Development of a subacute ruminal acidosis risk score and its prediction using milk mid-infrared spectra in early-lactation cows.

A routine monitoring for subacute ruminal acidosis (SARA) on the individual level could support the minimization of economic losses and the ensuring of animal welfare in dairy cows. The objectives of this study were (1) to develop a SARA risk score (SRS) by combining information from different data acquisition systems to generate an integrative indicator trait, (2) the investigation of associations of the SRS with feed analysis data, blood characteristics, performance data, and milk composition, including the fatty acid (FA) profile, (3) the development of a milk mid-infrared (MIR) spectra-based prediction equation for this novel reference trait SRS, and (4) its application to an external data set consisting of MIR data of test day records to investigate the association between the MIR-based predictions of the SRS and the milk FA profile. The primary data set, which was used for the objectives (1) to (3), consisted of data collected from 10 commercial farms with a total of 100 Holstein cows in early lactation. The data comprised barn climate parameters, pH and temperature logging from intrareticular measurement boluses, as well as jaw movement and locomotion behavior recordings of noseband-sensor halters and pedometers. Further sampling and data collection included feed samples, blood samples, milk performance, and milk samples, whereof the latter were used to get the milk MIR spectra and to estimate the main milk components, the milk FA profile, and the lactoferrin content. Because all measurements were characterized by different temporal resolutions, the data preparation consisted of an aggregation into values on a daily basis and merging it into one data set. For the development of the SRS, a total of 7 traits were selected, which were derived from measurements of pH and temperature in the reticulum, chewing behavior, and milk yield. After adjustment for fixed effects and standardization, these 7 traits were combined into the SRS using a linear combination and directional weights based on current knowledge derived from literature studies. The secondary data set was used for objective (4) and consisted of test day records of the entire herds, including performance data, milk MIR spectra and MIR-predicted FA. At farm level, it could be shown that diets with higher proportions of concentrated feed resulted in both lower daily mean pH and higher SRS values. On the individual level, an increased SRS could be associated with a modified FA profile (e.g., lower levels of short- and medium-chain FA, higher levels of C17:0, odd- and branched-chain FA). Furthermore, a milk MIR-based partial least squares regression model with a moderate predictability was established for the SRS. This work provides the basis for the development of routine SARA monitoring and demonstrates the high potential of milk composition-based assessment of the health status of lactating cows.

Modeling reticular and ventral ruminal pH of lactating dairy cows using ingestion and rumination behavior.

The prevention and control of metabolic and digestive diseases is an enormous challenge in dairy farming. Subacute ruminal acidosis (SARA) is assumed to be the most severe feed-related disorder and it impairs both animal health and economic efficiency. Currently, ruminal pH as well as variables derived from the daily pH curve are the main indicators for SARA. The objective of this study was to explain the daily pH course in the ventral rumen and reticulum of dairy cows using ingestion pattern and rumination behavior data gathered by automated data recording systems. The data of 13 ruminally fistulated lactating cows were collected at the experimental station of the Friedrich-Loeffler-Institut (Brunswick, Germany). The data included continuous pH measurements, which were recorded simultaneously in the reticulum by pH-measuring boluses and in the ventral rumen by a separate data logger. In addition, rumination behavior was measured using jaw movement sensors, and feed and water intakes were recorded by transponder-assisted systems. Milk yield and body weight were determined during and after each milking, respectively. For statistical evaluation, the data were analyzed using time-series modeling with multiple linear mixed regressions. Before applying the developed mathematical statistical modeling, we performed a plausibility assessment to ensure data quality. The major part of the mathematical statistical modeling consisted of data preparation, where all variables were transformed into a uniform 1-min resolution. Signal transformations were used to model individual feed and water intakes as well as rumination behavior events over time. Our results indicated that diurnal pH curves of both the reticulum and ventral rumen could be predicted by the transformed feed and water intake rates. Rumination events were associated with a marginal temporal increase in pH. We observed that the pH of the ventral rumen was delayed by approximately 37 min compared with that of the reticulum, which was therefore considered in the modeling. With the models developed in this study, 67.0% of the variance of the reticular pH curves and 37.8% of the variance of the ruminal pH curves could be explained by fixed effects. We deduced that the diurnal pH course is, to a large extent, associated with the animal's individual feed intake and rumination behavior.

Statistical modeling of ruminal pH parameters from dairy cows based on a meta-analysis.

Adequate feeding of high-performance dairy cows is extremely important to avoid the digestive disorder subacute ruminal acidosis. Subacute ruminal acidosis is defined as a status with a below-average ruminal pH that does not cause direct clinical symptoms at the individual level but is relevant for animal welfare due to a higher risk of secondary health problems at the herd level. The main objective of this study was to apply meta-analytical methods in an exploratory approach to investigate the association between pH parameters of the ventral rumen with milk and diet parameters. Data from 32 studies using continuous pH measurement in the ventral rumen of lactating cows were included in the meta-analysis. Available information extracted from all studies was categorized into parameters associated with management, cow, diet, milk, and pH. The statistical analysis was divided into 4 sections. First, a multiple imputation procedure based on a principal component model was applied, since approximately 19% of the data set consisted of missing values due to heterogeneity in provided information between the studies included in the analysis. In a second step, all potential predictors for the pH parameters, including the daily mean pH, the time with a pH below 5.8, and the pH range, were examined for their prediction suitability using multi-level mixed effects meta-regression models. These analyses were performed on the raw and the imputed data. Because the results of both approaches were consistent, the imputing procedure was considered to be appropriate. Third, automated variable selection was applied to all 3 pH parameters separately for the predictor groups milk and diet using the imputed data set. Thereby, multi-model inference was used to estimate the relative importance of the selected variables. Finally, a functional relationship between the 3 pH parameters was established. The fat to protein ratio of milk, milk fat, and milk protein showed significant associations in meta-regression analysis for all 3 pH parameters when used as a single predictor. Out of the group of diet-specific variables, the acid detergent fiber, neutral detergent fiber, nonfiber carbohydrate, starch content, as well as the forage to concentrate ratio, showed the highest significance in the models. In particular, the multi-model inference showed that the protein, fat, and lactose content of the milk can best quantify the association to the daily mean pH and the time with a pH below 5.8 in a multiple regression model.

Biochemical alterations in the Musculus triceps brachii and Musculus longissimus thoracis during early postmortem period in pigs.

Muscle-to-meat-transition is influenced by alterations of the energy metabolism. Porcine Musculus triceps brachii (MT) consisted of more fast-twitch-glycolytic muscle fibers and samples, collected 0, 10 and 20 min after slaughter (p.m.), showed higher mitochondrial respiratory activities and ATP concentrations than Musculus longissimus thoracis (LT) samples. Enzyme activities in MT were higher at 0 min (glycogen phosphorylase (GP)), 10 min (GP, citrate synthase (CS)) and at 20 min p.m. (CS). However, LT results were higher at 0 min (lactate dehydrogenase (LDH)), 10 min (phosphofructokinase (PFK), LDH) and at 20 min p.m. (PFK, F0F1-ATPase (F0F1)). Between 0 min and 10 min p.m. CS activities decreased in LT and MT samples, PFK increased in LT and GP in MT samples. Between 10 min and 20 min p.m. PFK and LDH decreased in LT and GP in MT samples, whereas F0F1 increased in LT and CS in MT samples. The data indicate that muscles with different mitochondria contents show clearly different energy metabolism characteristics.

Analysis of porcine body size variation using re-sequencing data of miniature and large pigs.

BACKGROUND: Domestication has led to substantial phenotypic and genetic variation in domestic animals. In pigs, the size of so called minipigs differs by one order of magnitude compared to breeds of large body size. We used biallelic SNPs identified from re-sequencing data to compare various publicly available wild and domestic populations against two minipig breeds to gain better understanding of the genetic background of the extensive body size variation. We combined two complementary measures, expected heterozygosity and the composite likelihood ratio test implemented in "SweepFinder", to identify signatures of selection in Minipigs. We intersected these sweep regions with a measure of differentiation, namely FST, to remove regions of low variation across pigs. An extraordinary large sweep between 52 and 61 Mb on chromosome X was separately analyzed based on SNP-array data of F2 individuals from a cross of Goettingen Minipigs and large pigs. RESULTS: Selective sweep analysis identified putative sweep regions for growth and subsequent gene annotation provided a comprehensive set of putative candidate genes. A long swept haplotype on chromosome X, descending from the Goettingen Minipig founders was associated with a reduction of adult body length by 3% in F2 cross-breds. CONCLUSION: The resulting set of genes in putative sweep regions implies that the genetic background of body size variation in pigs is polygenic rather than mono- or oligogenic. Identified genes suggest alterations in metabolic functions and a possible insulin resistance to contribute to miniaturization. A size QTL located within the sweep on chromosome X, with an estimated effect of 3% on body length, is comparable to the largest known in pigs or other species. The androgen receptor AR, previously known to influence pig performance and carcass traits, is the most obvious potential candidate gene within this region.

Genetic approach to select against embryo mortality caused by Enterococcus faecalis infection in laying hens.

Selection to reduce susceptibility to Enterococcus faecalis infection in laying hens may contribute to the prevention of amyloid arthropathy since it is mainly induced by this bacterium. Therefore, the aim of the present study was to investigate the possibility to select more laying hens that are resistant against E. faecalis infection through the embryo lethality assay (ELA), which is proposed as an alternative model to replace the adult avian challenge assay. Ten-day-old embryos of 500 Lohmann Brown layers were inoculated into the allantoic cavity with an infectious dose of 2.5 colony-forming units (cfu)/mL of the avian E. faecalis strain K923/96 in 3 ELAs. The embryonic mortality rate (EMR) was determined by candling the eggs daily over a period of 4 d. The average EMR estimated during the 3 ELAs was 50% and the highest EMR occurred 3 to 4 d post inoculation. The estimated heritability for embryonic survivability to the infection was h2 = 0.12-0.14, calculated with the logistic and probit link function, respectively, indicating that the selection of more laying hens that are resistant to E. faecalis infection is feasible. A highly negative genetic correlation was estimated between embryonic survivability and laying performance at the peak of lay (rg = -0.22) and at the end of the production (rg = -0.65), as well as with breaking strength (rg = -0.30 to -0.37). A positive correlation was found between egg weight and the embryonic survivability (rg = +0.16), and no genetic correlation was found with body weight and dynamic stiffness. Therefore, although it was demonstrated that it is possible to breed for E. faecalis resistance, special care should be taken to monitor and to take all traits and their genetic correlations into account in order to achieve a balanced genetic progress. Besides, the ELA does not require that the hens are exposed to pathogens thereby saving labor and cost. Therefore, it could be feasible that ELA be implemented in selection programs.

Temperature alterations during embryogenesis have a sex-dependent influence on growth properties and muscle metabolism of day-old chicks and 35-day-old broilers.

Broiler eggs were either incubated at 37.8°C during the whole incubation period (control), or at higher (38.8°C, group H) and lower temperatures (36.8°C, group L) from embryonic day (ED) 7 up to ED 10 (ED 7 to 10) or from ED 10 up to ED 13 (ED 10 to 13). Before and after this temperature treatment the eggs were incubated at 37.8°C. The day-old chicks were weighted, sexed and fed up to day 35. On days 1 and 35 samples were taken from the breast and leg muscles for analyzing of the mitochondrial respiratory activity (MRA) and from the breast muscles for analysis of the cross-sectional areas (CSA) and the glycogen phosphorylase (GP), phosphofructokinase (PFK), lactate dehydrogenase (LDH), citrate synthase (CS) and cytochrome oxidase (COX) activities. Statistical analysis showed that treatment (control, group H, group L), sex and their interaction, but not the treatment period (ED 7 to 10; ED 10 to 13), significantly influenced the results. Group H chicks had lower (P⩽0.05) body and heart weights but higher (P⩽0.05) liver weights, CSA values, leg MRA as well as PFK, LDH, CS, GP and COX activities compared with the group L chicks. The results of the control chicks differ (P⩽0.05) from those of the group H (body, heart weight, COX), the group L chicks (liver weight, PFK, LDH, CS, GP) or the birds of both other groups (CSA). The group H broiler had higher (P⩽0.05) body and leg weights as well as LDH, CS, COX and GP activities than the group L broilers. The BWs and the LDH and GP results of the control broiler differ (P⩽0.05) from those of both other groups or from the results of the group H (CS) and group L broiler (COX). Female broilers had lower (P⩽0.05) body, breast and leg weights, but higher (P⩽0.05) CSA, LDH, CS and GP activities than the male animals. Analysis of treatment×sex interaction showed that group H hens had higher (P⩽0.05) body and breast weights, LDH and GP activities compared with the group L hens, whereas in the male broiler no effect of the interaction could be found, except for the lower (P⩽0.05) CSA values in the group H than group L cocks. The treatment effects are probably due to altered embryonic activity and related molecular mechanisms. The sex-related differences in the broiler indicate that these alterations already occur in the embryos and chicks, but become significant with the sexual dimorphism after hatch.

SNP g.1007A>G within the porcine DNAL4 gene affects sperm motility traits and percentage of midpiece abnormalities.

The flagellar beating of a spermatozoa's axoneme is caused by the varying activation and inactivation of dynein molecules. Dynein, axonemal, light chain 4 (DNAL4) is a functional candidate gene for sperm motility as it encodes a small subunit of the dyneins. We resequenced the porcine DNAL4 using three artificial insemination (AI) boars each with high (>68%) or low (<60%) motility, and detected 23 SNP. These were then genotyped for 82 AI boars. Using spermatological records, significantly negative genetic correlations between ejaculate volume (VOL) and the further spermatological parameters concentration (CONC) (r = -.43), motility of undiluted semen (MOTUD) (r = -.09), motility after 24 h (MOT1) (r = -.17) and after 48 hr (MOT2) (r = -.23) were estimated. Significantly positive correlations existed between CONC and MOT1 (r = .07) as well as MOT2 (r = .10), between MOTUD and MOT1 (r = .33), between MOTUD and MOT2 (r = .36), and finally between MOT1 and MOT2 (r = .70). Significantly negatively correlated were all motility traits with the parameters abnormal acrosome (AA) (MOTUD r = -.06; MOT1 r = -.08, and MOT2 r = -.1) and presence of cytoplasmic droplet (CD) (MOTUD r = -.07; MOT1 r = -.08; MOT2 r = -.07). Association analyses (single marker regression model; SMR) propose that SNP g.1007A>G, located in the second intron, reduces motility significantly (MOTUD -4.59%; MOT1 -10.33%; MOT2 -19.37%). According to the dominant-recessive model (DRM), genotype AA is always superior compared to genotypes AG and GG (i.e. MOTUD 67.67%, 64.16% and 53.91%; MOT1 54.17%, 43.75% and 28.44%; MOT2 44.12%, 24.91% and 4.97%). The average effect of gene substitution (g.1007A>G) on abnormal midpiece (AM) was 0.71%, the genotypic values-as expressed by LSmeans-were 0.1 (AA) and 0.81 (AG).

A reaction norm sire model to study the effect of metabolic challenge in early lactation on the functional longevity of dairy cows.

Due to the discrepancy of the high energy demand for rapidly increasing milk production and limited feed intake in the transition period around parturition, dairy cows require considerable metabolic adaptations. We hypothesize that some cows are genetically less suited to cope with these metabolic needs than others, leading to adverse follow-up effects on longevity. To test this, we designed a reaction norm model in which functional lifetime was linked to the metabolic challenge in the beginning of the first lactation. As challenge variables, we used either the sum of milk yield or the accumulated fat-to-protein ratio of the first 3 test-days (<120 d in milk), pre-adjusted for herd-test-day variance. We defined a random regression sire model, in which a random slope was estimated for each sire to assess whether a bull had robust (neutral or positive slopes) or non-robust (negative slopes) daughters. We fitted the model to data of ∼580,000 daughters of ∼5,000 Brown Swiss bulls with suitable observations available (≥10 daughters per bull). To validate our proposed model and assess the reliability of the estimated (co)variance components, we conducted an extensive bootstrap approach. For both challenge variables, we found the sire variance for the slope of the random regression to be significantly different from zero, suggesting a genetic component for metabolic adaptability. The results of the study show that the ability to cope with metabolic stress in the transition period has a genetic component, which can be used to breed metabolically robust dairy cows.

Distribution of Mycobacterium avium subsp. paratuberculosis in a Subclinical Naturally Infected German Fleckvieh Bull.

Although it has been known for years that Mycobacterium avium subsp. paratuberculosis (MAP) is detectable in the reproductive organs and semen of infected bulls, only few studies have been conducted on this topic worldwide. This study surveyed the MAP status of a bull, naturally infected due to close contact with its subclinically infected parents over a period of 4 years. From the age of 7 weeks to necropsy, faecal, blood and, after sexual maturity, semen samples were drawn repeatedly. Already at the first sampling day, MAP-DNA was detected in faeces by semi-nested PCR. True infection was confirmed by the detection of MAP-DNA in blood at the age of 40 weeks. In total, MAP-DNA was present in 25% faecal (34/139), 16% blood (23/140) and 5% semen (4/89) samples, including MAP-free intervals of up to 9 weeks. MAP genome equivalents (MAP-GE) of up to 6.3 × 106 /g faeces and 1.8 × 105 /ml blood were determined. Cultivation of MAP occurred only in three of 137 faecal and two of 109 blood, but never in semen samples. Over the whole period, the bull was a serological negative MAP shedder. During necropsy, 42 tissue samples were collected. Neither macroscopic nor histological lesions characteristic of a MAP infection were observed. Cultivation of MAP in tissue sections failed. However, MAP-DNA was spread widely in the host, including in tissues of the lymphatic system (7/15), digestive tract (5/14) and the urogenital tract (5/9) with concentrations of up to 3.9 × 106 MAP-GE/g tissue. The study highlighted the detection of MAP in male reproductive organs and semen. It supports the hypothesis that bulls may probably transmit MAP, at least under natural mating conditions. In artificial insemination, this might not be relevant, due to antibiotics included currently in semen extenders. However, the survivability of MAP in this microenvironment should be investigated in detail.

Changing the incubation temperature during embryonic myogenesis influences the weight performance and meat quality of male and female broilers.

Eggs of broilers were initially incubated at 37.8°C, then at 38.8°C (group H) and 36.8°C (group L) between embryonic days 7 to 10 (time A) and days 10 to 13 (time B) and further incubated at 37.8°C until hatching. The chicks were fattened until day 35 and then slaughtered. The effect of treatment, time, and sex and their interactions on carcass and meat quality traits were determined. No significant impact of the "treatment time" was analysed, but "treatment" and "sex" and their interactions influenced (P < 0.05) the different parameters. After hatching, group L broilers were heavier (P < 0.05), followed by slower growth compared to group H chicken. At slaughter day, body, carcass, and leg weights of group H broiler were higher (P < 0.05) and yield results lower (P < 0.05) compared to group L animals. pH, drip loss, shear force, and lightness values of group H broiler breast muscles were higher (P < 0.05) and grill loss and redness values lower (P < 0.05) compared to group L Musculus pectoralis superficialis (MPS). Body, carcass, MPS, and leg weights, leg yields and grill loss and lightness values of the male broiler were higher (P < 0.05) and drip loss results lower (P < 0.05) than the female birds. Male group H broiler showed lower (P < 0.05) carcass and MPS yields compared to the control and group L males, whereas females group H birds had higher (P < 0.05) carcass and MPS weights and lower leg yields (P < 0.05) than the female group L animals. The study shows that an increasing incubation temperature during early embryogenesis positively influences the growth and carcass traits of the broilers, accompanied with a partly negative impact on meat quality (drip loss, shear force, lightness). The growth effects were sex-dependent, as significant weight differences could be only found in female broilers. The results indicate that incubation temperature alteration influences molecular mechanisms in the muscle and other tissues with an impact on growth after hatch.

The growth response of ostrich (Struthio camelus var. domesticus) chicks fed on diets with three different dietary protein and amino acid concentrations.

1. Feeding costs are the largest expense in an ostrich production system, and protein is one of the more expensive components of the diet. This study evaluated the growth response of ostrich chicks on diets containing different concentrations of protein (amino acids). The diets were formulated to contain three concentrations of protein (one diet with 20% less protein than the conventional concentration, L; one diet with the conventional concentration of protein, M and one diet with 20% more protein than the conventional concentration, H) for each of the phase diets. The phase diets were pre-starter, starter, grower and finisher. 2. This study includes the analysis of ostrich body weight (BW) by modelling growth with linear polynomial and non-linear functions for all the data not separated for treatments. In total, 3378 BW recordings of 90 animals were collected weekly from hatch (d 0) to 287 d (41 weeks) of age. 3. Seven non-linear growth models and three linear polynomial models were fitted to the data. The growth functions were compared by using Akaike's information criterion (AIC). For the non-linear models, the Bridges and Janoschek models had the lowest AIC values for the H treatment, while the Richards curve had the lowest value for M and the von Bertalanffy for the L treatment. 4. For the linear polynomial models, the linear polynomial of the third degree had the lowest AIC values for all three treatments, thus making it the most suitable model for the data; therefore, the predictions of this model were used to interpret the growth data. Significant differences were found between treatments for growth data. 5. The results from this study can aid in describing the growth of ostriches subjected to optimum feeding conditions. This information can also be used in research when modelling the nutrient requirements of growing birds.

Footprints of recent selection and variability in breed composition in the Göttingen Minipig genome.

The Göttingen Minipig (GMP) developed at the University of Göttingen is a synthetic breed that is widely used in medical research and toxicology. It combines the high fertility of the Vietnamese potbellied pig, the low body weight of the Minnesota Minipig and the white coat colour of the German Landrace pig. The aim of this study was to find genomic regions that may have undergone selection since the creation of the breed in the 1960s. Therefore, the whole genome was screened for footprints of recent selection based on single nucleotide polymorphism (SNP) genotypes from the Illumina Porcine SNP60 BeadChip using two methods: the extended haplotype homozygosity (EHH) test and the estimation of the genomic proportion of the three original breeds at each SNP using a Bayesian approach. Local deviations from the average genome-wide breed composition were tested with a permutation-based empirical test. Results for a comprehensive whole-genome scan for both methods are presented. Several regions showing the highest P-values in the EHH test are related to breeding goals relevant in the GMP, such as growth (SOCS2, TXN, DDR2 and GRB10 genes) and white colour (PRLR gene). Additionally, the calculated proportion of the founder breeds diverged significantly in many regions from the pedigree-based expectations and the genome average. The results provide a genome-wide map of selection signatures in the GMP, which leads to a better understanding of selection that took place over the last decades in GMP breed development.

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).

Power and robustness of three whole genome association mapping approaches in selected populations.

Selection is known to influence the linkage disequilibrium (LD) pattern in livestock populations. Spurious LD may lead to a higher number of false-positive signals in whole genome association mapping experiments. We compared three approaches for whole genome association mapping in a simulation study: single marker regression (SMR), a two-step approach, which analyses residuals corrected for family effects with an SMR (GRAMMAR), and a combined linkage and LD approach, which applies the quantitative transmission disequilibrium test to the Mendelian sampling term (MTDT). Three different scenarios were simulated: idealized random mating, limited number of parents and directional selection. The number of false-positive associations increased when the number of parents was limited. Mapping accuracy was the worst in the scenario with directional selection for all approaches. As SMR produced a high number of false-positive signals in small populations, results of whole genome scans in livestock analysed with SMR should be considered with caution. GRAMMAR was the most accurate approach, but also the least powerful one. The Bonferroni-corrected significance threshold seemed to be too stringent for this approach. Results obtained with MTDT changed only slightly with selected populations. MTDT combined sufficient power with a manageable number of false-positive associations in all scenarios.

The effect of frizzle gene and dwarf gene on reproductive performance of broiler breeder dams under high and normal ambient temperatures.

In 3 experimental runs, the influence of genotype × temperature interactions on the reproductive traits (sexual maturity, egg production, fertility, hatchability, and chick production) of hens of a broiler breeder dam line carrying major genes for dwarfism (dw-) and frizzle (F) was investigated. In experiments 1 and 2, the hens were caged individually under hot (30°C) and temperate (19°C) temperatures, from wk 18 to 72 of age, whereas in experiment 3, hens were kept under moderate temperature (24°C). Hens in experiment 1 were heterozygous for the frizzle gene, and those in experiments 2 and 3 were homozygous, both with and without the dwarf gene. Hens without the above-mentioned major genes (ffDw-) served as control lines. In experiment 1, the frizzle gene (Ff) had no significant effect on sexual maturity, egg production, fertility, hatchability, and chick number under the 2 environmental conditions. In experiment 2, there was a significant interaction between feathering genotype (FF) and environmental temperature for all traits except sexual maturity. Under heat stress, there was a distinct reduction in all reproductive traits except sexual maturity for normally feathered hens compared with frizzle-feathered hens, whereas under temperate conditions, egg production and number of chicks of the FF genotype were reduced and sexual maturity was delayed. In experiments 1 and 2, the dw- gene showed a depressive effect on the growth of hens. In experiment 1, the interaction between dwarf genotype and environmental temperature for egg production was significant. Under temperate conditions, the egg production of dwarf hens was inferior to that of normally sized birds, whereas under hot temperatures, the egg production of the 2 body sizes did not differ. In experiment 2, for sexual maturity, egg production and fertility locus × locus interactions could be determined. The genotype combining the 2 major genes (FFdw-) proved to be inferior to the normally feathered dwarf type (ffdw-) for laying performance but superior in fertility. Under the conditions in experiment 3, the egg production of dwarf birds was significant reduced.

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 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.

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.