A. R. Sharifi

The pattern of linkage disequilibrium in German Holstein cattle

This study presents a second generation of linkage disequilibrium (LD) map statistics for the whole genome of the Holstein-Friesian population, which has a four times higher resolution compared with that of the maps available so far. We used DNA samples of 810 German Holstein-Friesian cattle genotyped by the Illumina Bovine SNP50K BeadChip to analyse LD structure. A panel of 40 854 (75.6%) markers was included in the final analysis. The pairwise r(2) statistic of SNPs up to 5 Mb apart across the genome was estimated. A mean value of r(2) = 0.30 +/- 0.32 was observed in pairwise distances of <25 kb and it dropped to 0.20 +/- 0.24 at 50-75 kb, which is nearly the average inter-marker space in this study. The proportion of SNPs in useful LD (r(2) > or = 0.25) was 26% for the distance of 50 and 75 kb between SNPs. We found a lower level of LD for SNP pairs at the distance < or =100 kb than previously thought. Analysis revealed 712 haplo-blocks spanning 4.7% of the genome and containing 8.0% of all SNPs. Mean and median block length were estimated as 164 +/- 117 kb and 144 kb respectively. Allele frequencies of the SNPs have a considerable and systematic impact on the estimate of r(2). It is shown that minimizing the allele frequency difference between SNPs reduces the influence of frequency on r(2) estimates. Analysis of past effective population size based on the direct estimates of recombination rates from SNP data showed a decline in effective population size to N(e) = 103 up to approximately 4 generations ago. Systematic effects of marker density and effective population size on observed LD and haplotype structure are discussed.

A genome‐wide scan for signatures of recent selection in Holstein cattle

The data from the newly available 50 K SNP chip was used for tagging the genome-wide footprints of positive selection in Holstein-Friesian cattle. For this purpose, we employed the recently described Extended Haplotype Homozygosity test, which detects selection by measuring the characteristics of haplotypes within a single population. To assess formally the significance of these results, we compared the combination of frequency and the Relative Extended Haplotype Homozygosity value of each core haplotype with equally frequent haplotypes across the genome. A subset of the putative regions showing the highest significance in the genome-wide EHH tests was mapped. We annotated genes to identify possible influence they have in beneficial traits by using the Gene Ontology database. A panel of genes, including FABP3, CLPN3, SPERT, HTR2A5, ABCE1, BMP4 and PTGER2, was detected, which overlapped with the most extreme P-values. This panel comprises some interesting candidate genes and QTL, representing a broad range of economically important traits such as milk yield and composition, as well as reproductive and behavioural traits. We also report high values of linkage disequilibrium and a slower decay of haplotype homozygosity for some candidate regions harbouring major genes related to dairy quality. The results of this study provide a genome-wide map of selection footprints in the Holstein genome, and can be used to better understand the mechanisms of selection in dairy cattle breeding.

Polymorphisms in the bovine HSP90AB1 gene are associated with heat tolerance in Thai indigenous cattle.

Heat shock proteins act as molecular chaperones that have preferentially been transcribed in response to severe perturbations of the cellular homeostasis such as heat stress. Here the traits respiration rate (RR), rectal temperature (RT), pack cell volume (PCV) and the individual heat tolerance coefficient (HTC) were recorded as physiological responses on heat stress (environmental temperatures) in Bos taurus (crossbred Holstein Friesian; HF) and B. indicus (Thai native cattle: White Lamphun; WL and Mountain cattle; MT) animals (n = 47) in Thailand. Polymorphisms of the heat shock protein 90-kDa beta gene (HSP90AB1) were evaluated by comparative sequencing. Nine single nucleotide polymorphisms (SNP) were identified, i.e. three in exons 10 and 11, five in introns 8, 9, 10 and 11, and one in the 3′UTR. The exon 11 SNP g.5082C>T led to a missense mutation (alanine to valine). During the period of extreme heat (in the afternoon) RR and RT were elevated in each of the three breeds, whereas the PCV decreased. Mountain cattle and White Lamphun heifers recorded significantly better physiologic parameters (p < 0.05) in all traits considered, including or particularly HTC than Holstein Friesian heifers. The association analysis revealed that the T allele at SNP g.4338T>C within intron 3 improved the heat tolerance (p < 0.05). Allele T was exclusively found in White Lamphun animals and to 84% in Mountain cattle. Holstein Friesian heifers revealed an allele frequency of only 18%. Polymorphisms within HSP90AB1 were not causative for the physiological responses; however, we propose that they should at least be used as genetic markers to select appropriate breeds for hot climates.

Different scalding techniques do not affect boar taint.

The prevention of unpleasant boar taint is the main reason for castration of male piglets. For animal welfare reasons, castration is announced to be banned in the European Community. This study aimed to investigate whether androstenone, skatole and indole in backfat of boars may be reduced by different scalding technologies. To discriminate ante and post mortem effects, carcasses were sampled before and after scalding in two abattoirs using either horizontal (TANK) or vertical (TUNNEL) scalding. Backfat samples were analysed using gas chromatography (androstenone) and liquid chromatography (skatole, indole). Neither TANK nor TUNNEL scalding did significantly reduce malodorous compounds. Skatole and androstenone in backfat obtained after scalding averaged 112 ± 123 ng/g and 1196 ± 885 ng/g melted fat, respectively; significant differences between abattoirs were observed for skatole. Increased skatole levels were tentatively assigned to longer transport duration. Concluding from recent consumer research and subsequent application of suggested sensory rejection thresholds for androstenone (2000 ng/g) and skatole (150 ng/g), nearly 30% of the carcasses may be unacceptably tainted.

Acute paretic syndrome in juvenile White Leghorn chickens resembles late stages of acute inflammatory demyelinating polyneuropathies in humans

BackgroundSudden limb paresis is a common problem in White Leghorn flocks, affecting about 1% of the chicken population before achievement of sexual maturity. Previously, a similar clinical syndrome has been reported as being caused by inflammatory demyelination of peripheral nerve fibres. Here, we investigated in detail the immunopathology of this paretic syndrome and its possible resemblance to human neuropathies.MethodsNeurologically affected chickens and control animals from one single flock underwent clinical and neuropathological examination. Peripheral nervous system (PNS) alterations were characterised using standard morphological techniques, including nerve fibre teasing and transmission electron microscopy. Infiltrating cells were phenotyped immunohistologically and quantified by flow cytometry. The cytokine expression pattern was assessed by quantitative real-time PCR (qRT-PCR). These investigations were accomplished by MHC genotyping and a PCR screen for Mareks disease virus (MDV).ResultsSpontaneous paresis of White Leghorns is caused by cell-mediated, inflammatory demyelination affecting multiple cranial and spinal nerves and nerve roots with a proximodistal tapering. Clinical manifestation coincides with the employment of humoral immune mechanisms, enrolling plasma cell recruitment, deposition of myelin-bound IgG and antibody-dependent macrophageal myelin-stripping. Disease development was significantly linked to a 539 bp microsatellite in MHC locus LEI0258. An aetiological role for MDV was excluded.ConclusionsThe paretic phase of avian inflammatory demyelinating polyradiculoneuritis immunobiologically resembles the late-acute disease stages of human acute inflammatory demyelinating polyneuropathy, and is characterised by a Th1-to-Th2 shift.

Genetic parameters and factors influencing survival to twenty-four hours after birth in Danish meat sheep breeds.

In this study, influential factors and (co)variance components for survival to 24 h after birth were determined and estimated for Texel, Shropshire, and Oxford Down, the most common sheep breeds in Denmark. Data from 1992 to 2006 containing 138,813 survival records were extracted from the sheep recording database at the Danish Agricultural Advisory Service. Estimation of (co)variance components was carried out using univariate animal models, applying logistic link functions. The logistic functions were also used for estimation of fixed effects. Both direct and maternal additive genetic effects, as well as common litter effects, were included in the models. The mean survival to 24 h after birth was 92.5, 91.7, and 88.5% for Texel, Shropshire, and Oxford Down, respectively. There was a curvilinear relationship between survival to 24 h after birth and birth weight, with survival less for light and heavy lambs. Male lambs, as well as lambs from ewes in the first parity or with difficult lambing, had the least survival to 24 h after birth. Survival to 24 h after birth was greater in twin-born Texel and Shropshire lambs compared with singletons and vice versa in Oxford Down. Estimates of direct heritability were in the range from 0.05 to 0.07. Maternal heritability estimates were slightly greater (0.06 and 0.07) than direct heritabilities in Texel and Shropshire and less (0.04) in Oxford Down. The estimated genetic correlations between direct and maternal effects for survival to 24 h after birth were negative, which will make breeding for this trait more difficult. However, on the basis of estimated genetic parameters, it can be concluded that it is possible to improve survival to 24 h after birth in meat sheep breeds by accounting for both direct and maternal genetic effects in breeding programs.

Analysis of relationship between bovine lymphocyte antigen DRB3.2 alleles, somatic cell count and milk traits in Iranian Holstein population.

The major histocompatibility complex (MHC) is a gene complex closely linked to the vertebrate immune system due to its importance in antigen recognition and immune response to pathogens. To improve our understanding of the MHC and disease resistance in dairy cattle, we gathered 5119 test day records of somatic cell count (SCC) and performance traits of 262 Holstein dairy cows to determine whether the DRB region of the MHC contains alleles that are associated with elevated SCC, milk yield, protein and fat percent of milk. To this purpose, genotyping of animals for DRB3 gene was investigated by polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP) assay. A two-step PCR was carried out so as to amplify a 284 base-pair fragment of exon 2 of the target gene. Second PCR products were treated with three restriction endonuclease enzymes RsaI, BstYI and HaeIII. Twenty-eight BoLA-DRB3 alleles were identified including one novel allele (*40). The results in general are in good accordance with allele frequencies of Holstein cattle populations reported by previous studies. Analyses of associations were modeled based on repeated measurement anova and generalized logistic linear methods for production traits and SCC data, respectively. The results of this study showed a significant relationship between the elevated SCC reflecting an increased probability of occurrence to subclinical mastitis and DRB3.2 allele *8 (p < 0.03). The results also revealed significant positive relationships of alleles*22 (p < 0.01) and allele*11 (p < 0.05) with milk fat percent as well as of alleles*24 (p < 0.03) and *22 (p < 0.05) with protein percent. The present study failed to find any association between milk yield and tested alleles. Because of the lack of consistency among results of similar studies, we suggest further investigations to determine the precise nature of these associations with the high polymorphic bovine MHC region to be performed based on haplotypes.

Consumer acceptance of fermented sausages made from boars is not distracted by respective information.

This study investigated the impact of two information conditions and two androstenone concentrations on the acceptability of fermented sausages made from boar meat. Two batches of salamis were produced by mixing bellies and lean meat resulting in average androstenone levels of 0.408 μg/g vs. 1.585 μg/g melted fat, respectively. Skatole levels were kept below 0.05 μg/g melted fat in the final products. The consumers were provided with either the information that the products consisted of 100% pork or 100% boar meat. In total, 478 visitors of an animal husbandry fair, assumed to be familiar with the consequences of not castrating male piglets, evaluated the salami following a monadic between-subject design. The information did not significantly affect the hedonic scores. The percentage of dislikes was very low, i.e. 3 vs. 6% (p=0.24) for salami LOW and HIGH, respectively. The batch with lower androstenone content was liked slightly but significantly better (p=0.03).

The effect of naked neck gene and ambient temperature and their interaction on reproductive traits of heavy broiler dams

High ambient temperature is a major factor for diminishing reproductive performance of broiler parent stocks. Homozygous naked neck (NaNa) broilers, which possess a higher adaptation to heat due to a reduction of feather coverage, exhibited higher growth rates and meat yield. This study was conducted to investigate the influence of genotype x temperature interactions on the reproduction traits of heavy broiler dams caused by different feathering genotypes induced by naked neck gene (Na). In an additional experiment, the effect of Na gene on embryonic activity using oxygen uptake was examined. Normal-feathered (nana) and NaNa hens were maintained in separate cages under high (30 degrees C) and moderate (19 degrees C) temperatures, with RH of 55% from the 18th to 72nd week of age. Egg production, fertility, hatchability, and the time of embryonic mortality were recorded. In comparison with the NaNa genotype, the nana hens showed clear performance depressions under thermal stress with respect to egg production (63%), fertility (20%), hatchability, and number of chicks (72%). Under temperate ambient temperature, there were no differences in laying performance and fertility between both genotypes, with the exception of hatchability due to an increase in embryonic mortality as a result of the Na gene and consequently in the complex trait number of chicks. The early embryonic mortality of eggs laid by nana hens exposed to heat stress is clearly higher than of eggs by nana hens kept under temperate ambient temperature. In contrast, there were no significant differences in early embryonic mortality of eggs of NaNa birds kept under high and temperate environmental temperatures, demonstrating that heat stress leads to reduced early embryonic livability. Embryonic mortality in the late developing stage is significantly increased, and the homozygous genotype is much more affected than the heterozygous embryo. The possible reason for the Na gene-induced embryonic mortality is still not clear. In this investigation, it is shown that the phenomenon cannot be explained by the oxygen consumption.

A single nucleotide polymorphism in the CYP2E1 gene promoter affects skatole content in backfat of boars of two commercial Duroc-sired crossbred populations.

The prevention of unpleasant boar taint is the main reason for castration of male piglets. This study aimed to investigate how the malodorous compound skatole is affected by a single nucleotide polymorphism (g.2412 C>T at -586 ATG) in the porcine cytochrome p450 II E1 (CYP2E1) gene. 119 boars of two commercial Duroc-sired crossbred populations raised at different farms were investigated. Skatole and androstenone in backfat averaged 114±125 ng/g and 1206±895 ng/g melted fat, respectively. The frequency of the genotypes CC, CT, and TT was 25, 52, and 23%, respectively. CC boars had the highest average skatole levels (175 ng/g) compared to CT (92 ng/g) and TT (93 ng/g). Applying suggested sensory threshold levels for skatole (>150 ng/g) and androstenone (>2000 ng/g), 30% of the carcasses may be unacceptably tainted while the proportion of tainted carcasses is significantly higher within genotype CC (56.7%) compared to genotypes CT (24.3%) and TT (14.8%). Effective reduction of tainted carcasses appears feasible applying marker assisted selection.