Henner Simianer

Abstract: Due to consistent increases of inbreeding of on average 0.95% per generation in layer populations, selection tools should consider both genetic gain and genetic relationships in the long term. The optimum genetic contribution theory using official estimated breeding values for egg production was applied for 3 different lines of a layer breeding program to find the optimal allocations of hens and sires. Constraints in different scenarios encompassed restrictions related to additive genetic relationships, the increase of inbreeding, the number of selected sires and hens, and the number of selected offspring per mating. All these constraints enabled higher genetic gain up to 10.9% at the same level of additive genetic relationships or in lower relationships at the same gain when compared with conventional selection schemes ignoring relationships. Increases of inbreeding and genetic gain were associated with the number of selected sires. For the lowest level of the allowed average relationship at 10%, the optimal number of sires was 70 and the estimated breeding value for egg production of the selected group was 127.9. At the highest relationship constraint (16%), the optimal number of sires decreased to 15, and the average genetic value increased to 139.7. Contributions from selected sires and hens were used to develop specific mating plans to minimize inbreeding in the following generation by applying a simulated annealing algorithm. The additional reduction of average additive genetic relationships for matings was up to 44.9%. An innovative deterministic approach to estimate kinship coefficients between and within defined selection groups based on gene flow theory was applied to compare increases of inbreeding from random matings with layer populations undergoing selection. Large differences in rates of inbreeding were found, and they underline the necessity to establish selection tools controlling long-term relationships. Furthermore, it was suggested to use optimum genetic contribution theory for conservation schemes or, for example, the experimental line in our study.

Abstract: 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.

Abstract: 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.

Abstract: A Bayesian nonparametric form of regression based on Dirichlet process priors is adapted to the analysis of quantitative traits possibly affected by cryptic forms of gene action, and to the context of SNP-assisted genomic selection, where the main objective is to predict a genomic signal on phenotype. The procedure clusters unknown genotypes into groups with distinct genetic values, but in a setting in which the number of clusters is unknown a priori, so that standard methods for finite mixture analysis do not work. The central assumption is that genetic effects follow an unknown distribution with some "baseline" family, which is a normal process in the cases considered here. A Bayesian analysis based on the Gibbs sampler produces estimates of the number of clusters, posterior means of genetic effects, a measure of credibility in the baseline distribution, as well as estimates of parameters of the latter. The procedure is illustrated with a simulation representing two populations. In the first one, there are 3 unknown QTL, with additive, dominance and epistatic effects; in the second, there are 10 QTL with additive, dominance and additive x additive epistatic effects. In the two populations, baseline parameters are inferred correctly. The Dirichlet process model infers the number of unique genetic values correctly in the first population, but it produces an understatement in the second one; here, the true number of clusters is over 900, and the model gives a posterior mean estimate of about 140, probably because more replication of genotypes is needed for correct inference. The impact on inferences of the prior distribution of a key parameter (M), and of the extent of replication, was examined via an analysis of mean body weight in 192 paternal half-sib families of broiler chickens, where each sire was genotyped for nearly 7,000 SNPs. In this small sample, it was found that inference about the number of clusters was affected by the prior distribution of M. For a set of combinations of parameters of a given prior distribution, the effects of the prior dissipated when the number of replicate samples per genotype was increased. Thus, the Dirichlet process model seems to be useful for gauging the number of QTLs affecting the trait: if the number of clusters inferred is small, probably just a few QTLs code for the trait. If the number of clusters inferred is large, this may imply that standard parametric models based on the baseline distribution may suffice. However, priors may be influential, especially if sample size is not large and if only a few genotypic configurations have replicate phenotypes in the sample.

Abstract: A two-step procedure is presented for analysis of theta (FST) statistics obtained for a battery of loci, which eventually leads to a clustered structure of values. The first step uses a simple Bayesian model for drawing samples from posterior distributions of theta-parameters, but without constructing Markov chains. This step assigns a weakly informative prior to allelic frequencies and does not make any assumptions about evolutionary models. The second step regards samples from these posterior distributions as 'data' and fits a sequence of finite mixture models, with the aim of identifying clusters of theta-statistics. Hopefully, these would reflect different types of processes and would assist in interpreting results. Procedures are illustrated with hypothetical data, and with published allelic frequency data for type II diabetes in three human populations, and for 12 isozyme loci in 12 populations of the argan tree in Morocco.

Abstract: Summary This study aimed to assess genetic diversity within and between nine Vietnamese local chicken breeds and two Chinese breeds included for comparison. Genotyping 29 microsatellites revealed high diversity of both Vietnamese and Chinese breeds. Cluster analysis using the structure software suggested six clusters as the most likely grouping of the 11 breeds studied. These groups encompassed four homogeneous clusters, one formed by the two Chinese breeds and the other three representing a single breed each: the Mekong Delta breed Ac, the South Central Coast breed Choi, and the Red River Delta breed Dong Tao. The six remaining breeds formed two additional admixed clusters.

Abstract: The potential of the minipig as a platform for future developments in genomics, high density biology, transgenic technology, in vitro toxicology and related emerging technologies was reviewed. Commercial interests in the pig as an agricultural production species have driven scientific progress in these areas. There is no equivalent economic driver for progress in the dog or the monkey. As a result the available knowledge-bases are much greater for pigs (than for dogs or monkeys) in many areas (physiology, disease, genetics, immunology etc). Fundamental genomic knowledge and phenotypic characterization in regard to the pig is well in advance of the dog or the monkey and basic knowledge of the pig is therefore likely to stay ahead of the other two species. While the emerging technologies are essentially "species neutral" and can in principle be applied to all species, for all the technologies that we examined, basic knowledge and technical capabilities are greater for the pig than the dog or monkey. In concrete terms, in application to safety testing we have seen that: (i) The Göttingen minipig is well positioned for the performance of toxicogenomics studies, (ii) The close sequence homology between pigs and humans suggest that minipigs will be useful for the testing of biotechnology products (and possibly for in silico toxicology) and (iii) the minipig is the only non-rodent toxicology model where transgenic animals can be readily generated, and reproductive technologies are well developed in the pig. These properties should also make the minipig an interesting model for the testing of biotechnology products. These factors all support the idea that the minipig is well placed to meet the challenges of the emerging technologies and the toxicology of the future; it also seems likely that the minipig can be an advantageous model for the testing of biotechnology products.

Abstract: 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.

Abstract: The Göttingen Minipig is a laboratory animal of worldwide importance. The breed was developed in the 1960's at the University of Göttingen, Germany, using the founder breeds Minnesota Minipigs, Vietnamese Potbelly Pig and German Landrace. After the initial period under free range conditions the population was stocked under high hygienic standards. In 1992 an exclusive licence contract was made between Ellegaard Göttingen Minipigs ApS in Denmark and the University of Göttingen. Since 2002 the production and marketing of Göttingen Minipigs in the USA is managed by Marshall Farms, Inc. under licence from Ellegaard Göttingen Minipigs A/S. Today, there are three Danish, one American and one German population. The genetic management for all populations is provided by the University of Göttingen. The main focus is the maintenance and reduction of inbreeding and genetic drift, the maintenance of a high degree of uniformity and genetic progress in the main selection traits. The main selection trait in the past was the number of piglets born alive. By producing many piglets per sow and year, a fast genetic exchange of breeding animals could be achieved leading to a minimised inbreeding in the populations. To satisfy the market demands of a small and easy to handle minipig and to overcome the problem of an antagonistic relationship between litter size and body weight, the trait body weight reduction was included in the selection scheme using a restricted selection index. It is planned for the future to include temperament traits in the breeding scheme. Due to fast developments in genome-based breeding applications, these new methods can soon be implemented for an efficient control of genetic drift and inbreeding or even for genome-based selection.

Abstract: The genetic diversity of the world's livestock populations is decreasing, both within and across breeds. A wide variety of factors has contributed to the loss, replacement or genetic dilution of many local breeds. Genetic variability within the more common commercial breeds has been greatly decreased by selectively intense breeding programmes. Conservation of livestock genetic variability is thus important, especially when considering possible future changes in production environments. The world has more than 7500 livestock breeds and conservation of all of them is not feasible. Therefore, prioritization is needed. The objective of this article is to review the state of the art in approaches for prioritization of breeds for conservation, particularly those approaches that consider molecular genetic information, and to identify any shortcomings that may restrict their application. The Weitzman method was among the first and most well-known approaches for utilization of molecular genetic information in conservation prioritization. This approach balances diversity and extinction probability to yield an objective measure of conservation potential. However, this approach was designed for decision making across species and measures diversity as distinctiveness. For livestock, prioritization will most commonly be performed among breeds within species, so alternatives that measure diversity as co-ancestry (i.e. also within-breed variability) have been proposed. Although these methods are technically sound, their application has generally been limited to research studies; most existing conservation programmes have effectively primarily based decisions on extinction risk. The development of user-friendly software incorporating these approaches may increase their rate of utilization.

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Abstract: Free ranging chickens reared by smallholder farmers represent genetic diversity suited for particular environments and shaped by the socio-economic and cultural values of the farming systems. This study sought to investigate the existence of chicken strains and evaluate the breeding goals and strategies used by village chicken farmers in Zimbabwe. A semi-structured questionnaire was administered to 97, 56, 70, 104 and 37 households randomly selected from five agro-ecological-zones I-V, respectively. Fifteen chicken strains mostly defined by morphological traits were reported in the five eco-zones. Production criteria such as body size, and fertility were highly ranked (ranging from 1.3-2.6) by farmers across all the eco-zones, while cultural traits were the least preferred production traits. As a common breeding practice, farmers chose the type of hens and cocks to retain for breeding purposes and these randomly mixed and mated with others from community flocks. Chicken body size was ranked the major determinant in choosing breeding animals followed by mothering ability, and fertility. More households culled chickens associated with poor reproductive performance, poor growth rates and those intolerant to disease pathogens. The focus on many negatively correlated production traits and the absence of farmer records compromises breeding strategies in these production systems.

Abstract: The objective of this study was to compare a conventional dairy cattle breeding program characterized by a progeny testing scheme with different scenarios of genomic breeding programs. The ultimate economic evaluation criterion was discounted profit reflecting discounted returns minus discounted costs per cow in a balanced breeding goal of production and functionality. A deterministic approach mainly based on the gene flow method and selection index calculations was used to model a conventional progeny testing program and different scenarios of genomic breeding programs. As a novel idea, the modeling of the genomic breeding program accounted for the proportion of farmers waiting for daughter records of genotyped young bulls before using them for artificial insemination. Technical and biological coefficients for modeling were chosen to correspond to a German breeding organization. The conventional breeding program for 50 test bulls per year within a population of 100,000 cows served as a base scenario. Scenarios of genomic breeding programs considered the variation of costs for genotyping, selection intensity of cow sires, proportion of farmers waiting for daughter records of genotyped young bulls, and different accuracies of genomic indices for bulls and cows. Given that the accuracies of genomic indices are greater than 0.70, a distinct economic advantage was found for all scenarios of genomic breeding programs up to factor 2.59, mainly due to the reduction in generation intervals. Costs for genotyping were negligible when focusing on a population-wide perspective and considering additional costs for herdbook registration, milk recording, or keeping of bulls, especially if there is no need for yearly recalculation of effects of single nucleotide polymorphisms. Genomic breeding programs generated a higher discounted profit than a conventional progeny testing program for all scenarios where at least 20% of the inseminations were done by genotyped young bulls without daughter records. Evaluation of levels of annual genetic gain for individual traits revealed the same potential for low heritable traits (h(2) = 0.05) compared with moderate heritable traits (h(2) = 0.30), preconditioning highly accurate genomic indices of 0.90. The final economic success of genomic breeding programs strongly depends on the complete abdication of any forms of progeny testing to reduce costs and generation intervals, but such a strategy implies the willingness of the participating milk producers.

Abstract: 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.

Abstract: 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.

Abstract: In many farm animal populations, high-density single nucleotide polymorphism (SNP) genotypes are becoming available on a large scale, and routine estimation of breeding values is implemented for a multiplicity of traits. We propose to apply the basic principle of the quantitative transmission disequilibrium test (QTDT) to estimated Mendelian sampling terms. A two-step procedure is suggested, where in the first step additive breeding values are estimated with a mixed linear model and the Mendelian sampling terms are calculated from the estimated breeding values. In the second step, the QTDT is applied to these estimated Mendelian sampling terms. The resulting test is expected to yield significant results if the SNP is in sufficient linkage disequilibrium and linkage with quantitative trait loci (QTL). This principle is illustrated with a simulated data set comprising 4665 individuals genotyped for 6000 SNP and 15 true QTL. Thirteen of the fifteen QTL were significant on a genome-wide 0.1% error level. Results for the empirical power are derived from repeated samples of 1000 and 3000 genotyped individuals, respectively. General properties and potential extensions of the methodology are indicated. Owing to its computational simplicity and speed, the suggested procedure is well suited to scan whole genomes with high-density SNP coverage in samples of substantial size and for a multiplicity of different traits.

Abstract: In this study we compared different statistical procedures for estimating SNP effects using the simulated data set from the XII QTL-MAS workshop. Five procedures were considered and tested in a reference population, i.e., the first four generations, from which phenotypes and genotypes were available. The procedures can be interpreted as variants of ridge regression, with different ways for defining the shrinkage parameter. Comparisons were made with respect to the correlation between genomic and conventional estimated breeding values. Moderate correlations were obtained from all methods. Two of them were used to predict genomic breeding values in the last three generations. Correlations between these and the true breeding values were also moderate. We concluded that the ridge regression procedures applied in this study did not outperform the simple use of a ratio of variances in a mixed model method, both providing moderate accuracies of predicted genomic breeding values.

Abstract: The Goettingen minipig is a laboratory animal with increasing popularity in medical research. To get a genetically smaller minipig, a new breeding scheme with a focus on weight reduction has to be developed. Therefore, 19 505 body weight measurements of 3461 Goettingen minipigs were analysed with multiple trait models and random regression models (RRM) for the estimation of genetic parameters. Heritabilities were moderate with slightly higher values estimated with the RRM. Genetic correlations between body weight measurements at different ages were decreasing with increasing time lag between the measurements. An operational breeding goal for relative weight reduction RWR is suggested in which the weight reduction in each age class is expressed as per cent of the actual body weight and is weighted according to the proportion of animals sold in this age class. Expected genetic progress was calculated for two different selection ages (80 and 150 days). Selection at age 150 days leads to an expected genetic progress of 3.9 % RWR per year. And it is shown how the selection for RWR will modify the shape of the growth curve. On the basis of these results, a new breeding scheme with a focus on weight reduction can be implemented, which also has to account for correlated undesirable effects, like decline of fertility and increased rate of inbreeding.

Abstract: Relationships between claw disorders and test-day milk yield recorded in 2005 on 5,360 Holstein cows, kept on 11 large-scale dairy farms in eastern Germany, were analyzed in a Bayesian framework with standard linear and threshold models and recursive linear and threshold models. Four different claw disorders, digital dermatitis (DD), sole ulcer (SU), wall disorder (WD), and interdigital hyperplasia (IH), were scored as binary traits within 200 d after calving and analyzed separately. Incidences of disorders were 13.7% for DD, 16.5% for SU, 9.8% for WD, and 6.7% for IH. Heritabilities of disorders were greater when applying threshold or recursive threshold models than with linear or linear recursive models. Posterior means of genetic correlations between test-day milk production and claw disorders ranged from 0.17 to 0.44, suggesting that breeding strategies focusing on increased milk yield will increase incidences of disorders as a correlated response. A progressive path of lagged relationships was postulated for recursive models describing first the influence of test-day milk yield (MY1) on claw disorders and second, the effect of the disorder on milk production level at the following test day (MY2). In recursive models, structural coefficients describe recursive relationships at the phenotypic level. The structural coefficient lambda21 was the gradient of disease (trait 2) with respect to MY1 (trait 1) for a model with a recursive effect of trait 1 on trait 2. The increase of disease incidence of the 4 different disorders per 1-kg increase of MY1 ranged from lambda21 = 0.006 to lambda21 = 0.024 on the visible scale when applying recursive linear models, and from lambda21 = 0.003 to lambda21 = 0.016 on the underlying liability scale for recursive threshold models. The rate of change in MY2 (trait 3) with respect to the previous claw disorder is given by lambda32 for a model with a recursive effect from trait 2 to trait 3. Structural coefficients lambda32 ranged from -0.12 to -0.68 predicting that a 1-unit increase in the incidence of any disorder reduces milk yield at the following test day by up to 0.67 kg. Rank correlations between sire posterior means for the same claw disorders among different models were >0.84, but some changes in rank of sires in distinct top-10 lists were observed. Structural equation models are of increasing importance in genetic evaluations, and this study showed the possible application of recursive systems, even for categorical data.

Abstract: Genetic diversity within livestock species is threatened by extinction of breeds and by genetic drift; the need to conserve genetic diversity by conservation schemes is widely accepted. To maintain the between-breed diversity, breeds are usually kept separately in live conservation schemes. However, in some cases it might be very difficult or even impossible to conserve a highly endangered breed in a closed population. If this breed is important for diversity, it might be beneficial to merge it with one or more breeds to conserve a part of the diversity that is contributed by this breed. The present study introduces a general framework that may enable one to decide when it is beneficial to form a synthetic breed that includes highly endangered breeds to maximize conserved diversity and when to keep the breeds separate. Expected future diversities were estimated using a kinship-based diversity measure together with extinction probabilities of the breeds. Using a small hypothetical data set, the pattern of diversity and its 2 components, within-breed and between-breed diversity, were analyzed in detail when forming a synthetic breed. The suggested approach was applied to a data set of 13 central European red and yellow cattle breeds. The results suggested forming a synthetic breed by combining a nonendangered breed with 1 of the 2 highly endangered breeds, which would result in a slight increase in conserved diversity.

Abstract: The aims of the study were to evaluate the relationships among milk urea nitrogen and nonreturn rates at the phenotypic scale, and to estimate genetic parameters among milk urea nitrogen, milk yield, and fertility traits in the early period of lactation. Milk yield, protein percentage, the interval from calving to first service, and 56- and 90-d nonreturn rates were available from 73,344 Holstein cows from 2,178 different herds located in a region in northwestern Germany. Generalized linear models with a logit link function were applied to assess the phenotypic relationships. Bivariate threshold-threshold, linear-threshold, and linear-linear models, fitted in a Bayesian framework, were used to estimate genetic correlations among traits. Milk yield, protein percentage, and milk urea nitrogen were means from test-day 1 (on average 20.8 d in milk) and test-day 2 (on average 53.1 d in milk) after calving. An increase in milk urea nitrogen was associated with decreasing 56-d nonreturn rates on the phenotypic scale. At fixed levels of milk urea nitrogen, greater values of protein percentage, indicating a surplus of energy in the feed, were positively associated with nonreturn rates. Heritabilities were 0.03 for 56- and 90-d nonreturn rates, 0.07 for interval from calving to first service, 0.13 for milk urea nitrogen, and 0.19 for milk yield. Service sire explained a negligible part (below 0.15%) of the total variance for nonreturn rates. Genetic correlations between the interval from calving to first service and nonreturn rates were close to zero. The genetic correlation between nonreturn rates was 0.94, suggesting that a change from nonreturn after 90 d to nonreturn after 56 d in the national genetic evaluation would not result in any loss of information. The genetic correlation between milk yield and nonreturn after 56 d was -0.31, and between milk yield and calving to first service was 0.14, both indicating an antagonistic relationship between production and reproduction. The genetic correlation between milk yield and milk urea nitrogen was 0.44, reflecting an energy deficiency in early lactation. The genetic correlations between milk urea nitrogen and nonreturn rates were too weak (-0.19 for 56-d nonreturn rate, and -0.23 for 90-d nonreturn rate) to justify the use of milk urea nitrogen as an additional trait in genetic selection for fertility, as demonstrated by selection index calculations.

Abstract: This study sought to assess mitochondrial DNA (mtDNA) diversity and phylogeographic structure of chickens from five agro-ecological zones of Zimbabwe. Furthermore, chickens from Zimbabwe were compared with populations from other geographical regions (Malawi, Sudan and Germany) and other management systems (broiler and layer purebred lines). Finally, haplotypes of these animals were aligned to chicken sequences, taken from GenBank, that reflected populations of presumed centres of domestication. A 455-bp fragment of the mtDNA D-loop region was sequenced in 283 chickens of 14 populations. Thirty-two variable sites that defined 34 haplotypes were observed. In Zimbabwean chickens, diversity within ecotypes accounted for 96.8% of the variation, indicating little differentiation between ecotypes. The 34 haplotypes clustered into three clades that corresponded to (i) Zimbabwean and Malawian chickens, (ii) broiler and layer purebred lines and Northwest European chickens, and (iii) a mixture of chickens from Zimbabwe, Sudan, Northwest Europe and the purebred lines. Diversity among clades explained more than 80% of the total variation. Results indicated the existence of two distinct maternal lineages evenly distributed among the five Zimbabwean chicken ecotypes. For one of these lineages, chickens from Zimbabwe and Malawi shared major haplotypes with chicken populations that have a Southeast Asian background. The second maternal lineage, probably from the Indian subcontinent, was common to the five Zimbabwean chicken ecotypes, Sudanese and Northwest European chickens as well as purebred broiler and layer chicken lines. A third maternal lineage excluded Zimbabwean and other African chickens and clustered with haplotypes presumably originating from South China.

Abstract: A new approach is suggested to perform joint haplotype reconstruction and haplotype frequency estimation in families consisting of multiple full sibs where only one parent is genotyped. It can also deal with the mixed data structures with 0 and 1 parent genotyped. The approach is based on the maximum likelihood principle using the expectation-maximization algorithm and thus combines pedigree information within families and linkage disequilibrium information between families with assumption of no recombination. In a simulation study of single nucleotide polymorphisms, the new algorithm termed PMCHAP (parent multiple children haplotyping) is shown to provide significantly better results than an approximation used so far, especially providing better estimates with increasing family sizes. It will be especially helpful for research in multiparous species like pigs, dogs, fish, and many lab animals where it is easy to collect families with multiple siblings.

Abstract: National estimated breeding values of bulls from 1998 through 2006 from 12 different German artificial insemination (AI) organizations were used to determine the differences in expected and realized selection intensities for cow sire selection, considering the total merit index as well as subindexes for production, conformation, somatic cell count, fertility, and functional herd life. The expected selection intensity was derived from a Gaussian distribution and from the replacement rate describing the percentage of bulls graduated as cow sires from the total amount of progeny-tested young bulls within the AI organization and by birth year. Realized selection intensities for all indexes were derived from the selection differential of cow sires, defined as the deviation of the average index of selected cow sires from the average index of the total number of progeny-tested young bulls. A low replacement rate of cow sires was associated with relatively high realized selection intensities for the total merit, production, and conformation indexes, but was not related to the somatic cell count, fertility, and functional herd life indexes. The controlling value, defined as the ratio of realized to expected selection intensities, indicates the effectiveness of cow sire selection for different traits. Low controlling values (i.e., low realized selection intensities in combination with moderate or high expected selection intensities) suggest improvements in the step of cow sire selection, especially when discussing the total merit index. Analysis of variance revealed significant differences in expected selection intensities, realized selection intensities, and controlling values for the total merit, production, and conformation indexes between AI organizations and birth years of bulls. Artificial insemination organizations applying well-defined breeding policies (e.g., high controlling values for the total merit index) were successful in the national competition when evaluated according to the national top lists for the respective indexes, regardless of the active population size. The suggested method also allows for comparison of the importance of different indexes in selection decisions. Furthermore, controlling values can monitor additional potential in the improvement of cow sire selection with respect to improvement of the genetic level in the whole population. The development of appropriate selection tools or controlling instruments is of increasing concern for monitoring selection policies in the short term as well as for establishing sustainable breeding policies.

Abstract: To overcome limitations of diversity measures applied to livestock breeds marker based estimations of kinship within and between populations were proposed. This concept was extended from the single locus consideration to chromosomal segments of a given length in Morgan. Algorithms for the derivation of haplotype kinship were suggested and the behaviour of marker based haplotype kinship was investigated theoretically. In the present study the results of the first practical application of this concept are presented. Full sib pairs of three sub-populations of the Goettingen minipig were genotyped for six chromosome segments. After haplotype reconstruction the haplotypes were compared and mean haplotype kinships were estimated within and between populations. Based on haplotype kinships a distance measure is proposed which is approximatively linear with the number of generations since fission. The haplotype kinship distances, the respective standard errors and the pedigree-based expected values are presented and are shown to reflect the true population history better than distances based on single-locus kinships. However the marker estimated haplotype kinship reveals variable among segments. This leads to high standard errors of the respective distances. Possible reasons for this phenomenon are discussed and a pedigree-based approach to correct for identical haplotypes which are not identical by descent is proposed.

Abstract: The Goettingen minipig developed at the University of Goettingen, Germany, is a special breed for medical research. As a laboratory animal it has to be as small and light as possible to facilitate handling during experiments. For achieving the breeding goal of small body size in the future, the growth pattern of the minipig was studied. This study deals with the analysis of minipig BW by modeling growth with linear and nonlinear functions and comparing the growth of the minipigs with that of normal, fattening pigs. Data were provided by Ellegaard Goettingen minipigs, Denmark, where 2 subpopulations of the Goettingen basis population are housed. In total 189,725 BW recordings of 33,704 animals collected from birth (d 0) to 700 d of age were analyzed. Seven nonlinear growth functions and 4 polynomial functions were applied. The growth models were compared by using the Akaike's information criterion (AIC). Regarding the whole growth curve, linear polynomials of third and fourth order of fit had the smallest AIC values, indicating the best fit for the minipig BW data. Among the nonlinear functions, the logistic model had the greatest AIC value. A comparison with fattening pigs showed that the minipigs have a nearly linear BW development in the time period from birth to 160 d. Fattening pigs have very low weight gains in their first 7 wk in relation to a specific end weight. After 7 wk, fattening pigs have increased growth, resulting in a growth curve that is more sigmoid than the growth curve of the minipig. Based on these results, further studies can be conducted to analyze the growth with random regression models and to estimate variance components for optimizing the strategies in minipig breeding.

Abstract: The Goettingen minipig is a laboratory animal especially developed for medical research. For easy and comfortable handling during experiments, and to minimize costs, a low BW is essential. To breed for an even smaller minipig, genetic parameters for BW were estimated using a random regression model (RRM). The RRM was calculated using random animal, common litter environment, and permanent environment effects, respectively. Regressions for the random effects in the RRM were modeled using Legendre polynomials from second to fourth order of fit in different combinations. The model was applied to a data set that focused on the time period from 30 to 400 d of age. Eight age classes were built to consider heterogeneous residual variances. The heritabilities were moderate and ranged from 0.211 (375 d of age) to 0.254 (275 d of age). The variances initially decreased and then increased toward the end of the examined time period for permanent environment and litter effects. Genetic and phenotypic correlations between BW in different age classes decreased with increasing distance between age classes. The major eigenfunction showed positive values throughout the whole trajectory (i.e., a selection for low BW had positive effects on this trait throughout the whole range of time). On the basis of the estimated genetic parameters, a breeding scheme can be created to develop genetically smaller Goettingen minipigs in the future.

Abstract: The degree to which village chickens are integrated in the smallholder farming systems differs depending on the socio-economic, cultural and biological factors within each system. The objective of this study was to characterise the village chicken farming systems and identify possible threats to, and opportunities for, local chickens in the agro-ecological zones of Zimbabwe. A pre-tested questionnaire was administered to households randomly selected from five districts, Risitu (n=97), Hurungwe (n=56), Gutu (n=77), Gokwe-South (n=104) and Beitbridge (n=37) in eco-zones I-V, respectively. Age of head of household averaged 47 years (SD = 14.3). Land holdings per household averaged 4.82 ha (SD = 3.6). Overall, 17.7 percent of the households ranked livestock as the major source of income compared to 70.8 percent who ranked crops as the main contributor. Chicken flock size averaged 16.7 (SD = 12.4), and the highest flock sizes were observed in eco-zones I and IV. Households owning cattle, goats and other livestock assigned less important ranks to chickens. Chickens were usedmainly for the provision of meat and eggs whilst the use of chicken feathers and investment were uncommon practises. Results indicate that more support is necessary for village chickens in the non-cropping regions of the country.

Abstract: The aim of this study was to analyse racing performance data in Irish greyhounds with regard to genetic and environmental variation. Estimation of heritabilities for racing time (RT) and ranking, and the prediction of breeding values for all greyhounds in the investigated data were carried out. Data from 42,785 races in Ireland in the years 2000-2003 were available. These results were obtained from 42,880 greyhounds on 20 race tracks over a distance of 480 m. Three traits were analysed, RT, ranking and a scaled logarithmic function for RT (ART), which was used to adjust racing time to be normally distributed. The data were analysed with a bivariate animal model. The estimated heritabilities were moderate for RT (0.31) and ART (0.38), but very low for ranking (0.10). The repeatabilities were 0.56 (RT), 0.51 (ART) and 0.13 (ranking). The genetic correlations were very high, 0.99 (RT-ranking) and 0.96 (ART-ranking), while the phenotypic correlation was lower, 0.60 (RT-ranking) and 0.62 (ART-ranking). The genetic trend for the traits as well as the phenotypic change of the average RT was positive.

Abstract: Recent literature has suggested that haplotype inference through close relatives, especially from nuclear families, can be an alternative strategy in determining linkage phase and estimating haplotype frequencies. In the case of no possibility to obtain genotypes for parents, and only full-sib information being used, a new approach is suggested to infer phase and to reconstruct haplotypes. We present a maximum-likelihood method via an expectation-maximization algorithm, called FSHAP, using only full-sib information when parent information is not available. FSHAP can deal with families with an arbitrary number of children, and missing parents or missing genotypes can be handled as well. In a simulation study we compare FSHAP with another existing expectation-maximization (EM)-based approach (FAMHAP), the conditioning approach implemented in FBAT and GENEHUNTER, which is only pedigree based and assumes linkage equilibrium. In most situations, FSHAP has the smallest discrepancy of haplotype frequency estimation and the lowest error rate in haplotype reconstruction, only in some cases FAMHAP yields comparable results. GENEHUNTER produces the largest discrepancy, and FBAT produces the highest error rate in offspring in most situations. Among the methods compared, FSHAP has the highest accuracy in reconstructing the diplotypes of the unavailable parents. Potential limitations of the method, e.g., in analyzing very large haplotypes, are indicated and possible solutions are discussed.

Abstract: The primary aim of this study was to estimate variance components for traits related to embryo transfer (ET) by applying generalized linear mixed models (GLMM) for different distributions of traits (normal, binomial, and Poisson) in a synergistic context. Synergistic models were originally developed for traits affected by several genotypes, denoted as maternal, paternal, and direct effects. In the case of ET, the number of flushed ova (FO) only depends on a donor's maternal genetic effect, whereas paternal fertility must be considered for other embryo survival traits, such as the number of transferable embryos (TE), the number of degenerated embryos (DE), the number of unfertilized oocytes (UO), and the percentage of transferable embryos (PTE). Data for these traits were obtained from 4,196 flushes of 2,489 Holstein cows within 4 regions of northwest Germany from January 1998 through October 2004. Estimates of maternal heritability were 0.231 for FO, 0.096 for TE, 0.021 for DE, 0.135 for UO, and 0.099 for PTE, whereas the relative genetic impact of the paternal component was near zero. Estimates of the genetic correlations between the maternal and the paternal component were slightly negative, indicating a genetic antagonism. For the analysis of pregnancy after ET, 8,239 transfers to 6,819 different Holstein-Friesian recipients were considered by applying threshold methodology. The direct heritability for pregnancy in the recipient after ET was 0.056. The relative genetic impact of maternal and paternal components on pregnancy of recipients describing a donor's and a sire's ability to produce viable embryos was below 1%. The genetic correlations of the direct effect of the recipient with the sire of embryos (paternal effect) and the donor cow (maternal effect) for pregnancy after ET were -0.32 and -0.14, respectively. With the exception of FO and PTE (-0.17), estimates of genetic correlations among traits for the maternal site were distinctly positive, especially between FO and TE (0.74). Based on this high genetic correlation and due to the higher heritability for FO, indirect selection on FO will increase selection response in TE by about 22% compared with direct selection on TE. The negative genetic correlation of -0.27 between TE and lactation milk yield indicates the need for development of an index for bull dams in multiple ovulation and embryo transfer (MOET) breeding schemes combining production as well as traits related to ET.

Abstract: The objective of this study was to investigate the population structure of village chickens found in the five agro-ecological zones of Zimbabwe. Twenty-nine microsatellites were genotyped for chickens randomly selected from 13 populations, including the five eco-zones of Zimbabwe (n = 238), Malawi (n = 60), Sudan (n = 48) and six purebred lines (n = 180). A total of 280 alleles were observed in the 13 populations. Forty-eight of these alleles were unique to the Zimbabwe chicken ecotypes. The average number (+/-SD) of alleles/locus was 9.7 +/- 5.10. The overall heterozygote deficiency in the Zimbabwe chickens (F(IT) +/- SE) was 0.08 +/- 0.01, over 90% of which was due to within-ecotype deficit (F(IS)). Small Nei's standard genetic distances ranging from 0.02 to 0.05 were observed between Zimbabwe ecotypes compared with an average of 0.6 between purebred lines. The structure software program was used to cluster individuals to 2 </= K </= 7 assumed clusters. The most probable clustering was found at K = 6. Ninety-seven of 100 structure runs were identical, in which Malawi, Sudan and purebred lines split out as independent clusters and the five Zimbabwe ecotypes clustered into one population. The within-ecotype marker-estimated kinships (mean = 0.13) differed only slightly from the between-ecotype estimates. Results from this study lead to a rejection of the hypothesis that village chickens are substructured across agro-ecological zones but indicated high genetic diversity within the Zimbabwe chicken population.

Abstract: BACKGROUND: Inguinal and scrotal hernias are of great concern to pig producers, and lead to poor animal welfare and severe economic loss. Selection against these conditions is highly preferable, but at this time no gene, Quantitative Trait Loci (QTL), or mode of inheritance has been identified in pigs or in any other species. Therefore, a complete genome scan was performed in order to identify genomic regions affecting inguinal and scrotal hernias in pigs. Records from seedstock breeding farms were collected. No clinical examinations were executed on the pigs and there was therefore no distinction between inguinal and scrotal hernias. The genome scan utilised affected sib pairs (ASP), and the data was analysed using both an ASP test based on Non-parametric Linkage (NPL) analysis, and a Transmission Disequilibrium Test (TDT). RESULTS: Significant QTLs (p < 0.01) were detected on 8 out of 19 porcine chromosomes. The most promising QTLs, however, were detected in SSC1, SSC2, SSC5, SSC6, SSC15, SSC17 and SSCX; all of these regions showed either statistical significance with both statistical methods, or convincing significance with one of the methods. Haplotypes from these suggestive QTL regions were constructed and analysed with TDT. Of these, six different haplotypes were found to be differently transmitted (p < 0.01) to healthy and affected pigs. The most interesting result was one haplotype on SSC5 that was found to be transmitted to hernia pigs with four times higher frequency than to healthy pigs (p < 0.00005). CONCLUSION: For the first time in any species, a genome scan has revealed suggestive QTLs for inguinal and scrotal hernias. While this study permitted the detection of chromosomal regions only, it is interesting to note that several promising candidate genes, including INSL3, MIS, and CGRP, are located within the highly significant QTL regions. Further studies are required in order to narrow down the suggestive QTL regions, investigate the candidate genes, and to confirm the suggestive QTLs in other populations. The haplotype associated with inguinal and scrotal hernias may help in achieving selection against the disorder.

Abstract: The epistatic kinship describes the probability that chromosomal segments of length x in Morgan are identical by descent. It is an extension from the single locus consideration of the kinship coefficient to chromosomal segments. The parameter reflects the number of meioses separating individuals or populations. Hence it is suggested as a measure to quantify the genetic distance of subpopulations that have been separated only few generations ago. Algorithms for the epistatic kinship and the extension of the rules to set up the rectangular relationship matrix are presented. The properties of the epistatic kinship based on pedigree information were investigated theoretically. Pedigree data are often missing for small livestock populations. Therefore, an approach to estimate epistatic kinship based on molecular marker data are suggested. For the epistatic kinship based on marker information haplotypes are relevant. An easy and fast method that derives haplotypes and the respective frequencies without pedigree information was derived based on sampled full-sib pairs. Different parameters of the sampling scheme were tested in a simulation study. The power of the method decreases with increasing segment length and with increasing number of segments genotyped. Further, it is shown that the efficiency of the approach is influenced by the number of animals genotyped and the polymorphism of the markers. It is discussed that the suggested method has a considerable potential to allow a phylogenetic differentiation between close populations, where small sample size can be balanced by the number, the length, and the degree of polymorphism of the chromosome segments considered.

Abstract: Although funds for livestock conservation are limited there is little known about the optimal allocation of conservation funds. A new algorithm was used to allocate Mio US dollar 1, 2, 3, 5 or unlimited funds, discounted over 50 years, on 23 African cattle breeds conserved with four different possible conservation programs. Additionally, Mio US dollar 1 was preferably allocated to breeds with special traits. The conceptional in situ conservation programs strongly involve breeders and give them part of the responsibility for the conservation of the breed. Therefore, the pure in situ conservation was more efficient than cryoconservation or combined in situ and cryoconservation. The average annual discounted conservation cost for a breed can be as low as US dollar 1000 to US dollar 4400 depending on the design of the conservation program and the economic situation of the country of conservation. The choice of the breeds and the optimal conservation program and the amount of money allocated to each breed depend on many factors such as the amount of funds available, the conservation potential of each breed, the effects of the conservation program as well as its cost. With Mio US dollar 1, 64% of the present diversity could be maintained over 50 years, which is 13% more than would be maintained if no conservation measures were implemented. Special traits could be conserved with a rather small amount of the total funds. Diversity can not be conserved completely, not even with unlimited funds. A maximum of 92% of the present diversity could be conserved with Mio US dollar 10, leaving 8% of the diversity to unpredictable happenings. The suggested algorithm proved to be useful for optimal allocation of conservation funds. It allocated the funds optimally among breeds by identifying the most suited conservation program for each breed, also accounting for differences in currency exchange rates between the different countries.

Abstract: Milking frequencies measured at official test days were used with repeated measurement analysis to reveal the environmental and genetic impact on the milking frequency of cows in automatic milking systems. Repeated measurements were 3 test-day observations per cow within days in milk (DIM) classes, with 1,216 cows in DIM class 1 (d 0 to 99), from 1,112 cows in DIM class 2 (d 100 to 199), and from 1,004 cows in DIM class 3 (d 200 to 299) kept in 15 farms. Selection criteria for models analyzing repeated measurements were Akaike and Schwarz Bayesian values, which favored the autoregressive [AR(1)] covariance structure over the compound symmetry model. Results from the AR(1) model indicated a significant impact of fixed herd and parity effects. Milking frequencies decreased with increasing parities and were greatest for first-parity cows. High daily milk yield was associated with higher milking frequencies. Heritabilities for milking frequency were 0.16, 0.19, and 0.22 in DIM classes 1, 2, and 3, respectively, from the AR(1) model. Higher heritabilities in the later stage of lactation were due to a substantial reduction of the residual variance. Genetic correlations between test-day milk yield and daily milking frequency were in the range of 0.46 to 0.57 for all DIM classes and between milking frequency and somatic cell score were near zero. For verification of results, milking frequencies of the same cows obtained from herd management programs were averaged within DIM classes. Heritabilities were slightly above the values from the AR(1) model. In conclusion, heritabilities for milking frequency in automatic milking systems are moderate enough to incorporate this behavioral trait in a combined breeding goal. The inevitable improvement of labor efficiency in dairy cattle farming demands such cows going easily and voluntarily in automatic milking systems.

Abstract: A fully Bayesian method for quantitative genetic analysis of data consisting of ranks of, e.g., genotypes, scored at a series of events or experiments is presented. The model postulates a latent structure, with an underlying variable realized for each genotype or individual involved in the event. The rank observed is assumed to reflect the order of the values of the unobserved variables, i.e., the classical Thurstonian model of psychometrics. Parameters driving the Bayesian hierarchical model include effects of covariates, additive genetic effects, permanent environmental deviations, and components of variance. A Markov chain Monte Carlo implementation based on the Gibbs sampler is described, and procedures for inferring the probability of yet to be observed future rankings are outlined. Part of the model is rendered nonparametric by introducing a Dirichlet process prior for the distribution of permanent environmental effects. This can lead to potential identification of clusters of such effects, which, in some competitions such as horse races, may reflect forms of undeclared preferential treatment.

Abstract: Recent literature has suggested that haplotype inference through close relatives, especially from nuclear families can be an alternative strategy in determining the linkage phase. In this paper, haplotype reconstruction and estimation of haplotype frequencies via expectation maximization (EM) algorithm including nuclear families with only one parent available is proposed. Parent and his (her) child are treated as parent-child pair with one shared haplotype. This reduces the number of potential haplotype pairs for both parent and child separately, resulting in a higher accuracy of the estimation. In a series of simulations, the comparisons of PHASE, GENEHUNTER, EM-based approach for complete nuclear families and our approach are carried out. In all situations, EM-based approach for trio data is comparable but slightly worse error rate than PHASE, our approach is slightly better and much faster than PHASE for incomplete trios, the performance of GENEHUNTER is very bad in simple nuclear family settings and dramatically decreased with the number of markers being increased. On the other hand, the comparison result of different sampling designs demonstrates that sampling trios is the most efficient design to estimate haplotype frequencies in populations under same genotyping cost.

Abstract: Conservation of genetic diversity in farm animal species can be achieved by preventing extinction of breeds and by reducing genetic drift within breeds. It is suggested to use the expected number of alleles segregating in the species after a given time period as objective function in the design of conservation strategies. A formal approach is presented to predict this quantity based on marker information, accounting for extinction probability of breeds and effective population size within breeds as the major component of genetic drift. Based on this model, relative efficiency of different strategies of diversity conservation can be quantified. Formulas are given to derive the marginal expected number of alleles with respect to genetic drift within population and extinction probability, respectively. The suggested approach is illustrated with an example of 13 European cattle breeds. With the assumed parameters, drift is shown to be the major force leading to loss of alleles, and different breeds are prioritized for activities to reduce risk of extinction and for measures to reduce genetic drift, respectively. Although different aspects of the model need to be further refined, the suggested methodology provides a general and flexible tool to derive the optimum conservation strategy in various scenarios.

Abstract: The primary aim of this study was to estimate heritabilities for different types of claw and foot disorders and the genetic relationship of disorders with milk yield and selected conformation traits by applying logistic models in Holstein dairy cattle. The study included data from 5634 Holstein cows kept on large-scale dairy farms in Eastern Germany. Dichotomous response variables were the presence or absence of the disorder in 2003. Cows that were present in herds for <6 wk in 2003 were excluded from the analysis. Incidences, disregarding repeated measurements, for digital dermatitis (DD), sole ulceration (SU), wall disorder (WD), and interdigital hyperplasia (IH) in rear legs were 13.2, 16.1, 9.6, and 6.3%, respectively. The herd effect was highly significant for all disorders. Incidences increased with increasing parities for SU and WD, but were highest among heifers for DD. High milk yield at the first 2 test d after calving was associated with a greater risk for claw and foot disorders in the same lactation. Estimates of heritability were 0.073 for DD, 0.086 for SU, 0.104 for WD, and 0.115 for IH. Genetically, health problems appear to occur in clusters (i.e., a cow showing one disease has an increased genetic risk of showing another claw disease). This phenomenon was also observed between claw and foot disorders and the somatic cell score. Genetic correlations between milk yield in early lactation and disorders were 0.240 for DD, 0.057 for SU, 0.270 for WD, and 0.336 for IH, indicating a physiological antagonism. Correlations between breeding values for claw and foot disorders of bulls and official breeding values for functional type traits were mostly favorable. Routine recording of claw data will offer a new chance to improve claw health within the population as was elaborated by different scenarios applying selection index procedures.

Abstract: Information on costs and benefits of conservation programmes for cattle is scarce in the literature and mainly available for Europe. This study aims at simulating cost of and benefits from different kinds of conservation programmes designed for indigenous African cattle. The programmes include installation of a herdbook and activities to promote the breed (HB), in situ conservation with a sire rotation scheme (IS), cryoconservation of semen (CC) and CC combined with in situ conservation (IC). The results indicate that cost of the analysed conservation programmes was generally higher than those reported in the literature for comparable schemes. If cost per effective population size conserved is considered, programmes analysed in this study do not appear to be more expensive. The proposed rotation scheme in IS can be applied to many different production systems and prove to be effective with regard to low increase in kinship. Reduction in extinction probability is found to be higher for conservation programmes that strongly involve farmers and give them part of the responsibility for the breeding population. IC was most efficient with regard to cost per effective population size conserved. However, if cost per reduction in endangerment is considered as criterion for the efficiency of a programme, IS, HB and CC are superior to IC. These findings suggest that decisions on conservation programmes should be based on multiple criteria, and not just on cost per effective population size.

Abstract: A total of 2122 single sperm from 35 bulls belonging to six different paternal half-sib groups were analysed with respect to two markers in the bovine pseudoautosomal region (PAR) and sex-specific loci on the X and Y chromosomes, respectively. A segregation ratio significantly different from 1:1 was observed in a test over all families, with a higher proportion of X-bearing gametes (53.5%). The analysis of recombination conducted separately for X- and Y-bearing sperm showed that X-bearing sperm cells possess highly significant individual and between-family variability in recombination rate, whereas Y-bearing sperm show linkage homogeneity. To test whether the two phenomena are related, different logistic regression models were fitted to the data. The results show that sex ratio significantly correlates with changes in recombination rate among X-bearing but not among Y-bearing sperm. Different hypotheses to explain these observations are discussed.

Abstract: Genetic mapping functions translate the observed recombination rate between two loci into the corresponding map distance in Morgan units. Different mapping functions give different weights to multiple crossing over and therefore lead to different results. This points out that not every function is best suited to fit a data set. The data used in this study originated from 2214 sperm from 37 Norwegian bulls, which were genotyped for 11 markers. The optimal functions for the chromosomes 6, 23 and the sex chromosome of cattle were derived using the maximum likelihood method, the likelihood ratio test and empirical discriminant analysis. It became apparent that for each chromosome a different function fitted the data best. These were the function of Rao et al. (Human Heredity 1977, 27, 99-104) with p = 0.63 for chromosome 6, the function of Goldgar & Fain (American Journal of Human Genetics 1988, 43, 38-45) with C0 = 0.42, C1 = 0.47, C2 = 0.07 and C3 = 0.04 for chromosome 23 and the function of Felsenstein (Genetics 1979, 91, 769-75) with K = 0.23 for the sex chromosome. The well known functions of Haldane (Journal of Genetics 1919, 8, 299-309) and Kosambi (Annals of Eugenics 1944, 12, 172-5) were shown to be suboptimal in most cases. A function is said to be multilocus feasible if the evaluation of the probability of all possible recombination events does not lead to negative values. The optimal function for chromosome 23 turned out to be multilocus feasible, whereas the functions for chromosome 6 and the sex chromosome were not. The choice of the correct mapping function is shown to have a considerable impact in mapping studies, when double recombinations have to be taken into account. Since there is no unique best mapping function, it is argued that it might be useful to use a simple parametric mapping function (like the one of Felsenstein 1979) and to estimate the respective parameter specifically for a given data set.

Abstract: We have conducted a study based on single sperm typing in a family design to assess patterns of variability of the male recombination rate in cattle. 2214 sperm of 37 bulls were typed for 11 loci on bovine Chromosomes (Chrs) 6, 23, and the sex chromosomes. Statistically significant individual variability of the recombination rate was observed for one interval in the pseudoautosomal region (PAR) of the bovine sex chromosomes; one marker interval on bovine Chr 23 exhibited individual variability that was close to significance. Thirty-five of the bulls were members of six paternal halfsib groups, and highly significant variability between families was found for one interval in the PAR. This variability may be due to DNA sequence differences in the PAR or to a genetic control of the recombination activity in this region. It is demonstrated that differences in the recombination rate of the magnitude observed in the present study may have a considerable impact on the power of QTL mapping experiments as well as on the sustainability of marker-assisted selection strategies.

Abstract: Evidence for close genetic linkage between the loci for serum albumin (ALB) and vitamin D binding protein (GC) in sheep is presented. No recombinants were found in 28 informative offspring of a single ram family. The recombination frequency between the two loci was estimated to be in the range of 0 to 10%. No sign of linkage was observed between the ALB-GC complex and transferrin.

Abstract: Data included observations on more than 200,000 first lactations of Norwegian cattle. Milk yield, fat and protein percentages, and observations on mastitis, ketosis, and presence of disease (binary coding of 0 or 1) were analyzed. Following Bayesian principles and applying the threshold concept, dispersion parameters for the binary traits (on the underlying scale) with continuous production traits were estimated. Heritabilities were .27, .34, and .43 for milk yield, fat percentage, and protein percentage, respectively. Heritabilities for the disease traits were .05 to .13 but may be inconsistent because of methodology problems with small sire by herd-year-season subclass size. Genetic correlations between milk yield and all three disease traits were above .5, indicating an undesirable relationship. Genetic correlations between ketosis and the content traits were -.38 to -.65; low component percentages were associated with high ketosis frequencies. Ignoring diseases in breeding programs may lead to undesirable correlated selection responses when selecting on milk yield.

Abstract: