The genetic consequences of dog breed formation—Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels

Abstract

Selective breeding for desirable traits in strictly controlled populations has generated an extraordinary diversity in canine morphology and behaviour, but has also led to loss of genetic variation and random entrapment of disease alleles. As a consequence, specific diseases are now prevalent in certain breeds, but whether the recent breeding practice led to an overall increase in genetic load remains unclear. Here we generate whole genome sequencing (WGS) data from 20 dogs per breed from eight breeds and document a ~10% rise in the number of derived alleles per genome at evolutionarily conserved sites in the heavily bottlenecked cavalier King Charles spaniel breed (cKCs) relative to in most breeds studied here. Our finding represents the first clear indication of a relative increase in levels of deleterious genetic variation in a specific breed, arguing that recent breeding practices probably were associated with an accumulation of genetic load in dogs. We then use the WGS data to identify candidate risk alleles for the most common cause for veterinary care in cKCs–the heart disease myxomatous mitral valve disease (MMVD). We verify a potential link to MMVD for candidate variants near the heart specific NEBL gene in a dachshund population and show that two of the NEBL candidate variants have regulatory potential in heart-derived cell lines and are associated with reduced NEBL isoform nebulette expression in papillary muscle (but not in mitral valve, nor in left ventricular wall). Alleles linked to reduced nebulette expression may hence predispose cKCs and other breeds to MMVD via loss of papillary muscle integrity.

PIK3CA is recurrently mutated in canine mammary tumors, similarly to in human mammary neoplasia

“…This included lowering the pool of normal (PON) threshold to 1 and setting the Nlod to 0. Further any variants present in two separate normal canine variant databases were removed as being potential germline variants 36,37 . Variants were excluded if there was ≤2 alternative reads supporting the alternative allele or if the coverage was more than the mean +5xSD.…”

Genetic Variants at the Nebulette Locus Are Associated with Myxomatous Mitral Valve Disease Severity in Cavalier King Charles Spaniels

“…MMVD accounts for 75% of all cardiac disease in domestic dogs, and the CKCS exhibits an unusually high prevalence of early-onset and severe MMVD [ 5 ]. Prevalence and incidence are both related to the breed and age of the animal [ 6 ]. Smaller breeds are generally at higher risk of MMVD, with particularly high incidences in Cavalier King Charles Spaniels (CKCS) [ 4 , 7 , 8 ].…”

“…The CKCS is reported to be one of the most heavily bottlenecked domestic dog breeds as a result of multiple decades of closed population breeding [ 6 , 11 ]. As a result, CKCSs carry up to 13% more derived alleles than other domestic dog breeds [ 6 ], and this is believed to contribute to high-risk states for certain diseases, including MMVD.…”

“…The CKCS is reported to be one of the most heavily bottlenecked domestic dog breeds as a result of multiple decades of closed population breeding [ 6 , 11 ]. As a result, CKCSs carry up to 13% more derived alleles than other domestic dog breeds [ 6 ], and this is believed to contribute to high-risk states for certain diseases, including MMVD. While the disease progression in CKCSs is not dissimilar to other dog breeds, the early onset of the disease in combination with rapid progression in some dogs leads to earlier mortalities and higher morbidity.…”

“…Most recently, a study featuring 20 United States and European CKCSs identified ten possible risk variants related to MMVD that are highly conserved in the breed [ 6 ]. Six of these variants were located in the NEBL gene, and the remaining four were located in the Latrophilin 2 (LPHN2) , Sorbin and SH3 Domain Containing 2 (SORBS2) , 5-Hydroxytryptamine Receptor 1F ( HTR1F ) and Hepatoma Derived Growth Factor-Like 1 ( HDGFL1) genes.…”