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Investigating the population structure and genetic differentiation of livestock guard dog breeds

  • D. Bigi (a1), S.P. Marelli (a2), L. Liotta (a3), S. Frattini (a2), A. Talenti (a2), G. Pagnacco (a2), M. Polli (a2) and P. Crepaldi (a2)...

Livestock guarding dogs are a valuable adjunct to the pastoral community. Having been traditionally selected for their working ability, they fulfil their function with minimal interaction or command from their human owners. In this study, the population structure and the genetic differentiation of three Italian livestock guardian breeds (Sila’s Dog, Maremma and Abruzzese Sheepdog and Mannara’s Dog) and three functionally and physically similar breeds (Cane Corso, Central Asian Shepherd Dog and Caucasian Shepherd Dog), totalling 179 dogs unrelated at the second generation, were investigated with 18 autosomal microsatellite markers. Values for the number of alleles per locus, observed and expected heterozygosity, Hardy–Weinberg Equilibrium, F stats, Nei’s and Reynold’s genetic distances, clustering and sub-population formation abilities and individual genetic structures were calculated. Our results show clear breed differentiation, whereby all the considered breeds show reasonable genetic variability despite small population sizes and variable selection schemes. These results provide meaningful data to stakeholders in specific breed and environmental conservation programmes.

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Bigi, D, Marelli, SP, Randi, E and Polli, M 2015. Genetic characterization of four native Italian shepherd dog breeds and analysis of their relationship to cosmopolitan dog breeds using microsatellite markers. Animal 9, 19211928.
Brzustowski, J 2001. GeneDist: population to population genetic distance calculator. Retrieved on 25 May 2017 from
Budowle, B, Garofano, P, Hellman, A, Ketchum, M, Kanthaswamy, S, Parson, W, van Haeringen, W, Fain, S and Broad, T 2005. Recommendations for animal DNA forensic and identity testing. International Journal of Legal Medicine 119, 295302.
Ceh, E and Dovc, P 2014. Population structure and genetic differentiation of livestock guard dog breeds from the Western Balkans. Journal of Animal Breeding and Genetics 131, 313325.
Coppinger, R and Schneider, R 1995. Evolution of working dogs. In: The domestic dog: its evolution, behaviour and interactions with people. Cambridge University Press, Cambridge, UK. pp. 2147.
Council of Europe 1986. European convention for the protection of vertebrate animals used for experimental and other scientific purposes CETS 123. Strasbourg. Retrieved on 18 December 2015 from
Evanno, G, Regnaut, S and Goudet, J 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14, 26112620.
Excoffier, L and Lischer, HEL 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10, 564567.
Felsenstein, J 1989. PHYLIP – Phylogeny Inference Package (Version 3.2). pp. 164–166. Retrieved on 28 November 2014 from
Gagliardi, R, Llambí, S, García, C and Arruga, MV 2011. Microsatellite characterization of Cimarron Uruguayo dogs. Genetics and Molecular Biology 34, 165168.
Goudet, J 2001. FSTAT, a program to estimate and test gene diversities and fixation indices. Version 2.9.3. Retrieved on 25 May 2017 from
Irion, DN, Schaffer, AL, Famula, TR, Eggleston, ML, Hughes, SS and Pedersen, NC 2003. Analysis of genetic variation in 28 dog breed populations with 100 microsatellite markers. Journal of Heredity 94, 8187.
Irion, DN, Schaffer, AL, Grant, S, Wilton, AN and Pedersen, NC 2005. Genetic variation analysis of the bali street dog using microsatellites. BMC Genetics 6, 6.
Jakobsson, M and Rosenberg, NA 2007. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23, 18011806.
Jordana, J, Piedrafita, J, Sanchez, A and Puig, P 1992. Comparative F statistics analysis of the genetic structure of ten Spanish dog breeds. Journal of Heredity 83, 367374.
Kim, KS, Tanabe, Y, Park, CK and Ha, JH 2001. Genetic variability in East Asian dogs using microsatellite loci analysis. Journal of Heredity 92, 398403.
Kopaliani, N, Shakarashvili, M, Gurielidze, Z, Qurkhuli, T and Tarkhnishvili, D 2014. Gene flow between wolf and shepherd dog populations in Georgia (Caucasus). Journal of Heredity 105, 345353.
Lee, E-W, Choi, S-K and Cho, G-J 2014. Molecular Genetic Diversity of the Gyeongju Donggyeong dog in Korea. Journal of Veterinary Medical Science 76, 13591365.
Nei, M 1972. Genetic distance between populations. The American Naturalist 106, 283292.
Parker, HG 2012. Genomic analyses of modern dog breeds. Mammalian Genome 23, 1927.
Parra, D, Méndez, S, Cañón, J and Dunner, S 2008. Genetic differentiation in pointing dog breeds inferred from microsatellites and mitochondrial DNA sequence. Animal Genetics 39, 17.
Peakall, R and Smouse, PE 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research –an update. Bioinformatics 28, 25372539.
Pedersen, N, Liu, H, Theilen, G and Sacks, B 2012. 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, 236248.
Pfahler, S and Distl, O 2013. A massive reduction of the genetic diversity in the Lundehund. Animal Genetics 45, 154.
Pritchard, JK, Stephens, M and Donnelly, P 2000. Inference of population structure using multilocus genotype data. Genetics 155, 945959.
Reynolds, J, Weir, BS and Cockerham, CC 1983. Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics 105, 767779.
Rice, WR 1989. Analyzing tables of statistical tests. Evolution 43, 223.
Rosenberg, NA 2003. Distruct: a program for the graphical display of population structure. Molecular Ecology Notes 4, 137138.
Sechi, S, Polli, M, Marelli, S, Talenti, A, Crepaldi, P, Fiore, F, Spissu, N, Dreger, DL, Zedda, M, Dimauro, C, Ostrander, EA, Di Cerbo, A and Cocco, R 2016. Fonni’s dog: morphological and genetic characteristics for a breed standard definition. Italian Journal of Animal Science 16, 2230.
Slatkin, M 1995. A measure of population subdivision based on microsatellite allele frequencies. Genetics 139, 457462.
Streitberger, K, Schweizer, M, Kropatsch, R, Dekomien, G, Distl, O, Fischer, MS, Epplen, JT and Hertwig, ST 2012. Rapid genetic diversification within dog breeds as evidenced by a case study on Schnauzers. Animal Genetics 43, 577586.
Suárez, NM, Betancor, E, Fregel, R and Pestano, J 2013. Genetic characterization, at the mitochondrial and nuclear DNA levels, of five Canary Island dog breeds. Animal Genetics 44, 432441.
Vilà, C, Savolainen, P, Maldonado, JE, Amorim, IR, Rice, JE, Honeycutt, RL, Crandall, KA, Lundeberg, J and Wayne, RK 1997. Multiple and ancient origins of the domestic dog. Science 276, 16871689.
Vonholdt, BM, Pollinger, JP, Lohmueller, KE, Han, E, Parker, HG, Quignon, P, Degenhardt, JD, Boyko, AR, Earl, DA, Auton, A, Reynolds, A, Bryc, K, Brisbin, A, Knowles, JC, Mosher, DS, Spady, TC, Elkahloun, A, Geffen, E, Pilot, M, Jedrzejewski, W, Greco, C, Randi, E, Bannasch, D, Wilton, A, Shearman, J, Musiani, M, Cargill, M, Jones, PG, Qian, Z, Huang, W, Ding, Z-L, Zhang, Y-P, Bustamante, CD, Ostrander, EA, Novembre, J and Wayne, RK 2010. Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature 464, 898902.
Weir, BS and Cockerham, CC 1984. Estimating F-Statistics for the analysis of population structure. Evolution 38, 1358.
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