Pedigree data indicate rapid inbreeding and loss of genetic diversity within populations of native, traditional dog breeds of conservation concern.

Increasing concern is directed towards genetic diversity of domestic animal populations because strong selective breeding can rapidly deplete genetic diversity of socio-economically valuable animals. International conservation policy identifies minimizing genetic erosion of domesticated animals as a key biodiversity target. We used breeding records to assess potential indications of inbreeding and loss of founder allelic diversity in 12 native Swedish dog breeds, traditional to the country, ten of which have been identified by authorities as of conservation concern. The pedigrees dated back to the mid-1900, comprising 5-11 generations and 350-66,500 individuals per pedigree. We assessed rates of inbreeding and potential indications of loss of genetic variation by measuring inbreeding coefficients and remaining number of founder alleles at five points in time during 1980-2012. We found average inbreeding coefficients among breeds to double-from an average of 0.03 in 1980 to 0.07 in 2012 -in spite of the majority of breeds being numerically large with pedigrees comprising thousands of individuals indicating that such rapid increase of inbreeding should have been possible to avoid. We also found indications of extensive loss of intra-breed variation; on average 70 percent of founder alleles are lost during 1980-2012. Explicit conservation goals for these breeds were not reflected in pedigree based conservation genetic measures; breeding needs to focus more on retaining genetic variation, and supplementary genomic analyses of these breeds are highly warranted in order to find out the extent to which the trends indicated here are reflected over the genomes of these breeds.