Czech J. Anim. Sci., 2019, 64(12):491-503 | DOI: 10.17221/226/2019-CJAS

Analysis of selection signatures in the beef cattle genomeOriginal Paper

Nina Moravčíková*,1, Radovan Kasarda1, Luboš Vostrý2,3, Zuzana Krupová3, Emil Krupa3, Kristína Lehocká1, Barbora Olšanská1, Anna Trakovická1, Rudolf Nádaský4, Radoslav Židek5, Ľubomír Belej5, Jozef Golian5
1 Department of Animal Genetics and Breeding Biology, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic
2 Department of Genetics and Breeding, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
3 Institute of Animal Science, Prague-Uhříněves, Czech Republic
4 Poľnohospodárske družstvo Špačince, Špačince, Slovak Republic
5 Department of Food Hygiene and Safety, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Nitra, Slovak Republic

This study aimed to evaluate the impact of selection on the genome structure of beef cattle through identification of selection signatures reflecting the breeding standard of each breed and to discover potential functional genetic variants to improve performance traits. Genotyping data of six beef breeds (Aberdeen Angus, Hereford, Limousin, Charolais, Piedmontese and Romagnola) were used to perform genome-wide scans for selection signatures. The approaches applied were based on an assumption that selection leads to linkage disequilibrium or to a decrease of genetic variability in genomic regions containing genotypes connected with favourable phenotypes. Thus, the selection signatures were analysed based on Wright's FST index, distribution of runs of homozygosity segments in the beef genome and determination of linkage disequilibrium variability between breeds. The number and length of detected selection signals were different depending on the breeds and methodological approaches. As expected due to the breeding goals of analysed breeds, common signals were located on autosomes 2, 6, 7, 13 and 20 close to the genes associated with coat colour (KIT, KDR), muscle development (GDF9, GHRH, GHR), double muscling (MSTN), meat tenderness (CAST) and intramuscular fat content (SCD). But, across the genomes of analysed breeds, unique selection signals were found as well. The subsequent analysis of those single nucleotide polymorphism markers can be beneficial for the genetic progress of studied breeds in future.

Keywords: artificial selection; local population; genomic autozygosity; linkage disequilibrium; Wright's statistic

Published: December 31, 2019  Show citation

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Moravčíková N, Kasarda R, Vostrý L, Krupová Z, Krupa E, Lehocká K, et al.. Analysis of selection signatures in the beef cattle genome. Czech J. Anim. Sci. 2019;64(12):491-503. doi: 10.17221/226/2019-CJAS.
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    References

    1. Barendse W., Harrison B.E., Hawken R.J., Ferguson D.M., Thompson J.M., Thomas M.B., Bunch R.J. (2007): Epistasis between calpain 1 and its inhibitor calpastatin within breeds of cattle. Genetics, 176, 2601-2610. Go to original source... Go to PubMed...
    2. Bellinge R.H., Liberles D.A., Iaschi S.P., O'Brien P.A., Tay G.K. (2005): Myostatin and its implications on animal breeding: A review. Animal Genetics, 36, 1-6. Go to original source... Go to PubMed...
    3. Berton M.P., Fonseca L.F., Gimenez D.F., Utembergue B.L., Cesar A.S., Coutinho L.L., de Lemos M.V., Aboujaoude C., Pereira A.S., Silva R.M., Stafuzza N.B., Feitosa F.L., et al. (2016): Gene expression profile of intramuscular muscle in Nellore cattle with extreme values of fatty acid. BMC Genomics, 17, 972. Go to original source... Go to PubMed...
    4. Chang C.C., Chow C.C., Tellier L.C., Vattikuti S., Purcell S.M., Lee J.J. (2015): Second-generation PLINK: Rising to the challenge of larger and richer datasets. GigaScience, 4, 7. Go to original source... Go to PubMed...
    5. Coleman L.W., Hickson R.E., Schreurs N.M., Martin N.P., Kenyon P.R., Lopez-Villalobos N., Morris S.T. (2016): Carcass characteristics and meat quality of Hereford sired steers born to beef-cross-dairy and Angus breeding cows. Meat Science, 121, 403-408. Go to original source... Go to PubMed...
    6. Dorshorst B., Henegar C., Liao X., Sallman Almen M., Rubin C.J., Ito S., Wakamatsu K., Stothard P., Van Doormaal B., Plastow G., Barsh G.S., Andersson L. (2015): Dominant red coat color in Holstein cattle is associated with a missense mutation in the coatomer protein complex, subunit alpha (COPA) gene. PLoS ONE, 10, e0128969. Go to original source... Go to PubMed...
    7. Fiems L.O. (2012): Double muscling in cattle: genes, husbandry, carcasses and meat. Animals, 2, 472-506. Go to original source... Go to PubMed...
    8. Fontanesi L., Scotti E., Russo V. (2010): Analysis of SNPs in the KIT gene of cattle with different coat colour patterns and perspectives to use these markers for breed traceability and authentication of beef and dairy products. Italian Journal of Animal Science, 9, e42. Go to original source...
    9. Kukuckova V., Moravcikova N., Ferencakovic M., Simcic M., Meszaros G., Solkner J., Trakovicka A., Kadlecik O., Curik I., Kasarda R. (2017): Genomic characterization of Pinzgau cattle: Genetic conservation and breeding perspectives. Conservation Genetics, 18, 893-910. Go to original source...
    10. Li X., Ekerljung M., Lundstrom K., Lunden A. (2013): Association of polymorphisms at DGAT1, leptin, SCD1, CAPN1 and CAST genes with color, marbling and water holding capacity in meat from beef cattle populations in Sweden. Meat Science, 94, 153-158. Go to original source... Go to PubMed...
    11. McTavish E.J., Decker J.E., Schnabel R.D., Taylor J.F., Hillis D.M. (2013): New World cattle show ancestry from multiple independent domestication events. Proceedings of the National Academy of Sciences of the United States of America, 110, 1398-1406. Go to original source... Go to PubMed...
    12. Moravcikova N., Simcic M., Meszaros G., Solkner J., Kukuckova V., Vlcek M., Trakovicka A., Kadlecik O., Kasarda R. (2018): Genomic response to natural selection within Alpine cattle breeds. Czech Journal of Animal Science, 63, 136-143. Go to original source...
    13. Qanbari S., Gianola D., Hayes B., Schenkel F., Miller S., Moore S., Thaller G., Simianer H. (2011): Application of site and haplotype-frequency based approach for detecting selection signatures in cattle. BMC Genomics, 12, 318. Go to original source... Go to PubMed...
    14. Randhawa I.A., Khatkar M.S., Thomson P.C., Raadsma H.W. (2016): A meta-assembly of selection signatures in cattle. PLoS ONE, 11, e0153013. Go to original source... Go to PubMed...
    15. Rothammer S., Seichter D., Forster M., Medugorac I. (2013): A genome-wide scan for signatures of differential artificial selection in ten cattle breeds. BMC Genomics, 14, 908. Go to original source... Go to PubMed...
    16. Sabeti P.C., Varilly P., Fry B., Lohmueller J., Hostetter E., Cotsapas C., Xie X., Byrne E.H., McCarroll S.A., Gaudet R., Schaffner S.F., Lander E.S., et al. (2007): Genome-wide detection and characterization of positive selection in human populations. Nature, 449, 913-918. Go to original source... Go to PubMed...
    17. Salem M.M.I., Thompson G., Chen S., Beja-Pereira A., Carvalheira J. (2018): Linkage disequilibrium and haplotype block structure in Portuguese Holstein cattle. Czech Journal of Animal Science, 63, 61-69. Go to original source...
    18. Sharifiyazdi H., Mirzaei A., Ghanaatian Z. (2018): Characterization of polymorphism in the FSH receptor gene and its impact on some reproductive indices in dairy cows. Animal Reproduction Science, 188, 45-50. Go to original source... Go to PubMed...
    19. Sorbolini S., Marras G., Gaspa G., Dimauro C., Cellesi M., Valentini A., Macciotta N.P. (2015): Detection of selection signatures in Piemontese and Marchigiana cattle, two breeds with similar production aptitudes but different selection histories. Genetics Selection Evolution, 47, 52. Go to original source... Go to PubMed...
    20. Tanq K.Q., Yang W.C., Li S.J., Yang L.G. (2013): Polymorphisms of the bovine growth differentiation factor 9 gene associated with superovulation performance in Chinese Holstein cows. Genetics and Molecular Research, 12, 390-399. Go to original source... Go to PubMed...
    21. Teo Y.Y., Fry A.E., Bhattacharya K., Small K.S, Kwiatkowski D.P., Clark T.G. (2009): Genome-wide comparisons of variation in linkage disequilibrium. Genome Research, 19, 1849-1860. Go to original source... Go to PubMed...
    22. The Bovine HapMap Consortium (2009): Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science, 324, 528-532. Go to original source... Go to PubMed...
    23. Utsunomiya Y.T., O'Brien A.M., Sonstegard T.S., Solkner J., Garcia J.F. (2015): Genomic data as the "hitchhiker's guide" to cattle adaptation: Tracking the milestones of past selection in the bovine genome. Frontiers in Genetics, 6, 1-13. Go to original source... Go to PubMed...
    24. Voight B.F., Kudaravalli S., Wen X., Pritchard J.K. (2006): A map of recent positive selection in the human genome. PLoS Biology, 4, e72. Go to original source... Go to PubMed...
    25. Wiener P., Gutierrez-Gil B. (2009): Assessment of selection mapping near the myostatin gene (GDF-8) in cattle. Animal Genetics, 40, 598-608. Go to original source... Go to PubMed...
    26. Wiener P., Edriss M.A., Williams J.L., Waddington D., Law A., Woolliams J.A., Gutierrez-Gil B. (2011): Information content in genome-wide scans: Concordance between patterns of genetic differentiation and linkage mapping associations. BMC Genomics, 12, 65. Go to original source... Go to PubMed...
    27. Yurnalis, Arnim, Putra D.E. (2017): Polymorphism of insulin-like growth factor 1 gene (IGF1/TasI, IGF1/SnaBI, IGF1/RsaI) and the association with daily gain of Pesisir cattle local breed from West Sumatera, Indonesia. Pakistan Journal of Biological Sciences, 20, 210-216. Go to original source... Go to PubMed...
    28. Zhang Y., Yang M., Li C., Xu Y., Sun J., Lei C., Lan X., Zhang C., Chen H. (2014a): Identification and genetic effect of a variable duplication in the promoter region of the cattle ADIPOQ gene. Animal Genetics, 45, 171-179. Go to original source... Go to PubMed...
    29. Zhang Y., Cong X., Wang A., Jiang H. (2014b): Identification of the STAC3 gene as a skeletal muscle-specifically expressed gene and a novel regulator of satellite cell differentiation in cattle. Journal of Animal Science, 92, 3284-3290. Go to original source... Go to PubMed...
    30. Zheng L., Zhang G.M., Dong Y.P., Wen Y.F., Dong D., Lei C.Z., Qi X.L., Chen H., Huo L.J., Huang Y.Z. (2019): Genetic variant of MYLK4 gene and its association with growth traits in Chinese cattle. Animal Biotechnology, 30, 30-35. Go to original source... Go to PubMed...

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