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In quail, two feather colour phenotypes i.e. fawn-2/beige and yellow are associated with the ASIP locus. The aim of our study was to characterize the structural modifications within this locus that explain the ye...
After publication of this work [1], we noted that there was an error in Table 3 Line 4.
The original article was published in Genetics Selection Evolution 2018 50:60
To date, the molecular mechanisms that underlie residual feed intake (RFI) in pigs are unknown. Results from different genome-wide association studies and gene expression analyses are not always consistent. Th...
In livestock, deleterious recessive alleles can result in reduced economic performance of homozygous individuals in multiple ways, e.g. early embryonic death, death soon after birth, or semi-lethality with inc...
In pigs, crossbreeding aims at exploiting heterosis, but heterosis is difficult to quantify. Heterozygosity at genetic markers is easier to measure and could potentially be used as an indicator of heterosis. T...
The animal model is a key tool in quantitative genetics and has been used extensively to estimate fundamental parameters, such as additive genetic variance or heritability. An implicit assumption of animal models...
In pig and poultry breeding programs, the breeding goal is to improve crossbred (CB) performance, whereas selection in the purebred (PB) lines is often based on PB performance. Thus, response to selection may ...
The identification of loci associated with resistance to mastitis or of the causative mutations may be helpful in breeding programs for dairy sheep as it is for cattle worldwide. Seven genomic regions that con...
Body weight (BW) at different ages are of increasing importance in dairy cattle breeding schemes, because of their strong correlation with energy efficiency traits, and their impact on cow health, longevity an...
Over many years, artificial selection has substantially improved milk production by cows. However, the genes that underlie milk production quantitative trait loci (QTL) remain relatively poorly characterised. ...
Use of whole-genome sequence data (WGS) is expected to improve identification of quantitative trait loci (QTL). However, this requires imputation to WGS, often with a limited number of sequenced animals for th...
The use of whole-genome sequence (WGS) data for genomic prediction and association studies is highly desirable because the causal mutations should be present in the data. The sequencing of 935 sheep from a ran...
The size and type of ears are important conformation characteristics that distinguish pig breeds. A significant quantitative trait locus (QTL) for ear size has been identified on SSC5 (SSC for Sus scrofa chromoso...
Epistatic genomic relationship matrices for interactions of any-order can be constructed using the Hadamard products of orthogonal additive and dominance genomic relationship matrices and standardization based...
Genome-wide marker data are used both in phenotypic genome-wide association studies (GWAS) and genome-wide prediction (GWP). Typically, such studies include high-dimensional data with thousands to millions of ...
In this work, we investigated sequence variation, evolutionary constraint, and selection at the CD163 gene in pigs. A functional CD163 protein is required for infection by porcine reproductive and respiratory syn...
Highly diversified in morphology and structure, feathers have evolved into various forms. Frizzle feathers, which result from a developmental defect of the feather, are observed in several domestic chicken bre...
In this paper, we extend multi-locus iterative peeling to provide a computationally efficient method for calling, phasing, and imputing sequence data of any coverage in small or large pedigrees. Our method, ca...
Catfish farming is the largest segment of US aquaculture and research is ongoing to improve production efficiency, including genetic selection programs to improve economically important traits. The objectives ...
Generally, populations differ in terms of environmental and genetic factors, which can create differences in allele substitution effects between populations. Therefore, a single genotype may have different add...
Inherent sources of error and bias that affect the quality of sequence data include index hopping and bias towards the reference allele. The impact of these artefacts is likely greater for low-coverage data th...
Coccidiosis is a major contributor to losses in poultry production. With emerging constraints on the use of in-feed prophylactic anticoccidial drugs and the relatively high costs of effective vaccines, there a...
Availability of whole-genome sequence data for a large number of cattle and efficient imputation methodologies open a new opportunity to include rare and low-frequency variants (RLFV) in genomic prediction in ...
Patterns of homozygosity can be influenced by several factors, such as demography, recombination, and selection. Using the goat SNP50 BeadChip, we genotyped 3171 goats belonging to 117 populations with a world...
Goat populations that are characterized within the AdaptMap project cover a large part of the worldwide distribution of this species and provide the opportunity to assess their diversity at a global scale. We ...
Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems an...
Genetic isolation of breeds may result in a significant loss of diversity and have consequences on health and performance. In this study, we examined the effect of geographic isolation on caprine genetic diver...
International standard panels of single nucleotide polymorphisms (SNPs) have replaced microsatellites in several species for parentage assessment and assignment (PA) purposes. However, such a resource is still...
Bacterial cold-water disease, which is caused by Flavobacterium psychrophilum, is one of the major diseases that affect rainbow trout (Oncorhynchus mykiss) and a primary concern for trout farming. Better knowledg...
The Correction to this article has been published in Genetics Selection Evolution 2019 51:11
Copy number variations (CNV) are an important source of genetic variation that has gained increasing attention over the last couple of years. In this study, we performed CNV detection and functional analysis f...
Cross-validation tools are used increasingly to validate and compare genetic evaluation methods but analytical properties of cross-validation methods are rarely described. There is also a lack of cross-validat...
The Correction to this article has been published in Genetics Selection Evolution 2019 51:69
A breeding program for commercial broiler chicken that is carried out under strict biosecure conditions can show reduced genetic gain due to genotype by environment interactions (G × E) between bio-secure (B) ...
The single-step single nucleotide polymorphism best linear unbiased prediction (ssSNPBLUP) method, such as single-step genomic BLUP (ssGBLUP), simultaneously analyses phenotypic, pedigree, and genomic informat...
High resistance (the ability of the host to reduce pathogen load) and tolerance (the ability to maintain high performance at a given pathogen load) are two desirable host traits for producing animals that are ...
Genomic prediction (GP) accuracy in numerically small breeds is limited by the small size of the reference population. Our objective was to test a multi-breed multiple genomic relationship matrices (GRM) GP mo...
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...
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Genetics Selection Evolution