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Canarian Black (CB) pigs belong to an autochthonous and endangered breed, which is spread throughout the Canarian archipelago. It is commonly accepted that they represent a relic of the pig populations that we...
Native populations of Atlantic salmon in Poland, from the southern Baltic region, became extinct in the 1980s. Attempts to restitute salmon populations in Poland have been based on a Latvian salmon population ...
In this article, we imagine a breeding scenario with a population of individuals that have been genotyped but not phenotyped. We derived a computationally efficient statistic that uses this genetic information...
Since 2010, four Charolais calves with a congenital mechanobullous skin disorder that were born in the same herd from consanguineous matings were reported to us. Clinical and histopathological examination reve...
Modern dairy cattle breeding goals include several production and more and more functional traits. Estimated breeding values (EBV) that are combined in the total merit index usually come from single-trait mode...
This is the first study based on a genome-wide association approach that investigates the links between ovine footrot scores and molecular polymorphisms in Texel sheep using the ovine 50 K SNP array (42 883 SN...
Genomic prediction of breeding values from dense single nucleotide polymorphisms (SNP) genotypes is used for livestock and crop breeding, and can also be used to predict disease risk in humans. For some traits...
A recursive algorithm to calculate the fifteen detailed coefficients of identity is introduced. Previous recursive procedures based on the generalized coefficients of kinship provided the detailed coefficients...
Genomic best linear unbiased prediction (GBLUP) is a statistical method used to predict breeding values using single nucleotide polymorphisms for selection in animal and plant breeding. Genetic effects are oft...
Nelore and Gir are the two most important indicine cattle breeds for production of beef and milk in Brazil. Historical records state that these breeds were introduced in Brazil from the Indian subcontinent, cr...
High-density genomic data is often analyzed by combining information over windows of adjacent markers. Interpretation of data grouped in windows versus at individual locations may increase statistical power, s...
Genomic selection is increasingly widely practised, particularly in dairy cattle. However, the accuracy of current predictions using GBLUP (genomic best linear unbiased prediction) decays rapidly across genera...
Seven donkey breeds are recognized by the French studbook and are characterized by a black, bay or grey coat colour including light cream-to-white points (LP). Occasionally, Normand bay donkeys give birth to d...
The development of a reliable method to predict heterosis would greatly improve the efficiency of commercial crossbreeding schemes. Extending heterosis prediction from the line level to the individual sire lev...
A better understanding of non-additive variance could lead to increased knowledge on the genetic control and physiology of quantitative traits, and to improved prediction of the genetic value and phenotype of ...
A number of methods are available to scan a genome for selection signatures by evaluating patterns of diversity within and between breeds. Among these, “extended haplotype homozygosity” (EHH) is a reliable app...
Genomic BLUP (GBLUP) can predict breeding values for non-phenotyped individuals based on the identity-by-state genomic relationship matrix (G). The G matrix can be constructed from thousands of markers spread acr...
While several studies have examined the accuracy of direct genomic breeding values (DGV) within and across purebred cattle populations, the accuracy of DGV in crossbred or multi-breed cattle populations has be...
Recently, artificial neural networks (ANN) have been proposed as promising machines for marker-based genomic predictions of complex traits in animal and plant breeding. ANN are universal approximators of compl...
We tested the hypothesis that optimum-contribution selection (OCS) with restrictions imposed during optimisation realises most of the long-term genetic gain realised by OCS without restrictions.
In previous studies on an Iberian x Landrace cross, we have provided evidence that supported the porcine ELOVL6 gene as the major causative gene of the QTL on pig chromosome 8 for palmitic and palmitoleic acid co...
The short-term impact of using different genomic prediction (GP) models in genomic selection has been intensively studied, but their long-term impact is poorly understood. Furthermore, long-term genetic gain o...
Cryptorchidism and scrotal/inguinal hernia are the most frequent congenital defects in pigs. Identification of genomic regions that control these congenital defects is of great interest to breeding programs, b...
Recently, genome-wide association studies (GWAS) have been reported on various pig traits. We performed a GWAS to analyze 22 traits related to growth and fatness on two pig populations: a White Duroc × Erhuali...
In livestock production, many animals are crossbred, with two distinct advantages: heterosis and breed complementarity. Genomic selection (GS) can be used to select purebred parental lines for crossbred perfor...
Beef cattle require dietary minerals for optimal health, production and reproduction. Concentrations of minerals in tissues are at least partly genetically determined. Mapping genomic regions that affect the m...
In crossbreeding programs, genomic selection offers the opportunity to make efficient use of information on crossbred (CB) individuals in the selection of purebred (PB) candidates. In such programs, reference ...
The reliability of whole-genome prediction models (WGP) based on using high-density single nucleotide polymorphism (SNP) panels critically depends on proper specification of key hyperparameters. A currently po...
Next-generation sequencing techniques, such as genotyping-by-sequencing (GBS), provide alternatives to single nucleotide polymorphism (SNP) arrays. The aim of this work was to evaluate the potential of GBS com...
Both genome-wide association (GWA) studies and genomic selection depend on the level of non-random association of alleles at different loci, i.e. linkage disequilibrium (LD), across the genome. Therefore, char...
Recently, a mutation was discovered in the DMRT3 gene that controls pacing in horses. The mutant allele A is fixed in the American Standardbred trotter breed, while in the French trotter breed, the frequency of t...
GBLUP (genomic best linear unbiased prediction) uses high-density single nucleotide polymorphism (SNP) markers to construct genomic identity-by-state (IBS) relationship matrices. However, identity-by-descent (...
Genomic selection (GS) allows estimation of the breeding value of individuals, even for non-phenotyped animals. The aim of the study was to examine the potential of identity-by-descent genomic selection (IBD-G...
We conducted a genome-wide linkage analysis to identify quantitative trait loci (QTL) that influence meat quality-related traits in a large F2 intercross between Landrace and Korean native pigs. Thirteen meat qua...
With dense genotyping, many choices exist for methods to detect quantitative trait loci (QTL) in livestock populations. However, no across-species study has been conducted on the performance of different metho...
Differences in linkage disequilibrium and in allele substitution effects of QTL (quantitative trait loci) may hinder genomic prediction across populations. Our objective was to develop a deterministic formula ...
SNP (single nucleotide polymorphisms) genotype data are increasingly available in cattle populations and, among other things, can be used to predict carriers of specific haplotypes. It is therefore convenient ...
Parentage control is moving from short tandem repeats- to single nucleotide polymorphism (SNP) systems. For SNP-based parentage control in cattle, the ISAG-ICAR Committee proposes a set of 100/200 SNPs but qua...
Farm animals are normally selected under highly controlled, non-limiting conditions to favour the expression of their genetic potential. Selection strategies can also focus on a single trait to favour the most...
The current availability of genotypes for very large numbers of single nucleotide polymorphisms (SNPs) is leading to more accurate estimates of inbreeding coefficients and more detailed approaches for detectin...
In developing dairy sectors, genetic improvement programs have limited resources and recording of herds is minimal. This study evaluated different methods to estimate lactation yield and sampling schedules wit...
The additive genetic correlation (r g ) is a key parameter in livestock genetic improvement. The standard error (SE) of an estimate of r g ...
Infection of livestock with bovine tuberculosis (bTB; Mycobacterium bovis) is of major economical concern in many countries; approximately 15 000 to 20 000 cattle are infected per year in Ireland. The objective o...
Inbreeding reduces the fitness of individuals by increasing the frequency of homozygous deleterious recessive alleles. Some insight into the genetic architecture of fitness, and other complex traits, can be ga...
Toll-like receptors (TLR) are essential activators of the innate part of the vertebrate immune system. In this study, we analysed the interspecific variability of three TLR (bacterial-sensing TLR4 and TLR5 and...
It is common for humans and model organisms to exhibit sexual dimorphism in a variety of complex traits. However, this phenomenon has rarely been explored in pigs.
Most studies on genomic prediction with reference populations that include multiple lines or breeds have used linear models. Data heterogeneity due to using multiple populations may conflict with model assumpt...
Genomic prediction faces two main statistical problems: multicollinearity and n ≪ p (many fewer observations than predictor variables). Principal component (PC) analysis is a multivariate statistical method that ...
In pig, limb bone length influences ham yield and body height to a great extent and has important economic implications for pig industry. In this study, an intercross population was constructed between the ind...
All progeny-tested bucks from the two main French dairy goat breeds (Alpine and Saanen) were genotyped with the Illumina goat SNP50 BeadChip. The reference population consisted of 677 bucks and 148 selection c...
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Genetics Selection Evolution