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In spite of the availability of single nucleotide polymorphism (SNP) array data, differentiation between observed homozygosity and that caused by mating between relatives (autozygosity) introduces major diffic...
Modern breeding strategies have resulted in significant differences in muscle mass between indigenous chicken and specialized broiler. However, the molecular regulatory mechanisms that underlie these differenc...
Although the accumulation of whole-genome sequencing (WGS) data has accelerated the identification of mutations underlying complex traits, its impact on the accuracy of genomic predictions is limited. Reliable...
It has been challenging to implement genomic selection in multi-breed tropical beef cattle populations. If commercial (often crossbred) animals could be used in the reference population for these genomic evalu...
Combining the results of within-population genome-wide association studies (GWAS) based on whole-genome sequences into a single meta-analysis (MA) is an accurate and powerful method for identifying variants as...
The Correction to this article has been published in Genetics Selection Evolution 2023 55:79
Heterosis is routinely exploited to improve animal performance. However, heterosis and its underlying molecular mechanism for feed intake and efficiency have been rarely explored in chickens. Feed efficiency c...
The single-step approach has become the most widely-used methodology for genomic evaluations when only a subset of phenotyped individuals in the pedigree are genotyped, where the genotypes for non-genotyped in...
Harmful social behaviours, such as injurious feather pecking in poultry and tail biting in swine, reduce animal welfare and production efficiency. While these behaviours are heritable, selective breeding is st...
Evolutionary studies have reported that non-genetic information can be inherited across generations (epigenetic marks, microbiota, cultural inheritance). Non-genetic information is considered to be a key eleme...
Genetic selection based on direct indicators of heat stress could capture additional mechanisms that are involved in heat stress response and enable more accurate selection for more heat-tolerant individuals. ...
China has one third of the worldwide indigenous pig breeds. The Henan province is one of the earliest pig domestication centers of China (about 8000 years ago). However, the precise genetic characteristics of ...
For centuries, morphology has been the most commonly selected trait in horses. A 3D video recording enabled us to obtain the coordinates of 43 anatomical landmarks of 2089 jumping horses. Generalized Procruste...
Artificial selection on quantitative traits using breeding values and selection indices in commercial livestock breeding populations causes changes in allele frequency over time at hundreds or thousands of cau...
Metabolomics measures an intermediate stage between genotype and phenotype, and may therefore be useful for breeding. Our objectives were to investigate genetic parameters and accuracies of predicted breeding ...
The Connemara pony (CP) is an Irish breed that has experienced varied selection by breeders over the last fifty years, with objectives ranging from the traditional hardy pony to an agile athlete. We compared t...
Flavobacterium columnare is the pathogen agent of columnaris disease, a major emerging disease that affects rainbow trout aquaculture. Selective breeding using genomic selection has potential to achieve cumulativ...
Maternal effects influence juvenile traits such as body weight and early growth in broilers. Ignoring significant maternal effects leads to reduced accuracy and inflated predicted breeding values. Including ge...
Most genomic prediction applications in animal breeding use genotypes with tens of thousands of single nucleotide polymorphisms (SNPs). However, modern sequencing technologies and imputation algorithms can gen...
Genomic prediction has become widespread as a valuable tool to estimate genetic merit in animal and plant breeding. Here we develop a novel genomic prediction algorithm, called deepGBLUP, which integrates deep...
Whole-genome sequence (WGS) data harbor causative variants that may not be present in standard single nucleotide polymorphism (SNP) chip data. The objective of this study was to investigate the impact of using...
In commercial pig production, reduction of harmful social behavioural traits, such as ear manipulation and tail biting, is of major interest. Moreover, farmers prefer animals that are easy to handle. The aim o...
Rumen microbes break down complex dietary carbohydrates into energy sources for the host and are increasingly shown to be a key aspect of animal performance. Host genotypes can be combined with microbial DNA s...
Skin damage is a trait of economic and welfare importance that results from social interactions between animals. These interactions may produce wound signs on the gilt’s skin as a result of damage behavior (i....
Porcine reproductive and respiratory syndrome (PRRS) remains one of the most important infectious diseases for the pig industry. A novel small-scale transmission experiment was designed to assess whether the W...
Livestock and poultry play a significant role in human nutrition by converting agricultural by-products into high-quality proteins. To meet the growing demand for safe animal protein, genetic improvement of li...
Identifying true positive variants in genome-wide associations (GWA) depends on several factors, including the number of genotyped individuals. The limited dimensionality of genomic information may give insigh...
Genomic selection has increased genetic gain in dairy cattle, but in some cases it has resulted in higher inbreeding rates. Therefore, there is need for research on efficient management of inbreeding in genomi...
The frequency of chromosomal rearrangements in Canadian breeding boars has been estimated at 0.91 to 1.64%. These abnormalities are widely recognized as a potential cause of subfertility in livestock productio...
Genome-wide association studies (GWAS) are an effective way to explore genotype–phenotype associations in humans, animals, and plants. Various GWAS methods have been developed based on different genetic or sta...
The breeding value of a crossbred individual can be expressed as the sum of the contributions from each of the contributing pure breeds. In theory, the breeding value should account for segregation between bre...
Bone damage has welfare and economic impacts on modern commercial poultry and is known as one of the major challenges in the poultry industry. Bone damage is particularly common in laying hens and is probably ...
Currently, meat cut traits are integrated in pig breeding objectives to gain extra profit. However, little is known about the heritability of meat cut proportions (MCP) and their correlations with other traits...
Genome-wide association studies (GWAS) aim at identifying genomic regions involved in phenotype expression, but identifying causative variants is difficult. Pig Combined Annotation Dependent Depletion (pCADD) ...
International evaluations combine data from different countries allowing breeders to have access to larger panels of elite bulls and to increase the accuracy of estimated breeding values (EBV). However, intern...
Inherited epidermolysis bullosa (EB) is a group of painful and life-threatening genetic disorders that are characterized by mechanically induced blistering of the skin and mucous membranes. Congenital skin fra...
Selective breeding is a promising solution to reduce the vulnerability of fish farms to heat waves, which are predicted to increase in intensity and frequency. However, limited information about the genetic ar...
This paper highlights the relationships between economic weights, genetic progress, and phenotypic progress in genomic breeding programs that aim at generating genetic progress in complex, i.e., multi-trait, b...
Single-step genomic best linear unbiased prediction (ssGBLUP) models allow the combination of genomic, pedigree, and phenotypic data into a single model, which is computationally challenging for large genotype...
In breeding programmes, the observed genetic change is a sum of the contributions of different selection paths represented by groups of individuals. Quantifying these sources of genetic change is essential for...
An essential component in the development of sustainable pig production is the reduction of nitrogen excretion in fattening pigs. Pig feeds typically contain high levels of dietary crude protein, and due to in...
Recently, crossbred animals have begun to be used as parents in the next generations of dairy and beef cattle systems, which has increased the interest in predicting the genetic merit of those animals. The pri...
Low-pass sequencing followed by sequence variant genotype imputation is an alternative to the routine microarray-based genotyping in cattle. However, the impact of haplotype reference panels and their interpla...
Canadienne cattle are the oldest breed of dairy cattle in North America. The Canadienne breed originates from cattle that were brought to America by the mid-seventeenth century French settlers. The herd book w...
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 addition...
Viral nervous necrosis (VNN) is a major disease that affects European sea bass, and understanding the biological mechanisms that underlie VNN resistance is important for the welfare of farmed fish and sustaina...
Gut microbial composition plays an important role in numerous traits, including immune response. Integration of host genomic information with microbiome data is a natural step in the prediction of complex trai...
Genetic diversity is a necessary condition for populations to evolve under natural adaptation, artificial selection, or both. However, genetic diversity is often threatened, in particular in domestic animal po...
The construction of covariance matrices that account for the genetic relationships among individuals, using pedigree or genotype data, is integral to genetic evaluations, which are now routinely used in the fi...
The original article was published in Genetics Selection Evolution 2022 54:66
The original article was published in Genetics Selection Evolution 2023 55:9
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