John W. James

A genealogical survey of Australian registered dog breeds.

Breeding practices were analysed for 32 registered dog breeds representing very small registries (120 Central Asian shepherd dogs) through to very large registries (252,521 German shepherd dogs) in Australia. The vast majority (91%) of registered kennels in Australia that were sampled did not regularly employ either close breeding or popular sire usage in their kennels and the weighted mean inbreeding coefficient of Australian pedigree dogs was <5%. Australian breed mean inbreeding coefficients ranged from 0% (Central Asian shepherd dog) to 10.1% (Bichon Frise). Breed effective population sizes ranged from 26 (Ibizan hound) to 1090 (Golden retriever), comparable with other species of domesticated animals. The relatively low levels of inbreeding suggest that pedigree dog disorders are unlikely to arise frequently from the use of popular sires or close breeding in Australian registered dog breeds. It is possible that deleterious allele fixation might be driven by founder effects, genetic drift or adverse selection practices, which were not assessed in this analysis. European popular sire definitions should be revisited for rare breeds.

Genotype by Environment Interaction in Farm Animals

Interactions between genotype and environment are discussed in relation to genetic improvement of farm animals. Different types of classification are considered, with emphasis on their implications. A variety of statistical methods which can be used for the analysis of interactions between genotype and environment are discussed. The use of correlated response theory to predict responses in the selection environment and in other environments is described. Some examples are given in illustration, but no attempt has been made at an exhaustive compilation of experimental data. The comparison of different strategies such as development of a separate strain for each environment and improvement of a single strain for average performance over all environments is summarised. The effect of selection on sensitivity to environmental change is discussed. Adaptation to, or fitness in, specific environments is often an important part of such interactions.

Development of a highly fecund inbred strain of mice

A highly fecund inbred mouse line has been established from the Quackenbush Swiss (QS) outbred strain by full-sib inbreeding combined with selection for high number of pups born alive (NBA) and low interlitter interval (ILI). After more than 50 generations of inbreeding and selection, this line, named QSi5, has an NBA of 13.4 and an ILI of 29 days, averaged over the first four parities, and a total productivity of 50.7 NBA. With its exceptional reproductive performance, this line will be very useful in the creation of resources (including advanced intercross lines) for analysis of quantitative trait loci for a wide range of traits, and for the cost-effective creation of congenic lines.

Heritability and Phenotypic Variation of Canine Hip Dysplasia Radiographic Traits in a Cohort of Australian German Shepherd Dogs

Canine Hip Dysplasia (CHD) is a common, painful and debilitating orthopaedic disorder of dogs with a partly genetic, multifactorial aetiology. Worldwide, potential breeding dogs are evaluated for CHD using radiographically based screening schemes such as the nine ordinally-scored British Veterinary Association Hip Traits (BVAHTs). The effectiveness of selective breeding based on screening results requires that a significant proportion of the phenotypic variation is caused by the presence of favourable alleles segregating in the population. This proportion, heritability, was measured in a cohort of 13,124 Australian German Shepherd Dogs born between 1976 and 2005, displaying phenotypic variation for BVAHTs, using ordinal, linear and binary mixed models fitted by a Restricted Maximum Likelihood method. Heritability estimates for the nine BVAHTs ranged from 0.14–0.24 (ordinal models), 0.14–0.25 (linear models) and 0.12–0.40 (binary models). Heritability for the summed BVAHT phenotype was 0.30±0.02. The presence of heritable variation demonstrates that selection based on BVAHTs has the potential to improve BVAHT scores in the population. Assuming a genetic correlation between BVAHT scores and CHD-related pain and dysfunction, the welfare of Australian German Shepherds can be improved by continuing to consider BVAHT scores in the selection of breeding dogs, but that as heritability values are only moderate in magnitude the accuracy, and effectiveness, of selection could be improved by the use of Estimated Breeding Values in preference to solely phenotype based selection of breeding animals.

Estimated Breeding Values for Canine Hip Dysplasia Radiographic Traits in a Cohort of Australian German Shepherd Dogs

Canine hip dysplasia (CHD) is a serious and common musculoskeletal disease of pedigree dogs and therefore represents both an important welfare concern and an imperative breeding priority. The typical heritability estimates for radiographic CHD traits suggest that the accuracy of breeding dog selection could be substantially improved by the use of estimated breeding values (EBVs) in place of selection based on phenotypes of individuals. The British Veterinary Association/Kennel Club scoring method is a complex measure composed of nine bilateral ordinal traits, intended to evaluate both early and late dysplastic changes. However, the ordinal nature of the traits may represent a technical challenge for calculation of EBVs using linear methods. The purpose of the current study was to calculate EBVs of British Veterinary Association/Kennel Club traits in the Australian population of German Shepherd Dogs, using linear (both as individual traits and a summed phenotype), binary and ordinal methods to determine the optimal method for EBV calculation. Ordinal EBVs correlated well with linear EBVs (r = 0.90–0.99) and somewhat well with EBVs for the sum of the individual traits (r = 0.58–0.92). Correlation of ordinal and binary EBVs varied widely (r = 0.24–0.99) depending on the trait and cut-point considered. The ordinal EBVs have increased accuracy (0.48–0.69) of selection compared with accuracies from individual phenotype-based selection (0.40–0.52). Despite the high correlations between linear and ordinal EBVs, the underlying relationship between EBVs calculated by the two methods was not always linear, leading us to suggest that ordinal models should be used wherever possible. As the population of German Shepherd Dogs which was studied was purportedly under selection for the traits studied, we examined the EBVs for evidence of a genetic trend in these traits and found substantial genetic improvement over time. This study suggests the use of ordinal EBVs could increase the rate of genetic improvement in this population.

Symmetry of hip dysplasia traits in the German Shepherd Dog in Australia

Canine hip dysplasia (CHD) is a common and debilitating developmental condition of the canine coxofemoral (hip) joint, exhibiting a multifactorial pattern of inheritance. British Veterinary Association hip traits (BVAHTs) are nine radiographic features of hips used in several countries to ordinally score both the right and left hip of potential breeding candidates to assess their suitability for breeding. The objective of this study was to examine some aspects of the relationship between contralateral scores for each BVAHT in a cohort of 13 124 Australian-registered German Shepherd Dogs. Goodman and Kruskal gamma coefficients of 0.48-0.95 and correlation coefficients of 0.50-0.74 demonstrate that the association between right and left hip scores varies between moderate and strong for BVAHTs. Principal component analysis of scores detected a sizeable left-versus-right effect, a finding supported by symmetry and quasi-symmetry analyses which found that seven of the nine BVAHTs display significant marginal asymmetry. Dogs showing asymmetry for one BVAHT are significantly more likely to display asymmetry at other BVAHTs. When asymmetry is expressed as a binary trait (either symmetrical or asymmetrical), it displays low to moderate heritability. Estimates of genetic correlations between right and left scores are very high for all BVAHTs (>0.945), suggesting right and left scores for each BVAHT are largely determined by the same set of genes. The marginal asymmetries are therefore more likely to be of environmental and non-additive genetic origin. In breeding programmes for CHD, we recommend that scores from both hips be used to estimate breeding values, with a term for side-of-hip included in the model to account for score variation owing to asymmetry.

Predicting the annual effective size of livestock populations

Effective population size (Ne) is an important parameter determining the genetic structure of small populations. In natural populations, the number of adults (N) is usually known and Ne can be estimated on the basis of an assumed ratio Ne/N, usually found to be close to 0.5. In farm animal populations, apart from using pedigrees or genetic marker information, Ne can be estimated from the number N of breeding animals, and a value of 1 is commonly assumed for the ratio Ne/N. The purpose of this paper is to show the relation between effective population size and breeding herd size in livestock species. With overlapping generations, Ne can be predicted knowing the number of individuals entering the population per generation and the variance of family size, the latter being directly related to the survival pattern (or replacement policy) in the breeding herd. Assuming an ideal survivorship leading to a geometric age distribution, it can be shown that the number of breeding animals tends to overestimate effective size, particularly in early-maturing species. The ratio of annual effective size to the number of breeding animals is shown to be equal to [1 + (a- 1)(1 - s)]2/(1 - s2), where a is the age at first offspring and s is the survival rate (including culling) of the parents between successive births. This expression shows to what extent inbreeding may be determined by demography or culling policy independently of the actual herd size. In many situations a fast replacement or an early culling will increase annual effective size. Consequences for the management of small populations are discussed.

Genetic Correlations among Canine Hip Dysplasia Radiographic Traits in a Cohort of Australian German Shepherd Dogs, and Implications for the Design of a More Effective Genetic Control Program

Canine hip dysplasia (CHD) is a common musculoskeletal disease in pedigree dog populations. It can cause severe pain and dysfunction which may require extensive medication and/or surgical treatment and often ultimately requires humane euthanasia. CHD has been found to be moderately heritable and, given its impact on welfare, should be considered an imperative breeding priority. The British Veterinary Association/Kennel Club scoring method is one of several measures used to assess the genetic propensity of potential breeding stock for dysplastic changes to the hips based on radiographic examination. It is a complex measure composed of nine ordinal traits, intended to evaluate both early and late dysplastic changes. It would be highly desirable if estimated breeding values (EBVs) for these nine traits were consolidated into a simpler, EBV-based, selection index more easily usable by breeders. A multivariate analysis on the phenotype scores from an Australian cohort of 13,124 German Shepherd Dogs (GSDs) returned genetic correlations between 0.48–0.97 for the nine traits which fell into two trait groups, Group 1 reflecting early changes (“laxity”) and Group 2 reflecting late changes (“osteoarthritis”). Principal components analysis of the ordinal EBVs suggested the same pattern, with strong differentiation between “laxity” and “osteoarthritis” traits in the second component. Taking account of all results, we recommend interim use of two selection indexes: the first being the average of ordinal EBVs for “laxity” traits and the second being the average of ordinal EBVs for “osteoarthritis” traits. The correlation between these two selection indexes (0.771–0.774) is sufficiently less than unity enabling the selection of dogs with different genetic propensity for laxity and for osteoarthritic CHD changes in GSDs; this may also be applicable in other breeds. Dogs with low propensity for severe osteoarthritic change in the presence of laxity may be of interest both in molecular research and breeding programs.

Lethal genetic disorder in Poll Merino/Merino sheep in Australia

OBJECTIVES Characterise a lethal genetic disorder in Poll Merino/Merino sheep DESIGN Pathological description of a new congenital multisystem disorder in a commercial sheep flock, and analysis of breeding data collected each lambing season between 2004 and mid-lambing season 2010. PROCEDURE Necropsies were conducted on six affected lambs and the mode of inheritance of the disorder was determined by pedigree and segregation analyses. RESULTS The affected lambs were dwarfs with multiple defects in several organs, including skeleton, heart, liver and kidneys. The disorder has been named brachygnathia, cardiomegaly and renal hypoplasia syndrome (BCRHS). Segregation analysis suggests the disorder is transmitted as an autosomal trait with a recessive mode of inheritance. An annual incidence of the disorder in the discovery flock of up to 2.5% was recorded. CONCLUSIONS As a lethal disorder, the occurrence of BCRHS raises potential ethical and economic concerns for Merino breeders. The development of a DNA test would be useful to investigate its distribution in the Australian wool-sheep population. As the disorder affects both the skeleton and several critical organs, including the heart, it may provide a potential animal model for investigating key developmental processes in humans and other animals.

Is gene loss in pedigree dogs surprisingly rapid

Factors affecting the probabilities of gene loss are discussed, with particular attention given to population expansion, sex ratio and inbreeding. Much of the variation in gene survival probabilities among breeds can be explained by differences in expansion rate, sex ratio and family size, with little or no influence of average inbreeding and population size.