Population structure and genetic diversity of Bovec sheep from Slovenia preliminary results M. Simčič, M. Žan Lotrič, D. Bojkovski, E. Ciani, I. Medugorac
Introduction Jezersko Solčava sheep Bovec sheep Istrian Pramenka Bela Krajina Pramenka
Bovec sheep Krainer Steinschaff Austria Plezzana Italy Foto: V. Rezar Descendant of the ancient Small White sheep Widespread in Alpine regions extensive production Adapted on mountain grazing during summer time
Bovec sheep in Slovenia Population size = 2,300 animals Breeding program since 2005 Dairy breed Seasonal fertility Lactation milk yield = 206 kg Milk is processed into Bovec cheese Protected designation of origin Foto: G. Gorjanc
Improved Bovec sheep in Slovenia Introgression Started in 1982 New breed Population size = 900 animals Better milk production Lactation milk yield = 291 kg Foto: G. Gorjanc Bovec sheep a part of the population http://www,ocflock,com/eastfriesian,html White East Frisian sheep Improved Bovec sheep
Objectives to obtain unbiased estimates for genetic diversity parameters to determine the origin and historical development to show the population structure to estimate the degree of admixture in the Bovec sheep population Foto: S, Volarič
Material Blood samples Bovec sheep (n = 44) Improved Bovec sheep (n = 9) Max 3 animals from each of 27 flocks (unrelated) Reference breeds genotypes International Sheep Genomics Consortium http://www.sheephapmap.org/
12 reference breeds (255 animals) 1. Bovec sheep 2. Improved Bovec sheep 3. Jezersko Solčava sheep 4. Istrian Pramenka 5. Bela Krajina Pramenka 6. White East Frisian sheep 7. Brown East Frisian sheep 8. Alpagota 9. Bergamasca 10. Biellese 11. Bundner Oberlander 12. Swiss White Alpine sheep 13. German Texel 14. Spanish Merino Geographically closed Slovenia Introgression Possible ancient common origin Similar type traits Outgroups
Methods Genotypisation Illumina Ovine SNP50 array standard procedures (http://www.ilumina.com) Quality control procedures excluded SNPs with: genotyping errors unknown chromosomal position call rate < 95% minor allele frequency < 0.025 the departure from Hardy Weinberg equilibrium Finally, 52,381 autosomal SNPs Missing genotypes imputed Beagle
Methods Genome wide relationships method of Powell et al. (2010) Genome divided into blocks of 4 SNPs inter marker distance > 50 kb to avoid an ascertainment bias of the OvineSNP50 array 4,972 blocks as alleles considered Genetic diversity parameters the total number of observed alleles mean number of alleles per block number of private alleles observed (H O ) and expected (H E ) heterozygosity
Methods Genetic relationships between breeds Nei genetic distances Neighbour network constructed and plotted SplitsTree4 Unsupervised clustering Admixture the best K the lowest cross validation error barplot generated with R
Results Bovec sheep: Mean inbreeding coefficient = 0.075 ±0.052 Mean IBD = 0.093 ±0.056 Relationship coefficient among breeds: Min (Bovec sheep German Texel) = 0.0505 Max (Bovec sheep Jezersko Solčava sheep) = 0.0253
Genetic diversity parameters 40000 35000 30000 25000 20000 15000 10000 5000 0 Total number of observed alleles 9 8 7 6 5 4 3 2 1 0 Mean number of alleles per block Number of private alleles Ho 1200 1000 800 600 400 200 0 0,85 0,80 0,75 0,70 0,65 0,60 0,55 0,50
Genetic distances Neighbour Net White East Frisian sheep Brown East Frisian sheep German Texel Swiss White Alpine sheep Improved Bovec sheep Bundner Oberlander Jezersko Solčava sheep Alpagota Spanish Merino Bergamasca Bela Krajina Pramenka Istrian Pramenka Bovec sheep Biellese Independent origin of the breed!
Population structure Unsupervised clustering Admixture (308 animals, K = 10) Bovec sheep is a distinct breed Introgression Alpagota Bergamasca Biellese Bundner Oberlander Improved Bovec sheep Bovec sheep Bela Krajina Pramenka Brown East Frisian sheep White East Frisian sheep German Texel Istrian Pramenka Jezersko Solčava sheep Spanish Merino Swiss White Alpine sheep
Bovec sheep > 98% purebred According to Admixture analysis
Conclusion Phylogenetic analyses demonstrated unique genetic identity of Bovec sheep preserved in the Alps Genetic distance matrix and unsupervised clustering showed independent origin of the breed The procedure is capable to detect purebred Bovec animals and could be used to prevent the uncontrolled introgression
Thank you for your attention! Foto: Š. Škander Mountain Mangart (2679 m)