that inflicts systemic physiological changes, it is logical to expect that it...
Preprint
Full-text available
Social insects are very successful invasive species, and the continued increase of global trade and transportation has exacerbated this problem. The yellow-legged hornet, Vespa velutina nigrithorax (henceforth Asian hornet), is drastically expanding its range in Western Europe. As an apex insect predator, this hornet poses a serious threat to the h...
Preprint
Full-text available
Background By entering the era of mega-scale genomics, we are facing many computational issues with standard genomic evaluation models due to their dense data structure and cubic computational complexity. Several scalable approaches have have been proposed to address this challenge, like the Algorithm for Proven and Young (APY). In APY, genotyped a...
Preprint
Full-text available
Poaceae is one of the largest and most abundant families of plants, and includes many polyploid species with great economic importance, among which forage grasses (FGs) and sugarcane (Saccharum spp., SU). FG and SU species have elevated genomic complexities and consequently limited genetic resources, which hinders the application of marker-assisted...
Preprint
Full-text available
Poaceae, among the most abundant plant families, includes many economically important polyploid species, such as forage grasses and sugarcane ( Saccharum spp.). These species have elevated genomic complexities and limited genetic resources, hindering the application of marker-assisted selection strategies. Currently, the most promising approach for...
Preprint
Full-text available
Rubber tree ( Hevea brasiliensis ) is the main feedstock for commercial rubber; however, its long vegetative cycle has hindered the development of more productive varieties via breeding programs. With the availability of H. brasiliensis genomic data, several linkage maps with associated quantitative trait loci (QTLs) have been constructed and sugge...
Preprint
Full-text available
Background Early simulations indicated that whole-genome sequence data (WGS) could improve prediction accuracy and its persistence across generations and breeds. However, results in real datasets have been ambiguous so far. Large data sets that capture most of the genome diversity in a population must be assembled so that allele substitution effect...
Preprint
Full-text available
Background It is expected that missense and loss-of-function (LOF) variants are responsible for phenotypic differences among breeds, genetic lines and varieties of livestock and crop species that have undergone diverse selection histories. However, there is still limited knowledge about the existing missense and LOF variation in livestock commercia...
Preprint
Full-text available
Background In breeding programmes, the observed genetic change is a sum of the contributions of different groups of individuals. Quantifying these sources of genetic change is essential for identifying the key breeding actions and optimizing breeding programmes. However, it is difficult to disentangle the contribution of individual groups due to th...
Preprint
Full-text available
Some of the most economically important traits in plant breeding show highly polygenic inheritance. Genetic variation is a key determinant of the rates of genetic improvement in selective breeding programs. Rapid progress in genetic improvement comes at the cost of a rapid loss of genetic variation. Germplasm available through expired Plant Variety...
Article
Full-text available
Genetic variance is a central parameter in quantitative genetics and breeding. Assessing changes in genetic variance over time as well as the genome is therefore of high interest. Here, we extend a previously proposed framework for temporal analysis of genetic variance using the pedigree-based model, to a new framework for temporal and genomic anal...
Article
Full-text available
Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and simulation is usually the only way of obtaining ground-truth data to evaluate inferences. Because of this, a large number of specialized simulation programs have been developed, each filling a particular niche, but with large...
Article
Full-text available
Background In this paper, we present the AlphaPart R package, an open-source implementation of a method for partitioning breeding values and genetic trends to identify the contribution of selection pathways to genetic gain. Breeding programmes improve populations for a set of traits, which can be measured with a genetic trend calculated from estima...
Article
Full-text available
Background Meiotic recombination results in the exchange of genetic material between homologous chromosomes. Recombination rate varies between different parts of the genome, between individuals, and is influenced by genetics. In this paper, we assessed the genetic variation in recombination rate along the genome and between individuals in the pig u...
Article
Full-text available
Background Body weight (BW) is an economically important trait in the broiler (meat-type chickens) industry. Under the assumption of polygenicity, a “large” number of genes with “small” effects is expected to control BW. To detect such effects, a large sample size is required in genome-wide association studies (GWAS). Our objective was to conduct a...
Article
Full-text available
Background: Backfat thickness is an important carcass composition trait for pork production and is commonly included in swine breeding programmes. In this paper, we report the results of a large genome-wide association study for backfat thickness using data from eight lines of diverse genetic backgrounds. Methods: Data comprised 275,590 pigs fro...
Article
Full-text available
Breeding has increased genetic gain for dairy cattle in advanced economies but has had limited success in improving dairy cattle in low- to middle-income countries (LMIC). Genetic evaluations are a central component of delivering genetic gain, because they separate the genetic and environmental effects of animals' phenotypes. Genetic evaluations ha...
Preprint
Full-text available
This paper introduces a single-stage genomic selection approach which directly integrates environmental covariates within a special factor analytic framework. The factor analytic approach of Smith et al. (2001) is an effective method of analysis for multi-environment trial (MET) datasets, but has limited biological interpretation since the underlyi...
Article
Full-text available
Varroa mites (Varroa destructor) are the most significant threat to beekeeping worldwide. They are directly or indirectly responsible for millions of colony losses each year. Beekeepers are somewhat able to control varroa populations through the use of physical and chemical treatments. However, these methods range in effectiveness, can harm honey b...
Preprint
Full-text available
Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and simulation is usually the only way of obtaining ground-truth data to evaluate inferences. Because of this necessity, a large number of specialised simulation programs have been developed, each filling a particular niche, but...
Article
Full-text available
In the context of genomic selection, we evaluated and compared breeding programs using either index selection or independent culling for recurrent selection of parents. We simulated a clonally propagated crop breeding program for 20 cycles using either independent culling or an economic index with two unfavourably correlated traits under selection....
Article
Full-text available
Inbreeding depression is the reduction of performance caused by mating of close relatives. In livestock populations, inbreeding depression has been traditionally estimated by regression of phenotypes on pedigree inbreeding coefficients. This estimation can be improved by utilising genomic inbreeding coefficients. Here we estimate inbreeding depress...
Preprint
Full-text available
Varroa mites ( Varroa destructor ) are the most significant threat to beekeeping worldwide. They are directly or indirectly responsible for millions of colony losses each year. Beekeepers are somewhat able to control Varroa populations through the use of physical and chemical treatments. However, these methods range in effectiveness, can harm honey...
Preprint
Full-text available
Advances in sequencing technologies mean that insights into crop diversification aiding future breeding can now be explored in crops beyond major staples. For the first time, we use a genome assembly of finger millet, an allotetraploid orphan crop, to analyze DArTseq single nucleotide polymorphisms (SNPs) at the sub-genome level. A set of 8,778 SNP...
Article
Full-text available
Invasive species are among the major driving forces behind biodiversity loss. Gene drive technology may offer a humane, efficient and cost-effective method of control. For safe and effective deployment it is vital that a gene drive is both self-limiting and can overcome evolutionary resistance. We present HD-ClvR in this modelling study, a novel co...
Article
Full-text available
This study demonstrated the feasibility of a genomic evaluation for the dairy cattle population for which the small national training population can be complemented with foreign information from international evaluations. National test-day milk yield data records for the Slovenian Brown Swiss cattle population were analyzed. Genomic evaluation was...
Article
Full-text available
This paper evaluates the potential of maximizing genetic gain in dairy cattle breeding by optimizing investment into phenotyping and genotyping. Conventional breeding focuses on phenotyping selection candidates or their close relatives to maximize selection accuracy for breeders and quality assurance for producers. Genomic selection decoupled pheno...
Article
Full-text available
Intercrop breeding programs using genomic selection can produce faster genetic gain than intercrop breeding programs using phenotypic selection. Intercropping is an agricultural practice in which two or more component crops are grown together. It can lead to enhanced soil structure and fertility, improved weed suppression, and better control of pes...
Article
Full-text available
This paper introduces AlphaSimR, an R package for stochastic simulations of plant and animal breeding programs. AlphaSimR is a highly flexible software package able to simulate a wide range of plant and animal breeding programs for diploid and autopolyploid species. AlphaSimR is ideal for testing the overall strategy and detailed design of breeding...
Article
Full-text available
We propose a novel Bayesian approach that robustifies genomic modelling by leveraging expert knowledge through prior distributions. The central component is the hierarchical decomposition of phenotypic variation into additive and non-additive genetic variation, which leads to an intuitive model parameterization that can be visualised as a tree. The...
Article
Full-text available
We introduce a hierarchical model to estimate haplotype effects based on phylogenetic relationships between haplotypes and their association with observed phenotypes. In a population there are many, but not all possible, distinct haplotypes and few observations per haplotype. Further, haplotype frequencies tend to vary substantially. Such data stru...
Article
Full-text available
Over the last two decades, the application of genomic selection has been extensively studied in various crop species, and it has become a common practice to report prediction accuracies using cross validation. However, genomic prediction accuracies obtained from random cross validation can be strongly inflated due to population or family structure,...
Article
Full-text available
Background: The coupling of appropriate sequencing strategies and imputation methods is critical for assembling large whole-genome sequence datasets from livestock populations for research and breeding. In this paper, we describe and validate the coupling of a sequencing strategy with the imputation method hybrid peeling in real animal breeding se...
Article
Full-text available
Background: For assembling large whole-genome sequence datasets for routine use in research and breeding, the sequencing strategy should be adapted to the methods that will be used later for variant discovery and imputation. In this study, we used simulation to explore the impact that the sequencing strategy and level of sequencing investment have...
Article
Full-text available
Background: We describe the latest improvements to the long-range phasing (LRP) and haplotype library imputation (HLI) algorithms for successful phasing of both datasets with one million individuals and datasets genotyped using different sets of single nucleotide polymorphisms (SNPs). Previous publicly available implementations of the LRP algorith...
Article
Full-text available
Background Breeders and geneticists use statistical models to separate genetic and environmental effects on phenotype. A common way to separate these effects is to model a descriptor of an environment, a contemporary group or herd, and account for genetic relationship between animals across environments. However, separating the genetic and environm...
Article
Full-text available
This paper presents an extension to a heuristic method for phasing and imputation of genotypes of descendants in bi‐parental populations so that it can phase and impute genotypes of parents that are ungenotyped or partially genotyped. The imputed genotypes of the parent are used to impute low‐density (LD) genotyped descendants to high‐density (HD)....
Preprint
Full-text available
Intercrop breeding programs using genomic selection can produce faster genetic gain than intercrop breeding programs using phenotypic selection. Intercropping is an agricultural practice in which two or more component crops are grown together. It can lead to enhanced soil structure and fertility, improved weed suppression, and better control of pes...
Preprint
Full-text available
This study demonstrates a framework for temporal and genomic analysis of additive genetic variance in a breeding programme. Traditionally we used specific experimental designs to estimate genetic variance for a specific group of individuals and a general pedigree-based model to estimate genetic variance for pedigree founders. However, with the pedi...
Preprint
Full-text available
Invasive species are among the major driving forces behind biodiversity loss. Gene drive technology may offer a humane, efficient and cost-effective method of control. For safe and effective deployment it is vital that a gene drive is both self-limiting and can overcome evolutionary resistance. We present HD-ClvR, a novel combination of CRISPR-base...
Preprint
Full-text available
Background: This paper evaluates the potential of maximizing genetic gain in dairy cattle breeding by optimizing investment into phenotyping and genotyping. Conventional breeding focuses on phenotyping selection candidates or their close relatives to achieve desired selection accuracy for breeders and quality for producers. Genomic selection decoup...