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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 st...
We tested the hypothesis that breeding schemes with a pre-selection step, in which carriers of a lethal recessive allele (LRA) were culled, and with optimum-contribution selection (OCS) reduce the frequency of...
Goat, one of the first domesticated livestock, is a worldwide important species both culturally and economically. The current goat reference genome, known as ARS1, is reported as the first nonhuman genome asse...
India is the largest milk producer globally, with the largest proportion of cattle milk production coming from smallholder farms with an average herd size of less than two milking cows. These cows are mainly u...
Various regions of the chicken genome have been under natural and artificial selection for thousands of years. The substantial diversity that exits among chickens from different geographic regions provides an ...
The Correction to this article has been published in Genetics Selection Evolution 2022 54:28
Efficient breeding programs are difficult to implement in honeybees due to their biological specificities (polyandry and haplo-diploidy) and complexity of the traits of interest, with performances being measur...
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....
Global warming has increased the frequency of heat stress in livestock. Although heat stress directly leads to negative effects on production and reproduction traits in dairy cattle, the transgenerational tran...
The advent of genomic information and the reduction in the cost of genotyping have led to the use of genomic information to estimate genomic inbreeding as an alternative to pedigree inbreeding. Using genomic m...
This paper reviews the localization of published potential causative variants in contemporary pig and cattle reference genomes, and the evidence for their causality. In spite of the difficulties inherent to th...
In broiler production, breast muscle weight and intramuscular fat (IMF) content are important economic traits. Understanding the genetic mechanisms that underlie these traits is essential to implement effectiv...
Analysis and prediction of complex traits using microbiome data combined with host genomic information is a topic of utmost interest. However, numerous questions remain to be answered: how useful can the micro...
The Correction to this article has been published in Genetics Selection Evolution 2021 53:97
With the completion of a single nucleotide polymorphism (SNP) chip for honey bees, the technical basis of genomic selection is laid. However, for its application in practice, methods to estimate genomic breedi...
Linkage disequilibrium (LD) is a key parameter to study the history of populations and to identify and fine map quantitative trait loci (QTL) and it has been studied for many years in animal populations. The a...
Fourier-transform mid-infrared (FT-MIR) spectroscopy provides a high-throughput and inexpensive method for predicting milk composition and other novel traits from milk samples. While there have been many genom...
Egg production traits are economically important in poultry breeding programs. Previous studies have shown that incorporating genomic data can increase the accuracy of genetic prediction of egg production. Our...
Managing beneficial Mendelian characteristics in dairy cattle breeding programs implies that the correlated genetic effects are considered to avoid possible adverse effects in selection processes. The Mendelia...
Environmental variance (VE) is partially under genetic control, which means that the VE of individuals that share the same environment can differ because they have different genotypes. Previously, a divergent sel...
Imputation to whole-genome sequence is now possible in large sheep populations. It is therefore of interest to use this data in genome-wide association studies (GWAS) to investigate putative causal variants an...
Twin and multiple births are rare in cattle and have a negative impact on the performance and health of cows and calves. Therefore, selection against multiple birth would be desirable in dairy cattle breeds su...
Genetic improvement of wool and growth traits is a major goal in the sheep industry, but their underlying genetic architecture remains elusive. To improve our understanding of these mechanisms, we conducted a ...
Mathematical models are needed for the design of breeding programs using genomic prediction. While deterministic models for selection on pedigree-based estimates of breeding values (PEBV) are available, these ...
The Correction to this article has been published in Genetics Selection Evolution 2021 53:81
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 gene...
Residual feed intake (RFI) is one measure of feed efficiency, which is usually obtained by multiple regression of feed intake (FI) on measures of production, body weight gain and tissue composition. If phenoty...
Expression of the cellular prion protein (PrPC) is crucial for the development of prion diseases. Amino acid changes in PrPC or a reduced amount of PrPC may modulate disease resistance. The relative abundance of ...
There is an increasing need to account for genotype-by-environment (G × E) interactions in livestock breeding programs to improve productivity and animal welfare across environmental and management conditions....
While the adoption of genomic evaluations in livestock has increased genetic gain rates, its effects on genetic diversity and accumulation of inbreeding have raised concerns in cattle populations. Increased in...
Feed efficiency is a major driver of the sustainability of pig production systems. Understanding the biological mechanisms that underlie these agronomic traits is an important issue for environment questions a...
During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine ca...
The genetic structure of a diverse set of 15 Indian indigenous breeds and non-descript indigenous cattle sampled from eight states was examined, based on 777 k single nucleotide polymorphism (SNP) genotypes ob...
In dairy cattle populations in which crossbreeding has been used, animals show some level of diversity in their origins. In rotational crossbreeding, for instance, crossbred dams are mated with purebred sires ...
Dense single nucleotide polymorphism (SNP) panels are widely used for genome-wide association studies (GWAS). In these panels, SNPs within a genomic segment tend to be highly correlated. Thus, association stud...
In all organisms, life-history traits are constrained by trade-offs, which may represent physiological limitations or be related to energy resource management. To detect trade-offs within a population, one pro...
Mature microRNAs (miRNAs) play an important role in repressing the expression of a wide range of mRNAs. The presence of polymorphic sites in miRNA genes and their corresponding 3′UTR binding sites can disrupt ...
Genomic relationship matrices are used to obtain genomic inbreeding coefficients. However, there are several methodologies to compute these matrices and there is still an unresolved debate on which one provide...
Homozygous recessive deleterious mutations can cause embryo/fetal or neonatal lethality, or genetic defects that affect female fertility and animal welfare. In livestock populations under selection, the freque...
Nellore cattle (Bos indicus) are well-known for their adaptation to warm and humid environments. Hair length and coat color may impact heat tolerance. The Nellore breed has been strongly selected for white coat, ...
Short tandem repeats (STRs) are genetic markers with a greater mutation rate than single nucleotide polymorphisms (SNPs) and are widely used in genetic studies and forensics. However, most studies in pigs have...
As cage-free production systems become increasingly popular, behavioral traits such as nesting behavior and temperament have become more important. The objective of this study was to estimate heritabilities fo...
Streptococcosis is a major bacterial disease in Nile tilapia that is caused by Streptococcus agalactiae infection, and development of resistant strains of Nile tilapia represents a sustainable approach towards co...
Migration of a population from its founder population is expected to cause a reduction of its genetic diversity and facilitates differentiation between the population and its founder population, as predicted b...
The most prolific duck genetic resource in the world is located in Southeast/South Asia but little is known about the domestication and complex histories of these duck populations.
The preconditioned conjugate gradient (PCG) method is the current method of choice for iterative solving of genetic evaluations. The relative difference between two successive iterates and the relative residua...
In breeding programs, recording large-scale feed intake (FI) data routinely at the individual level is costly and difficult compared with other production traits. An alternative approach could be to record FI ...
Susceptibility of European sea bass (Dicentrarchus labrax L.) to viral nervous necrosis (VNN) is well-known. Interest towards selective breeding as a tool to enhance genetic resistance in this species has increas...
An amendment to this paper has been published and can be accessed via the original article.
The original article was published in Genetics Selection Evolution 2020 52:63
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 ga...
The impact of individual genetic and genomic variations on immune responses is an emerging lever investigated in vaccination strategies. In our study, we used genetic and pre-vaccination blood transcriptomic d...
Over the past decade, Fourier transform infrared (FTIR) spectroscopy has been used to predict novel milk protein phenotypes. Genomic data might help predict these phenotypes when integrated with milk FTIR spec...
Postnatal piglet survival is important both in economic and animal welfare terms. It is influenced by the piglet’s own direct genetic effects and by maternal genetic effects of the dam, associated with milk pr...
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Genetics Selection Evolution