Calculation of identity-by-descent probabilities of short chromosome segments.

For some purposes, identity-by-descent (IBD) probabilities for entire chromosome segments are required. Making use of pedigree information, length of the segment and the assumption of no crossing-over, a generalization of a previously published graph theory oriented algorithm accounting for nonzero IBD of common ancestors is given, which can be viewed as method of path coefficients for entire chromosome segments. Furthermore, rules for setting up a gametic version of a segmental IBD matrix are presented. Results from the generalized graph theory oriented method, the gametic segmental IBD matrix and the segmental IBD matrix for individuals are identical.

Optimum multistage genomic selection in dairy cattle.

The availability of different single nucleotide polymorphism (SNP) chips and the development of imputation algorithms allow for multistage dairy cattle breeding schemes applying various genomic selection strategies. These SNP genotypes yield genomically estimated breeding values (GEBV) with different accuracies at different costs. Thus, the optimum allocation of investments to different selection paths and strategies to maximize the genetic gain per year (ΔG(a)) and its sensitivity to changes in cost and accuracies of GEBV is of great interest. This is even more relevant under the constraints of limited financial resources. With deterministic methods, optimum multistage breeding plans maximizing ΔG(a) were identified in which selection could take place on GEBV derived from high-density (GEBV(HD)) and low-density (GEBV(LD)) SNP genotypes. To account for the uncertainty of cost and accuracies of GEBV, these parameters were varied in a semi-continuous manner. Overall breeding costs were limited to the crucial expenses of a traditional breeding program with 50 progeny-tested young bulls per year. Results clearly show that, in an optimal selection strategy, selection on GEBV(LD) is predominantly used for the identification of future bull dams but the main part of ΔG(a) is still generated from selection of sires. The low selection intensity in the path dam to sire induced a higher sensitivity of ΔG(a) to changes in cost and accuracies of GEBV(LD) compared with the same changes of GEBV(HD). On the contrary, the genetic gain generated from selection of males was only affected by changes in accuracies of GEBV(HD) but almost unaffected by any changes in cost. Thus, changes in cost and accuracies of GEBV(LD) put the most pressure on the breeding scheme structure to maintain a high ΔG(a). Furthermore, genomic selection of bull dams produced by far the majority of breeding cost but the lowest genetic gain.

Analysis of birth weight variability in pigs with respect to liveborn and total born offspring.

Reduction in the variability of piglet birth weight within litter and increased piglet survival are key objective in schemes aiming to improve sow prolificacy. In previous studies, variation in birth weight was described by the sample standard deviation of birth weights within one litter, and the genetic impact has been proved. In this study, we additionally considered the sex effect on piglet's birth weight and on its variability. The sample variance of birth weights per litter separated by sex was assigned as a trait of the sow. Different transformations of the trait were fitted by linear and generalized linear mixed models. Based on 1111 litters from Landrace sows, the estimates of heritability for the different measures ranged from 11 to 12%. We analysed the influence of including birth weight of stillborn piglets on the variability of birth weight within litter. With omitted stillborns, the heritability was estimated approximately 2% higher than that in investigations of all born piglets, and the impact of sex on birth weight variability was increased. Because the proportion of intrapartum deaths is rather high, it is recommended to consider the total number of piglets born per litter when analysing birth weight variation.

Statistical tools to detect genetic variation for a sex dimorphism in piglet birth weight.

Sex differences in birth weight contribute to within-litter variability, which itself is connected to piglet survival. Therefore, we studied whether the sex difference in piglet birth weight is a genetically variable sex dimorphism. For that purpose a linear mixed model including sex-specific additive genetic effects was set up. A hypothesis testing problem was defined to detect whether these genetic effects significantly differ between sexes. In a second step, the effect of sex-linked genes was studied explicitly by partitioning the additive genetic effects into autosomal and gonosomal effects. Furthermore, a definition of heritability for the sex difference of a randomly chosen pair of littermates with opposite sex was given. The proposed models were applied separately to a Landrace and Large White data set. Significant genetic variability for the sex dimorphism was found in Landrace (P = 0.03) but not in Large White (P = 0.10). Heritability estimates were at 3 to 5% depending on the model. The X-chromosomal genetic variation was not significant (P > 0.18) at all, whereas the Y-chromosome significantly (P < 0.01) contributed to the genetic variation in Landrace with a corresponding SD of 34 g. It can be concluded that the sex dimorphism of piglet birth weight is genetically variable and a potential target of genetic improvement.

Differences in muscle and fat accretion in Japanese Black and European cattle.

The development of different muscles and adipose tissues during growth was investigated in commercial Japanese Black (JB) cattle and compared with breeds of the largest variation to be found in Europe. Animals, reared under typical conditions for Japanese and European beef production systems, gained similar body weights but different carcass composition at 24months of age. The carcass of JB contained more adipose tissue and the least proportion of muscle. The longissimus muscle of JB developed extraordinary amounts of 23.3% intramuscular fat (IMF) at 24months of age, compared from 0.6% to 4.7% in European breeds. The relationships between IMF content in the longissimus muscle and different adipose tissue weights indicate that a large amount of "waste fat" is accreted with every percent of IMF. However in JB, the good ability of IMF deposition is associated with relatively least development of "waste fat", as a result of unique breed characteristics combined with special feeding system.

Comparison of statistical models to analyse the genetic effect on within-litter variance in pigs.

Genetics affects not only the weight of piglets at birth but also the variability of birth weight within litter. Previous studies on this topic assigned the sample standard deviation of piglet birth weights within litter as an observation to the sow. However, the contribution of the difference in mean birth weight per sex on the within-litter variance has been neglected so far. This work deals with the genetic effect on within-litter variance when different statistical models with different distributional assumptions are used and considers the sex effect and appropriate weights per trait. Traits were formed from the pooled sample variance of male and female birth weights within litter. A linear model approach was fitted to the logarithmized within-litter variance and the sample standard deviation. A generalized linear model with gamma-distributed residuals and log-link function was applied to the untransformed sample variance. Models were compared by analysing data from 9439 litters from Landrace and Large White of a commercial breeding programme. The estimates of heritability for different traits ranged from 7% to 11%. Although the generalized linear mixed model is preferred from a mathematical view, the rank correlations between breeding values of the linear mixed models and the generalized linear mixed model were relatively high, i.e. 94% to 98%. By residual diagnostics, a linear mixed model using the weighted and pooled within-litter standard deviation was identified as most suitable.

Growth- and breed-related changes of muscle bundle structure in cattle.

The objective of this study was to investigate the changes in muscle fiber bundles of cattle of different breeds during growth. Different numbers of muscle fibers are surrounded by connective tissue to form bundles macroscopically visible as meat fibers or meat grain, a common meat quality trait. To determine the influence of breed and age on morphological characteristics of muscle fiber bundles, 4 cattle breeds with different growth impetus and muscularity were reared and slaughtered under experimental conditions. German Angus, a typical beef cattle; Galloway, a smaller beef type; Holstein Friesian, a dairy type; and double-muscled Belgian Blue, an extreme type for muscle growth, were used. Between 5 and 15 bulls of each breed were slaughtered at 2, 4, 6, 12, or 24 mo of age, and slices of semitendinosus muscle were removed. Muscle structure characteristics were determined by computerized image analysis. During growth, the muscle cross-sectional area enlarged (P < 0.001) about 5-fold in double-muscled Belgian Blue bulls and about 4-fold in the other breeds. This was a result of the enlargement (P < 0.001) of primary bundles and muscle fibers. The bundle size was similar (P > or = 0.15) in bulls of German Angus and Galloway in all age groups and was doubled (P < 0.001) in double-muscled Belgian Blue animals from 4 mo of age on. The Holstein Friesian bulls had the smallest (P < 0.001) muscle fiber bundles at 24 mo of age. The number of muscle fibers per bundle and the number of bundles per muscle remained nearly constant (P > 0.05) during growth. This supports the existing view that the structure of the muscle is already fixed in prenatal life. The double-muscled Belgian Blue bulls showed a more than 2.5-fold greater (P < 0.001) number of muscle fibers per primary bundle compared with the other breeds investigated. The larger muscle fiber bundles led to a smaller amount of connective tissue per muscle area in double-muscled cattle. The coarser grain of meat in double-muscled Belgian Blue bulls and in older animals was not related to greater shear force values.

Growth- and breed-related changes of marbling characteristics in cattle.

The objective of this study was to investigate the growth- and breed-related changes of marbling characteristics in cattle. Four cattle breeds with different growth impetus and muscularity were reared and slaughtered under experimental conditions. German Angus, as a typical beef cattle; Galloway, as a smaller, environmentally resistant beef cattle; Holstein-Friesian, as a dairy-type cattle; and double-muscled Belgian Blue, as an extreme type for muscle growth, were used. These 4 breeds were expected to have differences in muscle development and i.m. fat deposition. Between 5 and 15 bulls of each breed were slaughtered at 2, 4, 6, 12, or 24 mo of age. Marbling characteristics were determined and classified in LM and semitendinosus muscle by computerized image analysis. Among breeds, differences appeared in the quantity, structure, and distribution of the marbling flecks in both muscles. The deposition of fat in the double-muscled Belgian Blue bulls remained substantially inferior to that of the other breeds, up to the age of 24 mo. Marbling in German Angus bulls particularly showed larger (P < 0.05) marbling fleck areas. Galloway cattle had the greatest (P < 0.05) number and the most regular (P < 0.05) distribution of the marbling flecks in young animals. Furthermore, for marbling characteristics in Holstein-Friesian animals, a great number and slightly finer structure were observed compared with the other breeds investigated. Postnatal growth-related changes of marbling in LM were characterized by as much as a 40-fold increase in the number of marbling flecks from 2 to 24 mo of age but also by up to a 4-fold enlargement in the area of the marbling flecks. The structure of marbling flecks was determined by 2 development trends. On the one hand, the marbling flecks became larger (P < 0.05), and the structure became coarser, which was reflected by an increasing (P < 0.01) proportion of long marbling flecks as well as an increasing (P < 0.01) maximum skeleton line length. On the other hand, continually new small, round marbling flecks appeared. This caused a decrease (P < 0.01) in the proportion of the 3 largest marbling fleck areas. The distribution of the marbling flecks became more regular (P < 0.05) with increasing proportion and number of marbling flecks. The results suggest that hyperplasia of adipocytes plays an important role in marbling during growth of muscle in cattle.

The map expansion obtained with recombinant inbred strains and intermated recombinant inbred populations for finite generation designs.

The generation of special crosses between different inbred lines such as recombinant inbred strains (RIS) and intermated recombinant inbred populations (IRIP) is being used to improve the power of QTL detection techniques, in particular fine mapping. These approaches acknowledge the fact that recombination of linked loci increases with every generation, caused by the accumulation of crossovers appearing between the loci at each meiosis. This leads to an expansion of the map distance between the loci. While the amount of the map expansion of RIS and IRIP is known for infinite inbred generations, it is not known for finite numbers of generations. This gap was closed here. Since the recursive evaluation of the map expansion factors turned out to be complex, a useful approximation was derived.

Application of computer image analysis to measure pork marbling characteristics.

Sixty longissimus (L) muscle chops were selected according to marbling score in order to develop a technique for the quantitative description of marbling fat by means of computer image analysis (CIA) and study its relationship with intramuscular fat content and shear force variation in pork. L muscle samples were taken from gilts belonging to three genetic lines differing in carcass leanness, namely Large White (LW), Meishan-derived dam line (M) and Synthetic Genex 3000 (SG). SG gilts had leaner loins (P<0.001) than LW and M. However, the SG loins were more marbled (P<0.001) and had higher IMF content. In addition, CIA analysis showed that marbling fat was finer and better distributed in the SG line. CIA marbling characteristics were significantly correlated with both IMF content (P<0.001) and shear force values (P<0.05) demonstrating the reliability of this technique to assess the contribution of marbling characteristics to variations in pork eating quality.

Comparing mRNA levels of genes encoding leptin, leptin receptor, and lipoprotein lipase between dairy and beef cattle.

Body weight and fat mass vary distinctly between German Holstein (dairy cattle) and Charolais (beef cattle). The aim of this study was to determine whether the expression of the obese (Ob) gene and lipoprotein lipase (LPL) gene in fat tissues and expression of the long isoform leptin receptor (Ob-Rb) gene in the hypothalamus were different between these two cattle breeds. Body weight and the area of longissimus muscle cross-section of German Holstein were lower (P<0.001), while body fat content, as well as the omental and perirenal fat mass were higher (P<0.001), compared to Charolais. Plasma insulin and leptin levels between two cattle breeds were determined by radioimmunoassay. Compared to Charolais, plasma insulin concentrations were significantly higher (P<0.01), and plasma leptin levels were tended to be higher (P<0.1) in German Holstein. Ob mRNA levels in subcutaneous and perirenal fat depots, but not in the omental fat depot, were significantly higher (P<0.05) in German Holstein than in Charolais. LPL mRNA expression in the perirenal fat depot of German Holstein was greater in abundance than that of Charolais. No significantly different LPL mRNA levels were found in subcutaneous and omental fat depots, and Ob-Rb mRNA levels in the hypothalamus between these two cattle breeds (P<0.05). Both Ob and LPL expression was greater in perirenal and omental fat depots than in the subcutaneous fat depot (P<0.05). Data indicated that in bovine the Ob and LPL gene expression levels in perirenal fats are an important index that is associated with body fat content, while Ob-Rb in hypothalamus is not.

Comparison of methods used for recovering the line origin of alleles in a cross between outbred lines.

Here, we introduce the idea of probabilities of line origins for alleles in general pedigrees as found in crosses between outbred lines. We also present software for calculating these probabilities. The proposed algorithm is based on the linear regression method of Haley, Knott and Elsen (1994) combined with the Markov chain Monte Carlo (MCMC) method for estimating quantitative trait locus coefficients used as regressors. We compared the relative precision of our method and the original method as proposed by Haley et al. (1994). The scenarios studied varied in the allelic distribution of marker alleles in parental lines and in the frequency of missing marker genotypes. We found that the MCMC method achieves a higher accuracy in all scenarios considered. The benefits of using MCMC approximation are substantial if the frequency of missing marker data is high or the number of marker alleles is low and the allelic frequency distribution is similar in both parental lines.

Models for chromatid interference with applications to recombination data.

Genetic interference means that the occurrence of one crossover affects the occurrence and/or location of other crossovers in its neighborhood. Of the three components of genetic interference, two are well modeled: the distribution of the number and the locations of chiasmata. For the third component, chromatid interference, there exists only one model. Its application to real data has not yet been published. A further, new model for chromatid interference is presented here. In contrast to the existing model, it is assumed that chromatid interference acts only in the neighborhood of a chiasma. The appropriateness of this model is demonstrated by its application to three sets of recombination data. Both models for chromatid interference increased fit significantly compared to assuming no chromatid interference, at least for parts of the chromosomes. Interference does not necessarily act homogeneously. After extending both models to allow for heterogeneity of chromatid interference, a further improvement in fit was achieved.

Growth- and breed-related changes of muscle fiber characteristics in cattle.

The objective of this study was to investigate the growth- and breed-related changes of muscle fiber characteristics in cattle and their importance to meat quality. Four cattle breeds with different growth impetus and muscularity were reared and slaughtered under experimental conditions. German Angus as a beef type, Galloway as a hardy type, Holstein Friesian as a dairy type, and double-muscled Belgian Blue as an extreme type for muscle growth were used. Between 5 and 17 bulls of each breed were slaughtered at 0, 2, 4, 6, 12, 18, and 24 mo of age. Muscle fiber traits were determined and classified by computerized image analysis, and several measures of meat quality were also determined, including shear force value, meat color, and i.m. fat content. The postnatal growth of semitendinosus muscle in cattle was characterized by a nearly 10-fold increase of muscle fiber area from birth to 24 mo of age. In the first few months after birth, a transformation of type IIA fibers into IIB fibers was found, whereas type I fibers were nearly unaffected by age. The apparent total muscle fiber number of semitendinosus muscle did not increase during postnatal life. These results confirm that the fiber number is determined in embryonic development. Throughout the study, the double-muscled Belgian Blue (BBDM) bulls had almost twice the fiber number of the other breeds, emphasizing a more extensive hyperplasia of muscle fibers during embryonic development in BBDM compared with the other three breeds. The apparent number of type I fibers was, however, not affected by breed, which suggests that the additional fibers found in BBDM postnatally were type IIB and IIA fibers. We did not find significant differences in muscle fiber total number, muscle fiber type frequencies, or meat quality characteristics among breeds, with the exception of BBDM. Having pooled the four breeds, paler meat was related to a higher frequency of type IIB fibers, a lower area of type IIA and type I fiber, and a higher total muscle fiber number. These findings based on data of double muscling give us some hints for biological causes for the variation of meat quality. Further investigation, in particular within each breed, is necessary to identify the superior fiber traits for bovine meat production.

Differential immunodiagnosis between cystic hydatid disease and other cross-reactive pathologies.

We assessed an Echinococcus granulosus hydatid fluid antigen-ELISA (EgHF-ELISA) as a serologic prescreening test for E. granulosus infections, supplemented by more specific confirmatory tests, including arc-5 immunoprecipitation and antigen B subunit 8-kD immunoblotting. The diagnostic sensitivity of the EgHF-ELISA was 91%. With regard to the test specificity of the EgHF-ELISA (overall = 82%), we observed relatively frequent cross-reactions in tumor patients (6%) and in patients with other parasitic diseases. Cestode-related cross-reactivity can be resolved by the complementary use of E. multilocularis-specific antigens or Taenia solium cysticercosis-specific immunoblotting. Immunoblotting based upon the detection of antibody reactivity to the 8-kD antigen of EgHF, or if appropriately detectable, to the 29-kD and 34-kD bands exhibited a 91% diagnostic sensitivity and an overall specificity of 97% or 94%, respectively. Thus, immunoblotting provided a 99% discrimination between seropositive pre-operative cystic hydatid disease cases and cross-reactive non-cestode parasitic infections or malignancies.

Effects of nicotine abstinence and menstrual phase on task performance.

Both menstrual phase and nicotine have been shown to affect task performance. Though conflicting results have been reported, at least one well-controlled study has demonstrated that women at midluteal phase show superior performance on speech articulation and speeded motor coordination tests, but poorer performance on perceptual-spatial tests, than during menses. Smokers have demonstrated superior performance on numerous tasks following nicotine than following placebo. To explore the separate and combined influence of these factors, we studied 13 regularly-menstruating smokers using a two (smoking vs. 12 hours' abstinence) by two (menstrual vs. midluteal phase) factorial design. During each session, subjects completed a test battery including two speeded motor coordination tasks, a computerized reaction time test, and the Stroop (1935) color/word test. Subjects completed the Stroop color and color-word tasks significantly faster after ad lib smoking than after overnight abstinence. No other significant differences emerged. Our findings replicate, in an all-female sample, previous reports that speed of cognitive processing is reduced by nicotine abstinence (or enhanced by nicotine administration). Our failure to observe menstrual cycle effects raises the possibility that the anti-estrogenic effects of smoking may attenuate phase differences in performance.

Severe acute oxidant exposure: morphological damage and aerobic metabolism in the lung.

Groups of male rats were exposed to acute doses of oxygen, ozone, or paraquat which produced equivalent mortality (25-30%) over a 28 day post-exposure period. Quantitative evaluation of morphological changes indicated the primary response to be edema and inflammation with only slight fibrosis being apparent by the end of the observation period. Aerobic pulmonary metabolism was inhibited in lungs from animals exposed to oxygen and ozone as evidenced by decreased oxygen consumption; however, this was transient and O2 consumption returned to normal within 24 hours after removal from the exposure chamber. Conversely, treatment with paraquat caused an immediate, transient stimulation of O2 consumption. Glucose metabolism was unaltered by the gas exposures and, as previously reported, was initially stimulated by paraquat treatment. In vitro, only paraquat altered both O2 consumption and glucose metabolism when added to lung slice preparations; ozone had no effect. Oxygen did not alter O2 consumption but caused a slight biphasic response in glucose metabolism. Aerobic metabolism is relatively unchanged by these doses of oxygen and ozone which result in the death of 25-30% of all treated animals. Even though paraquat produces similar morphologic changes, it may represent a more severe metabolic insult than "equivalent" doses of oxygen or ozone. Also, if interstitial pulmonary fibrosis is a desired result of experimental exposure, rats may not be a suitable model for oxidant induced lung injury.