Short tandem repeats and methylation in the promoter region affect expression of cystathionine beta-synthase gene in the laying hen.

Homocysteine can be converted to cysteine via the transsulfuration pathway where cystathionine beta-synthase (CBS) is a rate-limiting enzyme. Homocysteine is thought to play a role in bone remodelling and strength. Previous results indicated that some of the difference in bone strength of end-of-lay hens may be associated with CBS expression level.

Use and optimization of different sources of information for genomic prediction.

Background: Molecular data is now commonly used to predict breeding values (BV). Various methods to calculate genomic relationship matrices (GRM) have been developed, with some studies proposing regression of coefficients back to the reference matrix of pedigree-based relationship coefficients (A). The objective was to compare the utility of two GRM: a matrix based on linkage analysis (LA) and anchored to the pedigree, i.

Simultaneous fitting of genomic-BLUP and Bayes-C components in a genomic prediction model.

Background: The rapid adoption of genomic selection is due to two key factors: availability of both high-throughput dense genotyping and statistical methods to estimate and predict breeding values. The development of such methods is still ongoing and, so far, there is no consensus on the best approach. Currently, the linear and non-linear methods for genomic prediction (GP) are treated as distinct approaches.

Within- and across-breed genomic prediction using whole-genome sequence and single nucleotide polymorphism panels.

Background: Currently, genomic prediction in cattle is largely based on panels of about 54k single nucleotide polymorphisms (SNPs). However with the decreasing costs of and current advances in next-generation sequencing technologies, whole-genome sequence (WGS) data on large numbers of individuals is within reach. Availability of such data provides new opportunities for genomic selection, which need to be explored.

Stochastic modelling of optimum initial body weight, daily weight gain and effect of genetic changes in ovulation rate and age at sexual maturity on total egg production of broiler breeders.

1. A model that simulates the total production of eggs (TEP) in broiler breeders was used to predict the optimum initial (20 week) body weight (IBWexp), daily weight gains from 20 to 30 (DWGexp(20-30)) and 31 to 62 weeks of age (DWGexp(31-62)), age at photostimulation (affecting age at first egg, AFEexp), coefficients of variation of initial body weight (CV-IBWexp) and age at first egg (CV-AFEexp), and the effect of genetically increasing the numbers of yellow follicles at the onset of lay. 2.

Successful modification of a stochastic model of egg production in broiler breeders housed in temperate climates to predict flock productivity in tropical farms in Venezuela.

1. The production of hatching eggs in tropical flocks of broiler breeders was estimated from records of initial body weight and subsequent body weight gains from 6 flocks containing over 140,000 birds in Venezuela using a stochastic model developed in temperate climates. The model was then modified to account for the greater persistency of egg production in the tropical environment of Venezuela.

Cross-species utility of microsatellite markers in trichostrongyloid nematodes.

The development of microsatellite markers for parasitic nematodes has been hampered by technical difficulties in isolation and PCR amplification. We have investigated the potential for circumventing these problems using microsatellites from 3 trichostrongyloid species on a panel of 7 species. Ten of the 22 PCR primer pairs tested amplified in species other than the target species, usually in closely related species, and 2 new variable loci were discovered in the sheep parasite Trichostrongylus vitrinus.

Optimal design of genetic studies of gene expression with two-color microarrays in outbred crosses.

Combining global gene-expression profiling and genetic analysis of natural allelic variation (genetical genomics) has great potential in dissecting the genetic pathways underlying complex phenotypes. Efficient use of microarrays is paramount in experimental design as the cost of conducting this type of study is high. For those organisms where recombinant inbred lines are available for mapping, the "distant pair design" maximizes the number of informative contrasts over all marker loci.

Rapid and robust association mapping of expression quantitative trait loci.

We applied a simple and efficient two-step method to analyze a family-based association study of gene expression quantitative trait loci (eQTL) in a mixed model framework. This two-step method produces very similar results to the full mixed model method, with our method being significantly faster than the full model. Using the Genetic Analysis Workshop 15 (GAW15) Problem 1 data, we demonstrated the value of data filtering for reducing the number of tests and controlling the number of false positives.

Nutritional factors affecting poultry bone health.

Outlined are two main current research concerns relating to skeletal disorders in poultry: (a) osteoporosis in egg-laying hens; (b) leg problems caused by rapid bone growth in broiler chickens. Surveys indicate that 30% of caged laying hens suffer at least one lifetime fracture (a severe welfare issue). Modern hybrids produce one egg per d for 50 weeks.

Sequential genetic modification of the hprt locus in human ESCs combining gene targeting and recombinase-mediated cassette exchange.

Genetic modification of human embryonic stem cells (hESCs) will be an essential tool to allow full exploitation of these cells in regenerative medicine and in the study of hESC biology. Here we report multiple sequential modifications of an endogenous gene (hprt) in hESCs. A selectable marker flanked by heterospecific lox sites was first introduced by homologous recombination (HR) into the hprt gene.

The cholecystokinin type A receptor g.179A>G polymorphism affects feeding rate.

A polymorphism within the 5' untranslated region of the cholecystokinin type A receptor (CCKAR) gene has been shown to affect feed intake and growth in commercial pig lines. To further investigate the phenotype of animals carrying alternative alleles at this polymorphism, we genotyped animals from a distinct segregating commercial line and an experimental cross F(2) population, both with electronically recorded feeding pattern data. The data indicate that the daily feed intake increasing effect of the DQ496228:g.

Detection of quantitative trait loci for meat quality traits in cattle.

A whole-genome scan was carried out to detect quantitative trait loci (QTL) affecting sensory, organoleptic, physical and chemical properties of meat. The study used phenotypic data from 235 second-generation cross-bred bull calves of a Charolais x Holstein experimental population. Loin muscle samples were evaluated for yield force, intramuscular fat and nitrogen contents, myofibrillar fragmentation index, haem pigment concentration, moisture content and pH at 24 h postmortem.

Evolution of the chicken Toll-like receptor gene family: a story of gene gain and gene loss.

Background: Toll-like receptors (TLRs) perform a vital role in disease resistance through their recognition of pathogen associated molecular patterns (PAMPs). Recent advances in genomics allow comparison of TLR genes within and between many species. This study takes advantage of the recently sequenced chicken genome to determine the complete chicken TLR repertoire and place it in context of vertebrate genomic evolution.

Inbreeding in genome-wide selection.

Traditional selection methods, such as sib and best linear unbiased prediction (BLUP) selection, which increased genetic gain by increasing accuracy of evaluation have also led to an increased rate of inbreeding per generation (DeltaFG). This is not necessarily the case with genome-wide selection, which also increases genetic gain by increasing accuracy. This paper explains why genome-wide selection reduces DeltaFG when compared with sib and BLUP selection.

Genetic perspectives on host responses to porcine reproductive and respiratory syndrome (PRRS).

Porcine reproductive and respiratory syndrome (PRRS) is the most economically important disease in pig populations, worldwide. Current research, both in vitro and in vivo, has failed to provide industry with a reliable or effective method to combat the disease. In this paper the present knowledge of the genetics of the host response to porcine reproductive and respiratory syndrome virus (PRRSV) is reviewed.

Genetic effects on coat colour in cattle: dilution of eumelanin and phaeomelanin pigments in an F2-Backcross Charolais x Holstein population.

Background: In cattle, the gene coding for the melanocortin receptor 1 (MC1R) is known to be the main regulator of the switch between the two coat colour pigments: eumelanin (black pigment) and phaeomelanin (red pigment). Some breeds, such as Charolais and Simmental, exhibit a lightening of the original pigment over the whole body. The dilution mutation in Charolais (Dc) is responsible for the white coat colour of this breed.

Avian genomics in the 21st century.

The chicken has long been an important model organism for developmental biology, as well as a major source of protein with billions of birds used in meat and egg production each year. Chicken genomics has been transformed in recent years, with the characterisation of large EST collections and most recently with the assembly of the chicken genome sequence. As the first livestock genome to be fully sequenced it leads the way for others to follow--with zebra finch later this year.

The association between plasma levels of acute phase proteins, haptoglobin, alpha-1 acid glycoprotein (AGP), pig-MAP, transthyretin and serum amyloid A (SAA) in Large White and Meishan pigs.

During infection, the acute phase response triggers the release of acute phase proteins (APP), alpha-(1) acid glycoprotein (AGP), serum amyloid A (SAA) and Pig-MAP into the circulation, accompanied by a decrease in plasma levels of transthyretin. We quantified the association between these APP in 26 apparently healthy pigs from two breeds, 13 Large White and 13 Meishan (16 male; 10 female). There was a significant correlation between plasma levels of haptoglobin and Pig-MAP (r=0.

Stochastic model of egg production in broiler breeders.

A stochastic model was developed to simulate the egg production of broiler breeders in response to changes in BW. The first step involved the construction of a diagram incorporating dependent and independent variables and their relationships to ovulation rate and egg production from 8 equations based on experimental results. The model was based on existing experimental data, and stochastic processes were invoked for 4 input parameters.

Low mitochondrial variability in birds may indicate Hill-Robertson effects on the W chromosome.

Interference among loci subject to selection (the Hill-Robertson effect) may considerably reduce levels of adaptation and variability in genomic regions that lack recombination. Y- or W chromosomes are particularly vulnerable to such effects, since they represent large, non-recombining blocks of genetic material. In birds, the W chromosome and mitochondrial genomes are both maternally transmitted, and hence fail to recombine with each other, whereas in mammals the Y chromosome is paternally transmitted.

QTL modulating ear size and erectness in pigs.

Ear size and erectness are important conformation measurements in pigs. An F(2) population established by crossing European Large White (small, erect ears) with Chinese Meishan (large, flop ears) was used to study the genetic influence of the two ear traits for the first time. A linkage map incorporating 152 markers on 18 autosomal chromosomes was utilised in a genome scan for QTL.

Polymorphisms of the prion protein gene coding region in born-after-the-reinforced-ban (BARB) bovine spongiform encephalopathy cattle in Great Britain.

Polymorphisms of the prion protein gene are associated with differing susceptibilities to transmissible spongiform encephalopathy diseases, as shown for variant Creutzfeldt-Jakob disease in humans and scrapie in sheep, but not yet in cattle. Imposition of control measures in the UK, including a reinforced ruminant feed ban in 1996, has led to a reduction in the incidence of bovine spongiform encephalopathy (BSE). BSE-affected cattle born after 1996 in Great Britain have been termed born-after-the-reinforced-ban (BARB) cases.

Selection for carcass quality in hill sheep measured by X-ray computer tomography.

This paper describes an investigation of the use of computer tomography (CT) to genetically improve carcass composition and conformation in Scottish Blackface sheep. After 5 years of selection on an index designed to improve both composition and conformation (the 'CT index'), a large response was observed in the CT index, with genetic progress equivalent to 0.11 phenotypic standard deviations per year.