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Comparative Study
. 2016 Jan 29;11(1):e0147941.
doi: 10.1371/journal.pone.0147941. eCollection 2016.

Comparative Analysis of Genome Diversity in Bullmastiff Dogs

Sally-Anne Mortlock  1 , Mehar S Khatkar  1 , Peter Williamson  1
Affiliations
Comparative Study

Comparative Analysis of Genome Diversity in Bullmastiff Dogs

Sally-Anne Mortlock et al. PLoS One. .

Abstract

Management and preservation of genomic diversity in dog breeds is a major objective for maintaining health. The present study was undertaken to characterise genomic diversity in Bullmastiff dogs using both genealogical and molecular analysis. Genealogical analysis of diversity was conducted using a database consisting of 16,378 Bullmastiff pedigrees from year 1980 to 2013. Additionally, a total of 188 Bullmastiff dogs were genotyped using the 170,000 SNP Illumina CanineHD Beadchip. Genealogical parameters revealed a mean inbreeding coefficient of 0.047; 142 total founders (f); an effective number of founders (fe) of 79; an effective number of ancestors (fa) of 62; and an effective population size of the reference population of 41. Genetic diversity and the degree of genome-wide homogeneity within the breed were also investigated using molecular data. Multiple-locus heterozygosity (MLH) was equal to 0.206; runs of homozygosity (ROH) as proportion of the genome, averaged 16.44%; effective population size was 29.1, with an average inbreeding coefficient of 0.035, all estimated using SNP Data. Fine-scale population structure was analysed using NETVIEW, a population analysis pipeline. Visualisation of the high definition network captured relationships among individuals within and between subpopulations. Effects of unequal founder use, and ancestral inbreeding and selection, were evident. While current levels of Bullmastiff heterozygosity, inbreeding and homozygosity are not unusual, a relatively small effective population size indicates that a breeding strategy to reduce the inbreeding rate may be beneficial.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Inbreeding over time.
Mean inbreeding coefficients and number of equivalent complete generations of Bullmastiffs by year of birth from 1980 to 2013.
Fig 2
Fig 2. Genetic structure based on genotype data from Bullmastiff dogs.
High-definition network visualisation of population structure in Cytoscape. More closely related individuals are co-located. Thickness of edges is proportional to genetic distance while node size varies in proportion to number of edges, showing degree of relatedness of individuals within the dogs. Subpopulations are labelled 1 to 11.
Fig 3
Fig 3. Neighbour-joining tree of 31 diverse dog breeds.
Constructed using genetic distances calculated from >80,000 SNP loci genotyped. Each breed is represented with a unique colour.
See this image and copyright information in PMC

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