Genetic Heterogeneity and Diversity of North American Golden Retrievers Using a Low Density STR Marker Panel
Background: Many factors influence genetic diversity in the domestic dog. Much of the genetic diversity of the earliest dogs has been retained in populations of free-ranging, free-breeding village dogs, but in contrast, modern purebred dogs, which derive from breeding in closed populations with limited gene flow, exhibit reduced genetic heterogeneity and/or diversity. Inbreeding, artificial selection for performance and/or type, and geographic isolation, among other factors, also affect genetic diversity within present-day dog breeds.
Historically, pedigrees (studbooks, genealogical registries, etc.) have been used to track relationships between dogs within a breed or within a population. Such pedigrees allow for rough calculations of genetic diversity based on principles of Mendelian inheritance. However, with this method it is impossible to accurately gauge the genetic diversity retained in any one individual unless that animal’s pedigree extends back to the breed’s founders. Therefore pedigree-based coefficient of inbreeding (COI) percentages calculated over a few recent generations are limited in accuracy.
DNA analysis provides an alternate and more accurate way to assess genetic diversity and heterogeneity. The two DNA-based methods that are currently available make use of short tandem repeat (STR) markers and/or single nucleotide polymorphisms (SNPs). STRs are repetitive patterns found in DNA in which a short sequence of nucleotide base pairs, usually 1-6 base pairs, is tandemly repeated as a unit. SNPs are a type of genetic variation in which a single base pair is substituted at a specific location in the DNA. Each method has strengths and weaknesses, but both make use of modern genetic techniques and, compared to pedigrees, allow for deeper, more thorough assessment of the genetic diversity within an individual.
The Veterinary Genetics Laboratory has developed a panel of short tandem repeat (STR) markers that assesses genetic diversity across the genome and in the Dog Leukocyte Antigen (DLA) class I and II regions. These markers can be used to evaluate genetic diversity in pure breeds.
The research: A collaborative study involving Veterinary Genetics Laboratory researchers and other researchers at UC Davis used 33 autosomal short tandem repeat (STR) markers to evaluate genetic heterogeneity and diversity in a large sample of purebred Golden Retrievers. They also compared DNA-based internal relatedness values to coefficients of inbreeding (COI) calculated from 10 or 12 generation pedigrees.
The Golden Retriever breed is popular and encompasses two phenotypic lineage groups, conformation and performance, that have been shaped by artificial selection. Additionally, pedigrees that extend back 10 and 12 generations are publicly available. These aspects of the Golden Retriever make the breed an ideal study subject with which to determine the efficacy of DNA analysis in evaluating genetic diversity and heterogeneity in a pure breed of dog.
The results: The results of this study indicate that the modern Golden Retriever breed retains 46% of the known genetic diversity in all dogs as well as 12% and 22% of the DLA class I and class II haplotypes, respectively. These findings as well as other metrics including fixation index (0.035) suggest that the Golden Retriever breed is more diverse compared to other dog breeds. However, artificial selection for conformation or performance types has narrowed genomic and DLA diversity: specifically, Golden Retrievers selected for conformation contained fewer haplotypes than the performance lines. A comparison of coefficient of inbreeding values calculated from 10 and 12 generation pedigrees also supported lower diversity in conformation verses performance lines.
Taken together, these results demonstrate the efficacy of using a low density STR marker panel to accurately assess genetic heterogeneity and diversity in a pure breed.
References:
Leroy, G. (2011). Genetic diversity, inbreeding and breeding practices in dogs: results from pedigree analyses. Veterinary Journal, 189(2), 177-182. doi: 10.1016/j.tvjl.2011.06.016
Pedersen, N.C., Liu, H., Theilen, G.H., & Sacks, B.N. (2013). The effects of dog breed development on genetic diversity and the relative influences of performance and conformation breeding. Journal of Animal Breeding and Genetics, 130(3), 236-248. doi: 10.1111/jbg.12017
Ontiveros, E.S., Hughes, S., Penedo, M.C.T., Grahn, R.A., Stern, J.A. (2019). Genetic heterogeneity and diversity of North American golden retrievers using a low density STR marker panel. PLOS ONE 14(2): e0212171. doi: 10.1371/journal.pone.0212171