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Heterosis has been suggested to be caused by dominance effects. We performed a joint genome-wide association analysis (GWAS) using data from multi-breed and crossbred beef cattle to identify single nucleotide ...
Macroparasites, such as ticks, lice, and helminths, are a concern in livestock and aquaculture production, and can be controlled by genetic improvement of the host population. Genetic improvement should aim at...
In polytocous livestock species, litter size and offspring weight act antagonistically; in modern pig breeds, selection for increased litter size has resulted in lower mean birth weights, an increased number o...
Genetic connectedness is classically used as an indication of the risk associated with breeding value comparisons across management units because genetic evaluations based on best linear unbiased prediction re...
In this paper, we review the performance of various hidden Markov model-based imputation methods in animal breeding populations. Traditionally, pedigree and heuristic-based imputation methods have been used fo...
Runs of homozygosity (ROH) islands are stretches of homozygous sequence in the genome of a large proportion of individuals in a population. Algorithms for the detection of ROH depend on the similarity of haplo...
Records on groups of individuals rather than on single individuals could be valuable for predicting breeding values (BV) of the traits that are difficult or costly to measure individually, such as feed intake ...
Genomic models that link phenotypes to dense genotype information are increasingly being used for infering variance parameters in genetics studies. The variance parameters of these models can be inferred using...
In recent years, there has been increased interest in the study of the molecular processes that affect semen traits. In this study, our aim was to identify quantitative trait loci (QTL) regions associated with...
A common measure employed to evaluate the efficacy of livestock improvement schemes is the genetic trend, which is calculated as the means of predicted breeding values for animals born in successive time perio...
Cannibalism is an important welfare problem in the layer industry. Cannibalism is a social behavior where individual survival is affected by direct genetic effects (DGE) and indirect genetic effects (IGE). Pre...
The origin of native and locally developed Russian cattle breeds is linked to the historical, social, cultural, and climatic features of the diverse geographical regions of Russia. In the present study, we inv...
It has been known for almost a century that the belted phenotype in cattle follows a pattern of dominant inheritance. In 2009, the approximate position of the belt locus in Brown Swiss cattle was mapped to a 922-...
In the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still fa...
High levels of pairwise linkage disequilibrium (LD) in single nucleotide polymorphism (SNP) array or whole-genome sequence data may affect both performance and efficiency of genomic prediction models. Thus, th...
This study aimed at (1) deriving Bayesian methods to predict breeding values for ratio (i.e. feed conversion ratio; FCR) or linear (i.e. residual feed intake; RFI) traits; (2) estimating genetic parameters for...
Population stratification and cryptic relationships have been the main sources of excessive false-positives and false-negatives in population-based association studies. Many methods have been developed to mode...
In 2017, genomic selection was implemented in French dairy goats using the single-step genomic best linear unbiased prediction (ssGBLUP) method, which assumes that all single nucleotide polymorphisms explain t...
European sea bass (Dicentrarchus labrax) is one of the most important species for European aquaculture. Viral nervous necrosis (VNN), commonly caused by the redspotted grouper nervous necrosis virus (RGNNV), can ...
Russia has a diverse variety of native and locally developed sheep breeds with coarse, fine, and semi-fine wool, which inhabit different climate zones and landscapes that range from hot deserts to harsh northe...
In horned sheep breeds, breeding for polledness has been of interest for decades. The objective of this study was to improve prediction of the horned and polled phenotypes using horn scores classified as polle...
Genomic prediction (GP) across breeds has so far resulted in low accuracies of the predicted genomic breeding values. Our objective was to evaluate whether using whole-genome sequence (WGS) instead of low-dens...
Parentage assignment is usually based on a limited number of unlinked, independent genomic markers (microsatellites, low-density single nucleotide polymorphisms (SNPs), etc.). Classical methods for parentage a...
Indirect genetic effects (IGE) are important components of various traits in several species. Although the intensity of social interactions between partners likely vary over time, very few genetic studies have...
Optimal contributions selection (OCS) provides animal breeders with a framework for maximising genetic gain for a predefined rate of inbreeding. Simulation studies have indicated that the source of the selecti...
The replacement of fish oil (FO) and fishmeal with plant ingredients in the diet of farmed Atlantic salmon has resulted in reduced levels of the health-promoting long-chain polyunsaturated omega-3 fatty acids ...
This study aimed at (1) assessing the genomic stratification of experimental lines of Nelore cattle that have experienced different selection regimes for growth traits, and (2) identifying genomic regions that...
Avian influenza (AI) is a devastating poultry disease that currently can be controlled only by liquidation of affected flocks. In spite of typically very high mortality rates, a group of survivors was identifi...
mRNA-like long non-coding RNAs (lncRNAs) are a significant component of mammalian transcriptomes, although most are expressed only at low levels, with high tissue-specificity and/or at specific developmental s...
The distribution of the wild turkey (Meleagris gallopavo) extends from Mexico to southeastern Canada and to the eastern and southern regions of the USA. Six subspecies have been described based on morphological c...
Genome editing technologies provide new tools for genetic improvement and have the potential to become the next game changer in animal and plant breeding. The aim of this study was to investigate how genome ed...
Deleterious genetic variation can increase in frequency as a result of mutations, genetic drift, and genetic hitchhiking. Although individual effects are often small, the cumulative effect of deleterious genet...
In recent decades, Holstein–Friesian (HF) selection schemes have undergone profound changes, including the introduction of optimal contribution selection (OCS; around 2000), a major shift in breeding goal comp...
Increasing marker density was proposed to have potential to improve the accuracy of genomic prediction for quantitative traits; whole-sequence data is expected to give the best accuracy of prediction, since al...
Domestication of animals leads to large phenotypic alterations within a short evolutionary time-period. Such alterations are caused by genomic variations, yet the prevalence of modified traits is higher than e...
Pseudo-phenotypes, such as 305-day yields, estimated breeding values or deregressed proofs, are usually used as response variables for genome-wide association studies (GWAS) of milk production traits in dairy ...
Heat stress has a negative impact on pork production, particularly during the grow-finish phase. As temperature increases, feeding behaviour changes in order for pigs to decrease heat production. The objective...
Genomic prediction and quantitative trait loci (QTL) mapping typically analyze one trait at a time but this may ignore the possibility that one polymorphism affects multiple traits. The aim of this study was t...
The current large spectrum of sheep phenotypic diversity results from the combined product of sheep selection for different production traits such as wool, milk and meat, and its natural adaptation to new envi...
Genomic selection can be applied to select purebreds for crossbred performance (CP). The average performance of crossbreds can be considered as the summation of two components, i.e. the breed average (BA) of t...
Sex-linked slow (SF) and fast (FF) feathering rates at hatch have been widely used in poultry breeding for autosexing at hatch. In chicken, the sex-linked K (SF) and k+ (FF) alleles are responsible for the feathe...
For marker effect models and genomic animal models, computational requirements increase with the number of loci and the number of genotyped individuals, respectively. In the latter case, the inverse genomic re...
Throughout the world, harvesting of mussels Mytilus spp. is based on the exploitation of natural populations and aquaculture. Aquaculture activities include transfers of spat and live adult mussels between variou...
Average daily gain (ADG) in pigs is affected by the so-called social (or indirect) genetic effects (SGE). However, SGE may differ between sexes because boars grow faster than gilts and their social behaviours ...
Genomic prediction of the pig’s response to the porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV) would be a useful tool in the swine industry. This study investigated the accuracy of genomic ...
Profitability of breeding programs is a key determinant in the adoption of selective breeding, and can be evaluated using cost-benefit analysis. There are many options to design breeding programs, with or with...
The quantitative genetics theory argues that inbreeding depression and heterosis are founded on the existence of directional dominance. However, most procedures for genomic selection that have included dominan...
Formulae to predict the precision or accuracy of genomic estimated breeding values (GEBV) are important when modelling selection schemes. Simple versions of such formulae have been proposed in the past, based ...
After publication of our article [1], we found a typo in the formula to build the genomic relationship matrix using allele frequencies across all genotyped pigs (matrix) and the genomic relationship matrix usi...
The original article was published in Genetics Selection Evolution 2017 49:75
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Genetics Selection Evolution