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Genome-wide population structure and evolutionary history of the Frizarta dairy sheep 1

  • A. Kominakis (a1), A. L. Hager-Theodorides (a1), A. Saridaki (a2), G. Antonakos (a3) and G. Tsiamis (a2)...


In the present study, we used genomic data, generated with a medium density single nucleotide polymorphisms (SNP) array, to acquire more information on the population structure and evolutionary history of the synthetic Frizarta dairy sheep. First, two typical measures of linkage disequilibrium (LD) were estimated at various physical distances that were then used to make inferences on the effective population size at key past time points. Population structure was also assessed by both multidimensional scaling analysis and k-means clustering on the distance matrix obtained from the animals’ genomic relationships. The Wright’s fixation F ST index was also employed to assess herds’ genetic homogeneity and to indirectly estimate past migration rates. The Wright’s fixation F IS index and genomic inbreeding coefficients based on the genomic relationship matrix as well as on runs of homozygosity were also estimated. The Frizarta breed displays relatively low LD levels with r 2 and |Dʹ| equal to 0.18 and 0.50, respectively, at an average inter-marker distance of 31 kb. Linkage disequilibrium decayed rapidly by distance and persisted over just a few thousand base pairs. Rate of LD decay (β) varied widely among the 26 autosomes with larger values estimated for shorter chromosomes (e.g. β=0.057, for OAR6) and smaller values for longer ones (e.g. β=0.022, for OAR2). The inferred effective population size at the beginning of the breed’s formation was as high as 549, was then reduced to 463 in 1981 (end of the breed’s formation) and further declined to 187, one generation ago. Multidimensional scaling analysis and k-means clustering suggested a genetically homogenous population, F ST estimates indicated relatively low genetic differentiation between herds, whereas a heat map of the animals’ genomic kinship relationships revealed a stratified population, at a herd level. Estimates of genomic inbreeding coefficients suggested that most recent parental relatedness may have been a major determinant of the current effective population size. A denser than the 50k SNP panel may be more beneficial when performing genome wide association studies in the breed.


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In memory of Associate Professor Zafeiris Abas.



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Allendorf, FW and Phelps, SR 1981. Use of allelic frequencies to describe population structure. Canadian Journal of Fisheries and Aquatic Sciences 38, 15071514.
Al-Mamun, HA, Clark, SA, Kwan, P and Gondro, C 2015. Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep. Genetics Selection Evolution 47, 90.
Ardlie, KG, Kruglyak, L and Seielstad, M 2002. Patterns of linkage disequilibrium in the human genome. Nature Reviews Genetics 3, 299309.
Baloche, G, Legarra, A, Sallé, G, Larroque, H, Astruc, JM, Robert-Granié, C and Barillet, F 2014. Assessment of accuracy of genomic prediction for French Lacaune dairy sheep. Journal of Dairy Science 97, 11071116.
Beynon, SE, Slavov, GT, Farré, M, Sunduimijid, B, Waddams, K, Davies, B, Haresign, W, Kijas, J, MacLeod, IM, Newbold, CJ, Davies, L and Larkin, DM 2015. Population structure and history of the Welsh sheep breeds determined by whole genome genotyping. BMC Genetics 16, 65.
Bjelland, D, Weigel, K, Vukasinovic, N and Nkrumah, J 2013. Evaluation of inbreeding depression in Holstein cattle using whole-genome SNP markers and alternative measures of genomic inbreeding. Journal of Dairy Science 96, 46974706.
Dumont, BL and Payseur, BA 2008. Evolution of the genomic rate of recombination in mammals. Evolution 62, 276294.
Fisher, RA 1954. A fuller theory of junctions in inbreeding. Heredity 8, 187–197.
Fu, W, Dekkers, JC, Lee, WR and Abasht, B 2015. Linkage disequilibrium in crossbred and pure line chickens. Genetics Selection Evolution 47, 11.
García-Gámez, E, Sahana, G, Gutiérrez-Gil, B and Arranz, JJ 2012. Linkage disequilibrium and inbreeding estimation in Spanish Churra sheep. BMC Genetics 13, 43.
Hartl, DL and Clark, AG 2007. Principles of population genetics. Sinauer Associates Inc., Sunderland, MA, USA.
Hayes, BJ, Visscher, PM, McPartlan, HC and Goddard, ME 2003. Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Research 13, 635643.
Hill, WG 1981. Estimation of effective population size from data on linkage disequilibrium. Genetical Research 38, 209216.
Hill, WG and Robertson, A 1968. Linkage disequilibrium in finite populations. Theoretical and Applied Genetics 38, 226231.
Khatkar, MS, Nicholas, FW, Collins, AR, Zenger, KR, Cavanagh, JAL, Barris, W, Schnabel, RD, Taylor, JF and Raadsma, HW 2008. Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel. BMC Genomics 9, 187.
Kijas, JW, Lenstra, JA, Hayes, B, Boitard, S, Neto, LR, Cristobal, MS, Servin, B, McCulloch, R, Whan, V, Gietzen, K, Paiva, S, Barendse, W, Ciani, E, Raadsma, H, McEwan, J and Dalrymple, B 2012. Genome-wide analysis of the world’s sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biology 10, 2.
Kijas, JW, Porto-Neto, L, Dominik, S, Reverter, A, Bunch, R, McCulloch, R, Hayes, BJ, Brauning, R and McEwan, J 2014. Linkage disequilibrium over short physical distances measured in sheep using a high-density SNP chip. Animal Genetics 45, 754757.
Kominakis, A, Hager-Theodorides, AL, Zoidis, E, Saridaki, A, Antonakos, G and Tsiamis, G Combined GWAS and ‘Guilt By Association’ based prioritization analysis identified functional candidate genes for body size in sheep. Under review. Genetics Selection and Evolution.
Kominakis, A, Saridaki, A, Antonakos, G, Tsiamis, G and Bourtsis, A 2015. Genome-wide LD estimates in the Greek Frizarta dairy sheep. Poster Presented at Canadian Society of Animal Science Annual Meeting, 5–7 May 2015, Ottawa, ON, Canada.
Leroy, G, Mary-Huard, T, Verrier, E, Danvy, S, Charvolin, E and Danchin-Burge, C 2013. Methods to estimate effective population size using pedigree data: examples in dog, sheep, cattle and horse. Genetics Selection Evolution 45, 1.
Lewontin, RC 1964. The interaction of selection and linkage. I. general considerations; heterotic models. Genetics 49, 4967.
Long, JC 1991. The genetic structure of admixed populations. Genetics 127, 417428.
Lu, D, Sargolzaei, M, Kelly, M, Li, C, Vander Voort, G, Wang, Z, Plastow, G, Moore, S and Miller, SP 2012. Linkage disequilibrium in Angus, Charolais, and Crossbred beef cattle. Frontiers in Genetics 3, 152.
Mastrangelo, S, Di Gerlando, R, Tolone, M, Tortorici, L, Sardina, MT and Portolano, B 2014. Genome wide linkage disequilibrium and genetic structure in Sicilian dairy sheep breeds. BMC Genetics 15, 108.
Mastrangelo, S, Tolone, M, Di Gerlando, R, Fontanesi, L, Sardina, MT and Portolano, B 2016. Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds. Animal 10, 746754.
Meadows, JRS, Chan, EKF and Kijas, JW 2008. Linkage disequilibrium compared between five populations of domestic sheep. BMC Genetics 9, 61.
Meuwissen, THE, Hayes, BJ and Goddard, ME 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics 157, 18191829.
Mucha, S, Bunger, L and Conington, J 2015. Genome-wide association study of footrot in Texel sheep. Genetics Selection Evolution 47, 35.
Muñoz, M, Alves, E, Ramayo-Caldas, Y, Casellas, J, Rodríguez, C, Folch, JM, Siliõ, L and Fernández, AI 2012. Recombination rates across porcine autosomes inferred from high-density linkage maps. Animal Genetics 43, 620623.
Nei, M and Chakravarti, A 1977. Drift variances of FST and GST statistics obtained from a finite number of isolated populations. Theoretical Population Biology 11, 307325.
Neigel, JE 2002. Is FST obsolete? Conservation Genetics 3, 167173.
Petes, TD 2001. Meiotic recombination hot spots and cold spots. Nature Reviews Genetics 2, 360369.
Pfaff, CL, Parra, EJ, Bonilla, C, Hiester, K, McKeigue, PM, Kamboh, MI, Hutchinson, RG, Ferrell, RE, Boerwinkle, E and Shriver, MD 2001. Population structure in admixed populations: effect of admixture dynamics on the pattern of linkage disequilibrium. American Journal of Human Genetics 68, 198207.
Pritchard, JK, Stephens, M, Rosenberg, NA and Donnelly, P 2000. Association mapping in structured populations. American Journal of Human Genetics 67, 170181.
Qanbari, S, Pimentel, ECG, Tetens, J, Thaller, G, Lichtner, P, Sharifi, AR and Simianer, H 2010. The pattern of linkage disequilibrium in German Holstein cattle. Animal Genetics 41, 346356.
Reich, DE, Cargili, M, Boik, S, Ireland, J, Sabeti, PC, Richter, DJ, Lavery, T, Kouyoumjian, R, Farhadian, SF, Ward, R and Lander, ES 2001. Linkage disequilibrium in the human genome. Nature 411, 199204.
Sved, JA, Cameron, EC and Gilchrist, AS 2013. Estimating effective population size from linkage disequilibrium between unlinked loci: theory and application to fruit fly outbreak populations. PLoS ONE 8, 7.


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Genome-wide population structure and evolutionary history of the Frizarta dairy sheep 1

  • A. Kominakis (a1), A. L. Hager-Theodorides (a1), A. Saridaki (a2), G. Antonakos (a3) and G. Tsiamis (a2)...


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