The effect of genetic bottlenecks and inbreeding on the incidence of two major autoimmune diseases in standard poodles, sebaceous adenitis and Addison's disease.BACKGROUND
 Sebaceous adenitis (SA) and Addison's disease (AD) increased rapidly in incidence among Standard Poodles after the mid-twentieth century.  Previous attempts to identify specific genetic causes using genome wide association studies and interrogation of the dog leukocyte antigen (DLA) region have been non-productive.  However, such studies led us to hypothesize that positive selection for desired phenotypic traits that arose in the mid-twentieth century led to intense inbreeding and the inadvertent amplification of AD and SA associated traits.


 This hypothesis was tested with genetic studies of 761 Standard, Miniature, and Miniature/Standard Poodle crosses from the USA, Canada and Europe, coupled with extensive pedigree analysis of thousands more dogs.  Genome-wide diversity across the world-wide population was measured using a panel of 33 short tandem repeat (STR) loci.  Allele frequency data were also used to determine the internal relatedness of individual dogs within the population as a whole.  Assays based on linkage between STR genomic loci and DLA genes were used to identify class I and II haplotypes and disease associations.  Genetic diversity statistics based on genomic STR markers indicated that Standard Poodles from North America and Europe were closely related and reasonably diverse across the breed.  However, genetic diversity statistics, internal relatedness, principal coordinate analysis, and DLA haplotype frequencies showed a marked imbalance with 30 % of the diversity in 70 % of the dogs.  No single strong association was found between STR defined DLA class I or II haplotypes and SA or AD in the breed as a whole, although certain haplotypes present in a minority of the population appeared to confer moderate degrees of risk or protection against either or both diseases.  Dogs possessing minor DLA class I haplotypes were half as likely to develop SA or AD as dogs with common haplotypes.  Miniature/Standard Poodle crosses being used for outcrossing were more genetically diverse than Standard Poodles and genetically distinguishable across the genome and in the DLA class I and II region.


 CONCLUSIONS
 Ancestral genetic polymorphisms responsible for SA and AD entered Standard Poodles through separate lineages, AD earlier and SA later, and were increasingly fixed by a period of close linebreeding that was related to popular bloodlines from the mid-twentieth century.  This event has become known as the midcentury bottleneck or MCB.  Sustained positive selection resulted in a marked imbalance in genetic diversity across the genome and in the DLA class I and II region.  Both SA and AD were concentrated among the most inbred dogs, with genetic outliers being relatively disease free.  No specific genetic markers other than those reflecting the degree of inbreeding were consistently associated with either disease.  Standard Poodles as a whole remain genetically diverse, but steps should be taken to rebalance diversity using genetic outliers and if necessary, outcrosses to phenotypically similar but genetically distinct breeds.
C