Analysis of selection signatures in the beef cattle genome

https://doi.org/10.17221/226/2019-CJASCitation:Moravčíková N., Kasarda R., Vostrý L., Krupová Z., Krupa E., Lehocká K., Olšanská B., Trakovická A., Nádaský R., Židek R., Belej Ľ., Golian J. (2019): Analysis of selection signatures in the beef cattle genome. Czech J. Anim. Sci., 64: 491-503.
download PDF

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.

References:
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. https://doi.org/10.1534/genetics.107.074328
 
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. https://doi.org/10.1111/j.1365-2052.2004.01229.x
 
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. https://doi.org/10.1186/s12864-016-3232-y
 
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. https://doi.org/10.1186/s13742-015-0047-8
 
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. https://doi.org/10.1016/j.meatsci.2016.07.011
 
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. https://doi.org/10.1371/journal.pone.0128969
 
Fiems L.O. (2012): Double muscling in cattle: genes, husbandry, carcasses and meat. Animals, 2, 472–506. https://doi.org/10.3390/ani2030472
 
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. https://doi.org/10.4081/ijas.2010.e42
 
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. https://doi.org/10.1007/s10592-017-0935-9
 
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. https://doi.org/10.1016/j.meatsci.2013.01.010
 
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. https://doi.org/10.1073/pnas.1303367110
 
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. https://doi.org/10.17221/62/2017-CJAS
 
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. https://doi.org/10.1186/1471-2164-12-318
 
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. https://doi.org/10.1371/journal.pone.0153013
 
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.  https://doi.org/10.1186/1471-2164-14-908
 
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. https://doi.org/10.1038/nature06250
 
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. https://doi.org/10.17221/56/2017-CJAS
 
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. https://doi.org/10.1016/j.anireprosci.2017.11.006
 
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. https://doi.org/10.1186/s12711-015-0128-2
 
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. https://doi.org/10.4238/2013.February.8.3
 
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. https://doi.org/10.1101/gr.092189.109
 
The Bovine HapMap Consortium (2009): Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science, 324, 528–532. https://doi.org/10.1126/science.1167936
 
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. https://doi.org/10.3389/fgene.2015.00036
 
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.
 
Wiener P., Gutierrez-Gil B. (2009): Assessment of selection mapping near the myostatin gene (GDF-8) in cattle. Animal Genetics, 40, 598–608. https://doi.org/10.1111/j.1365-2052.2009.01886.x
 
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. https://doi.org/10.1186/1471-2164-12-65
 
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.  https://doi.org/10.3923/pjbs.2017.210.216
 
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. https://doi.org/10.1111/age.12112
 
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. https://doi.org/10.2527/jas.2014-7656
 
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. https://doi.org/10.1080/10495398.2018.1426594
 
download PDF

© 2020 Czech Academy of Agricultural Sciences