Potravinarstvo Slovak Journal of Food Sciences, Vol 9, No 1 (2015)

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Genome-wide selection signatures in Pinzgau cattle

Radovan Kasarda, Nina Moravčíková, Anna Trakovická, Gábor Mészáros, Ondrej Kadlečík


The aim of this study was to identify the evidence of recent selection based on estimation of the integrated Haplotype Score (iHS), population differentiation index (FST) and characterize affected regions near QTL associated with traits under strong selection in Pinzgau cattle. In total 21 Austrian and 19 Slovak purebreed bulls genotyped with Illumina bovineHD and  bovineSNP50 BeadChip were used to identify genomic regions under selection. Only autosomal loci with call rate higher than 90%, minor allele frequency higher than 0.01 and Hardy-Weinberg equlibrium limit of 0.001 were included in the subsequent analyses of selection sweeps presence. The final dataset was consisted from 30538 SNPs with 81.86 kb average adjacent SNPs spacing. The iHS score were averaged into non-overlapping 500 kb segments across the genome. The FST values were also plotted against genome position based on sliding windows approach and averaged over 8 consecutive SNPs. Based on integrated Haplotype Score evaluation only 7 regions with iHS score higher than 1.7 was found. The average iHS score observed for each adjacent syntenic regions indicated slight effect of recent selection in analysed group of Pinzgau bulls. The level of genetic differentiation between Austrian and Slovak bulls estimated based on FST index was low. Only 24% of FST values calculated for each SNP was greather than 0.01. By using sliding windows approach was found that 5% of analysed windows had higher value than 0.01. Our results indicated use of similar selection scheme in breeding programs of Slovak and Austrian Pinzgau bulls. The evidence for genome-wide association between signatures of selection and regions affecting complex traits such as milk production was insignificant, because the loci in segments identified as affected by selection were very distant from each other. Identification of genomic regions that may be under pressure of selection for phenotypic traits to better understanding of the relationship between genotype and phenotype is one of the challenges for livestock genetics.

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Akey, J. M., Zhang, G., Zhang, K., Jin, L., Shriver, M. D. 2002. Interrogating a high-density SNP map for signatures of natural selection. Genome Research, vol. 12, p. 1805-1814. http://dx.doi.org/10.1101/gr.631202

Barendse, W., Harrison, B., Bunch, R., Thomas, M., Turner, L. 2009. Genome wide signatures of positive selection: The comparison of independent samples and the identification of regions associated to traits. BMC Genomics, vol. 10, p. 178. http://dx.doi.org/10.1186/1471-2164-10-178 

Cole, J. B., VanRaden, P. M., O’Connell, J. R., Van Tassell, C. P., Sonstegard, T. S., Schnabel, R. D., Taylor, J. F., Wiggans, G. R. 2009. Distribution and location of genetic effects for dairy traits. Journal of Dairy Science, vol. 92, p. 2931-2946. http://dx.doi.org/10.3168/jds.2008-1762

de Simoni Gouveia, J. J., da Silva, M. V., Paiva, S. R., de Oliveira, S. M. 2014. Identification of selection signatures in livestock species. Genetics and Molecular Biology, vol. 37, p. 330-342. http://dx.doi.org/10.1590/s1415-47572014000300004

Dvořáková, V., Bartenschlager, H., Stratil, A., Horák, P., Stupka, R., Cítek, J., Sprysl, M., Hrdlicová, A., Geldermann, H. 2012. Association between polymorphism in FTO gene and growth and carcass traits in pig crosses. Genetic Selection Evolution, vol. 17, p. 13. http://dx.doi.org/10.1186/1297-9686-44-13 

Edel, C., Schwarzenbacher, H., Hamann, H., Neuner, S., Emmerling, R., Götz, K. U. 2011. The German-Austrian Genomic Evaluation System for Fleckvieh (Simmental) Cattle. [online] 2015-03-24. [cit. 2015-03-24] Available at: https://journal.interbull.org/index.php/ib/article/viewFile/1209/1319.

Flori, L., Fritz, S., Jaffrézic, F., Boussaha, M., Gut, I., Heath, S., Foulley, J. L., Gautier, M. 2009. The genome response to artificial selection: a case study in dairy cattle. PLoS One, vol. 4, p. e6595. http://dx.doi.org/10.1371/journal.pone.0006595

Gautier, M., Vitalis, R. 2012. rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure. Bioinformatics, vol. 28, p. 1176-1177. http://dx.doi.org/10.1093/bioinformatics/bts115

Gu, J., Orr, N., Park, S. D., Katz, L. M., Sulimova, G., MacHugh, D. E., Hill, E. W. 2009. A Genome Scan for Positive Selection in Thoroughbred Horses. PLoS One, vol. 4, p. e5767. http://dx.doi.org/10.1371/journal.pone.0005767

Hayes, B. J., Chamberlain, A. J., Maceachern, S., Savin, K., McPartlan, H., MacLeod, I., Sethuraman, L., Goddard, M. E. 2009. A genome map of divergent artificial selection between Bos taurus dairy cattle and Bos taurus beef cattle. Animal Genetics, vol. 40, vol. 176-184. PMid:19067671

Karim, L., Takeda, H., Lin, L., Druet, T., Arias, J. A. C., Baurain, D., Cambisano, N., Davis, S. R., Farnir, F., Grisart, B., Harris, B. L., Keehan, M. D., Littlejohn, M. D., Spelman, R. J., Georges, M., Coppieters, W. 2011. Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature. Nature Genetics, vol. 43,
p. 405-413. PMid:21516082

Kemper, K. E., Saxton, S. J., Bolormaa, S., Hayes, B. J., Goddard, M. E. 2014. Selection for complex traits leaves little or no classic signatures of selection. BMC Genomics, vol. 326, p. 246. http://dx.doi.org/10.1186/1471-2164-15-246

Mancini, G., Gargani, M., Chillemi, G., Nicolazzi, E. L., Marsan, P. A., Valentini, A., Pariset, L. 2014. Signatures of selection in five Italian cattle breeds detected by a 54K SNP panel. Molecular Biology Reports, vol. 41, p. 957-965. http://dx.doi.org/10.1007/s11033-013-2940-5

Matukumalli, L. K., Lawley, C. T., Schnabel, R. D., Taylor, J. F., Allan, M. F., Heaton, M. P., O’Connell, J., Moore, S. S., Smith, T. P., Sonstegard, T. S., Van Tassell, C. P. 2009. Development and Characterization of a High Density SNP Genotyping Assay for Cattle. PLoS One, vol. 4, p. e5350. http://dx.doi.org/10.1371/journal.pone.0005350

Maynard-Smith, J., Haigh, J. 1974. The hitch-hiking effect of a favourable gene. Genetical Research, vol. 23, p. 23-35. http://dx.doi.org/10.1017/s0016672300014634

Moradi, M. H., Nejati-Javaremi, A., Moradi-Shahrbabak, M., Dodds, K. G., McEwan, J. C. 2012. Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition. BMC Genetics, vol. 13, p. 10. http://dx.doi.org/10.1186/1471-2156-13-10

Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., Sham, P. C. 2007. PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics, vol. 81, p. 559-575. http://dx.doi.org/10.3410/f.1162373.622875

Qanbari, S., Gianola, D., Hayes, B., Schenkel. F, Miller, S., Moore, S., Thaller, G., Simianer, H. 2011. Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle. BMC Genomics, vol. 12, p. 318. http://dx.doi.org/10.1186/1471-2164-12-318

Qanbari, S., Pausch, H., Jansen, S., Somel, M., Strom, T. M., Fries, R., Nielsen, R., Simianer, H. 2014. Classic Selective Sweeps Revealed by Massive Sequencing in Cattle. PLoS Genetics, vol. 10, p. e1004148. http://dx.doi.org/10.1371/journal.pgen.1004148

Qanbari, S., Pimentel, E. C. G., Tetens, J., Thaller, G., Lichtner, P., Sharifi, A.R., Simianer, H. 2010a. A Genome-Wide Scan for Signatures of Recent Selection in Holstein Cattle. Animal Genetics, vol. 41, p. 377-389. PMid:20096028

Qanbari, S., Pimentel, E. C. G., Tetens, J., Thaller, G., Lichtner, P., Sharifi, A. R., Simianer, H. 2010b. The pattern of linkage disequilbriom in German Holstein cattle. Animal Genetics, vol. 41, p. 346-356. PMid:20055813

Ramey, H. R., Decker, J. E., McKay, S. D., Rolf, M. M., Schnabel, R. D., Taylor, J. F. 2013. Detection of selective sweeps in cattle using genome-wide SNP data. BMC Genomics, vol. 14, p. 382. http://dx.doi.org/10.1186/1471-2164-14-382

Sabeti, P. C., Reich, D. E., Higgins, J. M., Levine, H. Z., Richter, D. J., Schaffner, S. F., Gabriel, S. B., Platko, J. V., Patterson, N. J., McDonald, G. J., Ackerman, H. C., Campbell, S. J., Altshuler, D., Cooper, R., Kwiatkowski, D., Ward, R., Lander, E. S. 2002. Detecting recent positive selection in the human genome from haplotype structure. Nature, vol. 419, p. 832-837. PMid:12397357

Scheet, P., Stephens, M. 2006. A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase. American Journal of Human Genetics, vol. 78, p. 629-644. http://dx.doi.org/10.1086/502802

Simianer, H., Qanbari, S., Gianola, D. 2010. Detection of selection signatures within and between cattle populations. [online] 2015-03-24. [cit. 2015-03-24] Available at: http:// http://www.kongressband.de/wcgalp2010/assets/pdf/0618.pdf

SNP & Variation Suite (Version 8.x) [Software]. Bozeman, MT: Golden Helix, Inc. [cit. 2015-03-24] Available at http://www.goldenhelix.com

Su, G., Brøndum, R. F., Ma, P., Guldbrandtsen, B., Aamand, G. P., Lund, M. S. 2012. Comparison of genomic predictions using medium density (~54,000) and high density (~777,000) single nucleotide polymorphism markers panel in Nordic Holstein and Red Dairy Cattle populations. Journal of Dairy Science, vol. 95, p. 4657-4665. http://dx.doi.org/10.3168/jds.2012-5379 

Taimen, P., Berghäll, H., Vainionpää, R., Kallajoki, M. 2004. NuMA and nuclear lamins are cleaved during viral infection--inhibition of caspase activity prevents cleavage and rescues HeLa cells from measles virus-induced but not from rhinovirus 1B-induced cell death. Virology, vol. 320,
p. 85-98. http://dx.doi.org/10.1016/j.virol.2003.11.026 

Utsunomiya, Y. T., Pérez O'Brien, A. M., Sonstegard, T. S., Van Tassell, C. P., do Carmo, A. S., Mészáros, G., Sölkner, J., Garcia, J. F. 2013. Detecting loci under recent positive selection in dairy and beef cattle by combining different genome-wide scan methods. PLoS One, vol. 8, p. e64280. http://dx.doi.org/10.1371/journal.pone.0064280

Van Tassell, C. P., Smith, T. P., Matukumalli, L. K., Taylor, J. F., Schnabel, R. D., Lawley, C. T., Haudenschild, C. D., Moore, S. S., Warren, W. C., Sonstegard, T. S. 2008. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nature Methods, vol. 5, p. 247-252. PMid:18297082

Voight, B. F., Kudaravalli, S., Wen, X., Pritchard, J. K. 2006. A map of recent positive selection in the human genome. PLoS Biology, vol. 4, p. e72. PMid:16494531

Weir, B. S., Cardon, L. R., Anderson, A. D., Nielsen, D. M., Hill, W. G. 2005. Measures of human population structure show heterogeneity among genomic regions. Genome Research, vol. 15, p. 1468-1476. http://dx.doi.org/10.1101/gr.4398405

Weir, B. S., Cockerham, C. C. 1984. Estimating F-Statistics for the analysis of population structure. Evolution, vol. 38, p. 1358-1370. http://dx.doi.org/10.2307/2408641


Zhang, B., Zhang, Y., Zhang, L., Wang, J., Li, Z., Chen, H. 2011. Allelic polymorphism detected in the bovine FTO gene. Molecular Biotechnology, vol. 49, p. 257-262. http://dx.doi.org/10.1007/s12033-011-9400-z 


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