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Non-linear Bayesian genomic prediction models such as BayesA/B/C/R involve iteration and mostly Markov chain Monte Carlo (MCMC) algorithms, which are computationally expensive, especially when whole-genome seq...
Inbreeding coefficients can be estimated either from pedigree data or from genomic data, and with genomic data, they are either global or local (when the linkage map is used). Recently, we developed a new hid...
Deterministic formulas for the accuracy of genomic predictions highlight the relationships among prediction accuracy and potential factors influencing prediction accuracy prior to performing computationally in...
Molecular data is now commonly used to predict breeding values (BV). Various methods to calculate genomic relationship matrices (GRM) have been developed, with some studies proposing regression of coefficients...
Accurate genomic prediction requires a large reference population, which is problematic for traits that are expensive to measure. Traits related to milk protein composition are not routinely recorded due to co...
Genomic selection (GS) promises to accelerate genetic gain in plant breeding programs especially for crop species such as cassava that have long breeding cycles. Practically, to implement GS in cassava breedin...
Pedigree-based management of genetic diversity in populations, e.g., using optimal contributions, involves computation of the
Curly horses present a variety of curl phenotypes that are associated with various degrees of curliness of coat, mane, tail and ear hairs. Their origin is still a matter of debate and several genetic hypothese...
Because very large numbers of single nucleotide polymorphisms (SNPs) are now available throughout the genome, they are particularly suitable for the detection of genomic regions where a reduction in heterozygo...
Domestication, breed formation and intensive selection have resulted in divergent cattle breeds that likely exhibit their own genomic signatures. In this study, we used genotypes from 27,612 autosomal single n...
Our aim was to identify genomic regions via genome-wide association studies (GWAS) to improve the predictability of genetic merit in Holsteins for 10 calving and 28 body conformation traits. Animals were genot...
With the aim of identifying selection signals in three Merino sheep lines that are highly specialized for fine wool production (Australian Industry Merino, Australian Merino and Australian Poll Merino) and con...
Because of their high economic importance, growth traits in fish are under continuous improvement. For growth traits that are recorded at multiple time-points in life, the use of univariate and multivariate an...
Genomic evaluation is used to predict direct genomic values (DGV) for selection candidates in breeding programs, but also to estimate allele substitution effects (ASE) of single nucleotide polymorphisms (SNPs)...
This paper describes a heuristic method for allocating low-coverage sequencing resources by targeting haplotypes rather than individuals. Low-coverage sequencing assembles high-coverage sequence information fo...
Copy number variations (CNV) are known to play a major role in genetic variability and disease pathogenesis in several species including cattle. In this study, we report the identification and characterization...
Building an efficient reference population for genomic selection is an issue when the recorded population is small and phenotypes are poorly informed, which is often the case in sheep breeding programs. Using ...
Genomic prediction of purebred animals for crossbred performance can be based on a model that estimates effects of single nucleotide polymorphisms (SNPs) in purebreds on crossbred performance. For crossbred pe...
The Correction to this article has been published in Genetics Selection Evolution 2017 49:93
In statistical genetics, an important task involves building predictive models of the genotype–phenotype relationship to attribute a proportion of the total phenotypic variance to the variation in genotypes. M...
Cases of albinism have been reported in several species including cattle. So far, research has identified many genes that are involved in this eye-catching phenotype. Thus, when two paternal Braunvieh half-sib...
There is increasing interest in the definition, measurement and use of traits associated with water use and drinking behaviour, mainly because water is a finite resource and its intake is an important part of ...
Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on...
The Correction to this article has been published in Genetics Selection Evolution 2020 52:30
The increasing availability of whole-genome sequence data is expected to increase the accuracy of genomic prediction. However, results from simulation studies and analysis of real data do not always show an in...
In recent years, the commercial importance of changes in muscle function of broiler chickens and of the corresponding effects on meat quality has increased. Furthermore, broilers are more sensitive to heat str...
Genome-wide association studies (GWAS) were performed at the sequence level to identify candidate mutations that affect the expression of six major milk proteins in Montbéliarde (MON), Normande (NOR), and Hols...
Smallholder dairy farming in much of the developing world is based on the use of crossbred cows that combine local adaptation traits of indigenous breeds with high milk yield potential of exotic dairy breeds. ...
The effect of epistasis on response to selection is a highly debated topic. Here, we investigated the impact of epistasis on response to sequence-based selection via genomic best linear prediction (GBLUP) in a...
The original article was published in Genetics Selection Evolution 2017 49:59
A quantitative trait is controlled both by major variants with large genetic effects and by minor variants with small effects. Genome-wide association studies (GWAS) are an efficient approach to identify quant...
The rapid adoption of genomic selection is due to two key factors: availability of both high-throughput dense genotyping and statistical methods to estimate and predict breeding values. The development of such...
The application of genomic selection to sheep breeding could lead to substantial increases in profitability of wool production due to the availability of accurate breeding values from single nucleotide polymor...
Residual feed intake (RFI) was investigated as a measure of feed efficiency in a breeding population of Litopenaeus vannamei. Shrimp from 34 families were housed individually and feed efficiency and growth traits...
Whole-genome sequencing and imputation methodologies have enabled the study of the effects of genomic variants with low to very low minor allele frequency (MAF) on variation in complex traits. Our objective wa...
Much effort is put into identifying causative quantitative trait nucleotides (QTN) in animal breeding, empowered by the availability of dense single nucleotide polymorphism (SNP) information. Genomic selectio...
The Erratum to this article has been published in Genetics Selection Evolution 2017 49:65
Most rabbit production farms apply feed restriction at fattening because of its protective effect against digestive diseases that affect growing rabbits. However, it leads to competitive behaviour between cage...
Lethal recessive genetic variants are maintained at relatively low frequencies in a population in the heterozygous state, but by definition are fatal and therefore unobserved in the homozygous state. Since hap...
Enhancers are non-coding DNA sequences, which when they are bound by specific proteins increase the level of gene transcription. Enhancers activate unique gene expression patterns within cells of different typ...
This study uses simulation to explore and quantify the potential effect of shifting recombination hotspots on genetic gain in livestock breeding programs.
Fitting covariates representing the number of haplotype alleles rather than single nucleotide polymorphism (SNP) alleles may increase genomic prediction accuracy if linkage disequilibrium between quantitative ...
Infectious diseases in farm animals affect animal health, decrease animal welfare and can affect human health. Selection and breeding of host individuals with desirable traits regarding infectious diseases can...
The history of pig populations in Africa remains controversial due to insufficient evidence from archaeological and genetic data. Previously, a Western ancestry for West African pigs was reported based on loci...
Breed-specific effects are observed when the same allele of a given genetic marker has a different effect depending on its breed origin, which results in different allele substitution effects across breeds. In...
Parentage verification by molecular markers is mainly based on short tandem repeat markers. Single nucleotide polymorphisms (SNPs) as bi-allelic markers have become the markers of choice for genotyping project...
Cattle resistance to ticks is known to be under genetic control with a complex biological mechanism within and among breeds. Our aim was to identify genomic segments and tag single nucleotide polymorphisms (SN...
In recent years, there has been an increasing interest in the genetic determination of environmental variance. In the case of litter size, environmental variance can be related to the capacity of animals to ad...
This paper describes a method, called AlphaSeqOpt, for the allocation of sequencing resources in livestock populations with existing phased genomic data to maximise the ability to phase and impute sequenced ha...
Haplotype reconstruction (phasing) is an essential step in many applications, including imputation and genomic selection. The best phasing methods rely on both familial and linkage disequilibrium (LD) informat...
Optimum contribution selection (OCS) is effective for increasing genetic gain, controlling the rate of inbreeding and enables maintenance of genetic diversity. However, this diversity may be caused by high mig...
In crossbreeding programs, various genomic prediction models have been proposed for using phenotypic records of crossbred animals to increase the selection response for crossbred performance in purebred animal...
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Genetics Selection Evolution