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

Abstract

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.

The German Shorthair Pointer Dog Breed (Canis lupus familiaris): Genomic Inbreeding and Variability

“…The loss of genetic variability and the increase in inbreeding levels coupled with the consequent reduction in the effective population size in a high number of pedigree canine populations could be considered the main risk factor in conservation project definitions [12,15,[41][42][43][44]. In general, the reported results show low F PED in the studied subjects [44].…”

“…The loss of genetic variability and the increase in inbreeding levels coupled with the consequent reduction in the effective population size in a high number of pedigree canine populations could be considered the main risk factor in conservation project definitions [12,15,[41][42][43][44]. In general, the reported results show low F PED in the studied subjects [44]. The effectiveness of the molecular dissection of inbreeding is shown by the F ROH (equation 2) results, which reveal the genomic relationship among the studied individuals as demonstrated by different researchers [8,16,45].…”

Analysis of structure of the population, kinship coefficients and inbreeding trend depending on sex, type of breeding of Tatra Sheepherd dogs

“…This way of reducing the inbreeding is confirmed by studies concerning dog breeding and endangered breeds with small populations [13, 16, 33, 55]. These observations are alarming since reduced genetic variation and inbreeding are generally associated with the loss of the adaptive potential and reduced options of effective selection [10, 52, 56]. We note that this rapid genetic diversity loss is parallel to an increasing requirement of dogs for a number of different purposes in the modern society [8, 57-59].…”

“…Breeds like the Swedish lapphund and the Swedish vallhund, however, reach almost as high average F- 0.09 -in spite of pedigree sizes of several thousand individuals, census sizes of well over 1000, and over 50 founders. Similarly, the Swedish elkhound and the Drever have pedigrees comprising over 50,000 dogs, with over 10,000 defined as alive in 2012 but average F is over 0.07 [10]. A study of genealogical parameters for a number of breeds in Australia found that the mean inbreeding coefficient ranged from 0 to 0.101 across 32 analysed breeds [53].…”

Examination of the efficacy of small genetic panels in genomic conservation of companion animal populations

“…In many ways dogs are an ideal model for the study of genetic erosion and population recovery. Genetic diversity in many common domestic dog breeds has been declining systematically since the beginning of the 1800's, when modern breeding practices came into fashion (Jansson & Laikre, 2018). As such, inbreeding in domestic dog breeds is substantial and widespread (Freedman et al, 2014;Kettunen, Daverdin, Helfjord, & Berg, 2017;Pedersen, Pooch, & Liu, 2016;Sams & Boyko, 2018) and has led to an increase in recessive deleterious mutations of high effect (Jagannathan et al, 2019;Marsden et al, 2016) as well as general inbreeding depression (Chu et al, 2019).…”