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The main aim of single-step genomic predictions was to facilitate optimal selection in populations consisting of both genotyped and non-genotyped individuals. However, in spite of intensive research, biases st...
The dimensionality of genomic information is limited by the number of independent chromosome segments (Me), which is a function of the effective population size. This dimensionality can be determined approximatel...
Controlled mating procedures are widely accepted as a key aspect of successful breeding in almost all animal species. In honeybees, however, controlled mating is hard to achieve. Therefore, there have been sev...
Hamiltonian Monte Carlo is one of the algorithms of the Markov chain Monte Carlo method that uses Hamiltonian dynamics to propose samples that follow a target distribution. The method can avoid the random walk...
Whole-genome sequence (WGS) data could contain information on genetic variants at or in high linkage disequilibrium with causative mutations that underlie the genetic variation of polygenic traits. Thus far, g...
In honey bees, observations are usually made on colonies. The phenotype of a colony is affected by the average breeding value for the worker effect of the thousands of workers in the colony (the worker group) ...
As one of the important livestock species around the world, goats provide abundant meat, milk, and fiber to fulfill basic human needs. However, the genetic loci that underlie phenotypic variations in domestic ...
After publication of original article [1], the authors noticed that there was an error.
The original article was published in Genetics Selection Evolution 2018 50:53
After publication of this work [1], we noticed that there was an error: the formula to calculate the standard error of the estimated correlation
The original article was published in Genetics Selection Evolution 2019 51:50
For infectious diseases, the probability that an animal gets infected depends on its own susceptibility, and on the number of infectious herd mates and their infectivity. Together with the duration of the infe...
The detection of regions that affect quantitative traits (QTL), to implement selection assisted by molecular information, remains of particular interest in dairy sheep for which genetic gain is constrained by ...
Phenotypic records of group means or group sums are a good alternative to individual records for some difficult to measure, but economically important traits such as feed efficiency or egg production. Accuracy...
Following publication of original article [1], we noticed that there was an error: Eq. (3) on page 5 is the genomic relationship matrix that
The original article was published in Genetics Selection Evolution 2019 51:38
White spotting of the coat is a characteristic trait of various domestic species including cattle and other mammals. It is a hallmark of Holstein–Friesian cattle, and several previous studies have detected gen...
Two distinct populations have been extensively studied in Atlantic cod (Gadus morhua L.): the Northeast Arctic cod (NEAC) population and the coastal cod (CC) population. The objectives of the current study were t...
The pig breeding industry has undergone a large number of mergers in the past decades. Various commercial lines were merged or discontinued, which is expected to reduce the genetic diversity of the pig species...
Ribosomal DNA (rDNA) repeats are situated in the nucleolus organizer regions (NOR) of chromosomes and transcribed into rRNA for ribosome biogenesis. Thus, they are an essential component of eukaryotic genomes....
For genomic selection in populations with a small reference population, combining populations of the same breed or populations of related breeds is an effective way to increase the size of the reference popula...
Multi-trait single step genetic evaluation is increasingly facing the situation of having more individuals with genotypes than markers within each genotype. This creates a situation where the genomic relations...
Native cattle breeds are important genetic resources given their adaptation to the local environment in which they are bred. However, the widespread use of commercial cattle breeds has resulted in a marked red...
Mate allocation strategies that account for non-additive genetic effects can be used to maximize the overall genetic merit of future offspring. Accounting for dominance effects in genetic evaluations is easier...
Inbreeding decreases animal performance (inbreeding depression), but not all inbreeding is expected to be equally harmful. Recent inbreeding is expected to be more harmful than ancient inbreeding, because sele...
The objectives of this study were to (1) simultaneously estimate genetic parameters for BW, feed intake (FI), and body weight gain (Gain) during a FI test in broiler chickens using multi-trait Bayesian analysi...
In France, implementation of genomic evaluations in dairy cattle breeds started in 2009 and this has modified the breeding schemes drastically. In this context, the goal of our study was to understand the impa...
Salmonella infection is a serious concern in poultry farming because of its impact on both economic loss and human health. Chicks aged 20 days or less are extremely vulnerable to Salmonella pullorum (SP), which c...
The increase in accuracy of prediction by using genomic information has been well-documented. However, benefits of the use of genomic information and methodology for genetic evaluations are missing when genoty...
The Correction to this article has been published in Genetics Selection Evolution 2019 51:68
Breeding companies may want to maximize the rate of genetic gain from their breeding program within a limited budget. In salmon breeding programs, full-sibs of selection candidates are subjected to performance...
Feed efficiency (FE) has a major impact on the economic sustainability of pig production. We used a systems-based approach that integrates single nucleotide polymorphism (SNP) co-association and gene-expressio...
Infectious hematopoietic necrosis (IHN) is a disease of salmonid fish that is caused by the IHN virus (IHNV). Under intensive aquaculture conditions, IHNV can cause significant mortality and economic losses. C...
Meat production from the commercial crossbred Duroc × (Landrace × Yorkshire) (DLY) pig is predominant in the pork industry, but its meat quality is often impaired by low ultimate pH (pHu). Muscle glycogen leve...
Crossbreeding is widely used in pig production because of the benefits of heterosis effects and breed complementarity. Commonly, sire lines are bred for traits such as feed efficiency, growth and meat content,...
The Correction to this article has been published in Genetics Selection Evolution 2020 52:23
Experimental intercrosses between outbred founder populations are powerful resources for mapping loci that contribute to complex traits i.e. quantitative trait loci (QTL). Here, we present an approach and its ...
Random regression models (RRM) are widely used to analyze longitudinal data in genetic evaluation systems because they can better account for time-course changes in environmental effects and additive genetic v...
Columnaris disease (CD) is an emerging problem for the rainbow trout aquaculture industry in the US. The objectives of this study were to: (1) identify common genomic regions that explain a large proportion of...
Recessive loss-of-function (LOF) alleles at genes which are essential for life, can result in early embryonic mortality. Cattle producers can use the LOF carrier status of individual animals to make selection ...
This study aimed at estimating genetic parameters of sex-influenced production traits, evaluating the impact of genotype-by-sex interaction, and identifying the selection criteria that could be included in mul...
In modern dairy breeding programmes, high contributions from foreign sires are nearly always present. Genotyping, and therefore genomic selection (GS), concern only a subpopulation of the breeding programme’s ...
We tested the premise that optimum-contribution selection with pedigree relationships to control inbreeding (POCS) realises at least as much true genetic gain as optimum-contribution selection with genomic rel...
Pig and poultry breeding programs aim at improving crossbred (CB) performance. Selection response may be suboptimal if only purebred (PB) performance is used to compute genomic estimated breeding values (GEBV)...
The Correction to this article has been published in Genetics Selection Evolution 2019 51:63
This study aimed at identifying genomic regions that underlie genetic variation of worm egg count, as an indicator trait for parasite resistance in a large population of Australian sheep, which was genotyped w...
The Finnhorse was established as a breed more than 110 years ago by combining local Finnish landraces. Since its foundation, the breed has experienced both strong directional selection, especially for size and...
Milk quality in dairy cattle is routinely assessed via analysis of mid-infrared (MIR) spectra; this approach can also be used to predict the milk’s cheese-making properties (CMP) and composition. When this met...
In this paper, we evaluate the performance of using family-specific low-density genotype arrays to increase the accuracy of pedigree-based imputation. Genotype imputation is a widely used tool that decreases t...
This study aimed at (1) comparing the accuracies of genomic prediction for parasite resistance in sheep based on whole-genome sequence (WGS) data to those based on 50k and high-density (HD) single nucleotide p...
Heat stress negatively affects the welfare and production of chickens. High ambient temperature is considered one of the most ubiquitous abiotic environmental challenges to laying hens around the world. In thi...
The preconditioned conjugate gradient (PCG) method is an iterative solver of linear equations systems commonly used in animal breeding. However, the PCG method has been shown to encounter convergence issues wh...
Selection of cattle that are less sensitive to environmental variation in unfavorable environments and more adapted to harsh conditions is of primary importance for tropical beef cattle production systems. Und...
Single-step genomic best linear unbiased prediction (SSGBLUP) is a comprehensive method for genomic prediction. Point estimates of marker effects from SSGBLUP are often used for genome-wide association studies...
Selection of mice for decreased environmental variability of birth weight has achieved higher survivability and larger litter size as a correlated response to canalized selection, which suggests higher welfare...
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Genetics Selection Evolution