The evaluation of genomic diversity and selection signals in the autochthonous Slovak Spotted cattle

https://doi.org/10.17221/265/2020-CJASCitation:

Kasarda R., Moravčiková N., Olšanská B., Mészáros G., Vostrý L., Vostrá-Vydrová H., Lehocká K., Prišťák J., Candrák J. (2021): The evaluation of genomic diversity and selection signals in the autochthonous Slovak Spotted cattle. Czech J. Anim. Sci.,66:251-261.

download PDF

The aim of this study was to evaluate the effective population size based on linkage disequilibrium and the trend of inbreeding derived from runs of homozygosity (ROH) in the Slovak Spotted cattle. The ROH segments longer than 4 Mb were then analysed to identify selection signals. Eighty-five individuals were genotyped using the ICBF International Dairy and Beef chip (dams of sires) and Illumina BovineSNP50 BeadChip (sires). The ROH segments > 1 Mb occurred most often in the autosomal genome with an average number of 16.75 ± 7.23. The ROH segments > 16 Mb covering 0.41% of the genome pointed to the long-term effort of breeders to reduce inbreeding in the population of Slovak Spotted cattle. However, the average observed heterozygosity indicated a decrease in overall diversity in the current population. The decrease of heterozygosity per generation also confirmed the estimates of historical and recent effective population size (a decrease of 6.88 animals per generation). The predicted current effective population size was 58 animals. Twenty-one regions across 12 different autosomes were fixed due to the high selection pressure. Within these genomic regions were identified various genes associated with reproduction (SLC9C1, PTPN12), milk production (IGF1, ABCG2), beef production (IFRD1, PTPN4), developmental processes (FMNL2, GLI2), immune system (CD96, CSK) and coat colour (KIT). These selection signals detected in the genome of Slovak Spotted cattle confirm the constant effort of breeders to preserve the dual-purpose nature of this breed.

References:
Amaya A, Burgos W, Martinez R, Ceron-Munoz M. Linkage disequilibrium, population stratification and patterns of ancestry in Simmental cattle. Arch Zootec. 2020 Mar;69(266):148-54. https://doi.org/10.21071/az.v69i266.5109
 
Association of Slovak Spotted Cattle Breeders – Cooperative. The history of the breed [Internet]. [Levice (Slovak Republic)]: Association of Slovak Spotted Cattle Breeders – Cooperative; 2020 Sep. [cited 2020 Dec 26]. Available from: https://www.simmental.sk/about-breed/breed-objective.html.
 
Bahbahani H, Salim B, Almathen F, Al Enezi F, Mwacharo JM, Hanotte O. Signatures of positive selection in African Butana and Kenana dairy zebu cattle. PLOS One. 2018 Jan 4;13(1): 20 p. https://doi.org/10.1371/journal.pone.0190446
 
Barbato M, Orozco-terWengel P, Tapio M, Bruford MW. SNeP: A tool to estimate trends in recent effective population size trajectories using genome-wide SNP data. Front Genet. 2015 Mar 20;6: 6 p. https://doi.org/10.3389/fgene.2015.00109
 
Bjelland DW, Weigel KA, Vukasinovic N, Nkrumah JD. Evaluation of inbreeding depression in Holstein cattle using whole-genome SNP markers and alternative measures of genomic inbreeding. J Dairy Sci. 2013 Jul 1;96(7):4697-706. https://doi.org/10.3168/jds.2012-6435
 
Cesarani A, Gaspa G, Pauciullo A, Degano L, Vicario D, Macciotta NPP. Genome-wide analysis of homozygosity regions in european simmental bulls. J Anim Breed Genet. 2021 Jan;138(1):69-79. https://doi.org/10.1111/jbg.12502
 
Chang CC, Chow CC, Twllier LCAM, Vattikuti S, Purcell SM, Lee JJ. Second-generation PLINK: Rising to the challenge of larger and richer datasets. Gigascience. 2015 Dec 1;4(1): 16 p. https://doi.org/10.1186/s13742-015-0047-8
 
Ferencakovic M, Hamzic E, Gredler B, Solberg TR, Klemetsdal G, Curik I, Solkner J. Estimates of autozygosity derived from runs of homozygosity: Empirical evidence from selected cattle populations. J Anim Breed Genet. 2013 Aug;130(4):286-93. https://doi.org/10.1111/jbg.12012
 
Fisher RA. A fuller theory of “Junctions” in inbreeding. Heredity. 1954 Aug;8(2):187-97. https://doi.org/10.1038/hdy.1954.17
 
Fontanesi L, Scotti E, Russo V. 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. Ital J Anim Sci. 2010 Jan 1;9(2):217-21. https://doi.org/10.4081/ijas.2010.e42
 
Frankham R, Ballou JD, Briscoe DA. Introduction to conversation genetics. Cambridge: Cambridge University Press; 2002 Mar 14. 617 p.
 
Hazuchova E, Kadlecik O, Pavlik I, Kasarda R. Assessment of genetic diversity using characteristics based on the probability of gene origin in the Slovak Spotted breed. Acta Fytotech Zootech. 2013 Oct 3;16(2):31-7. https://doi.org/10.7251/AGRENG1703124K
 
Ilie DE, Gao Y, Nicolae I, Sun D, Li J, Han B, Gavojdian D. Evaluation of single nucleotide polymorphisms identified through the use of SNP assay in Romanian and Chinese Holstein and Simmental cattle breeds. Acta Biochim Pol. 2020 Sep 17;67(3):341-6. https://doi.org/10.18388/abp.2020_5080
 
Jasielczuk I, Gurgul A, Szmatola T, Zabek T, Pawlina K, Semik E, Bugno-Poniewierska M. Linkage disequilibrium and haplotype block structure in Limousin, Simmental and native Polish Red cattle. Livest Sci. 2016 Sep 1;191:57-63. https://doi.org/10.1016/j.livsci.2016.07.008
 
Kim ES, Cole JB, Huson H, Wiggans GR, Van Tassell CP, Crooker BA, Liu G, Da Y, Sonstegard TS. Effect of artificial selection on runs of homozygosity in U.S. Holstein cattle. PLOS One. 2013 Nov 14;8(11): 14 p. https://doi.org/10.1371/journal.pone.0080813
 
Kukuckova V, Moravcikova N, Ferencakovic M, Simcic M, Meszaros G, Solkner J, Trakovicka A, Kadlecik O, Curik I, Kasarda R. Genomic characterization of Pinzgau cattle: Genetic conservation and breeding perspectives. Conserv Genet. 2017 Aug;18(4):893-910. https://doi.org/10.1007/s10592-017-0935-9
 
Lencz T, Lambert C, DeRosse P, Burdick KE, Morgan TV, Kane JM, Kucherlapati R, Malhotra AK. Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia. Proc Natl Acad Sci USA. 2007 Dec 11;104(50):19942-7. https://doi.org/10.1073/pnas.0710021104
 
Li C, Sun D, Zhang S, Yang S, Alim MA, Zhang Q, Li Y, Liu L. Genetic effects of FASN, PPARGC1A, ABCG2 and IGF1 revealing the association with milk fatty acids in a Chinese Holstein cattle population based on a post genome-wide association study. BMC Genet. 2016 Dec;17(1): 16 p. https://doi.org/10.1186/s12863-016-0418-x
 
Makanjoula BO, Miglior F, Abdalla EA, Maltecca C, Schenkel FS, Baes CF. Effect of genomic selection on rate of inbreeding and coancestry and effective population size of Holstein and Jersey cattle populations. J Dairy Sci. 2020 Jun 1;103(6):5183-99. https://doi.org/10.3168/jds.2019-18013
 
Marchitelli C, Nardone A. Mutations and sequence variants in GDF9, BMP15, and BMPR1B genes in Maremmana cattle breed with single and twin births. Rend Lincei. 2015 Nov;26(3):553-60. https://doi.org/10.1007/s12210-015-0418-1
 
Matsumoto H, Kohara R, Sugi M, Usui A, Oyama K, Mannen H, Sasazakic S. The non-synonymous mutation in bovine SPP1 gene influences carcass weight. Heliyon. 2019 Dec;5(12): 5 p. https://doi.org/10.1016/j.heliyon.2019.e03006
 
McQuillan R, Leutenegger A, Abdel-Rahman R, Franklin CS, Pericic M, Barac-Lauc L, Smolej-Narancic N, Janicijevic B, Polasek O, Tenesa A, Macleod AK, Farrington SM, Rudan P, Hayward C, Vitart V, Rudan I, Wild SH, Dunlop MG, Wright AF, Campbell H, Wilson JF. Runs of homozygosity in European populations. Am J Hum Genet. 2008 Sep;83(3):359-72. https://doi.org/10.1016/j.ajhg.2008.08.007
 
Moravcikova N, Kasarda R, Kukuckova V, Kadlecik O. Effective population size and genomic inbreeding in Slovak Pinzgau cattle. Agric Conspec Sci. 2017 Dec 18;82(2):97-100.
 
Mullen MP, Mcclure MC, Kearney JF, Waters SM, Weld R, Flynn P, Creevey CJ, Cromie AR, Berry DP. Development of a custom SNP chip for dairy and beef cattle breeding, parentage, and research. Interbull Bull. 2013;47:58-66.
 
Randhawa IAS, Khatkar MS, Thomson PC, Raadsma HW. A meta-assembly of selection signatures in cattle. PLOS One. 2016 Apr 5;11(4): 30 p. https://doi.org/10.1371/journal.pone.0153013
 
Signer-Hasler H, Burren A, Neuditschko M, Frischknecht M, Garrick D, Stricker C, Gredler B, Bapst B, Flury C. Population structure and genomic inbreeding in nine Swiss dairy cattle populations. Genet Sel Evol. 2017 Dec;49(1): 13 p. https://doi.org/10.1186/s12711-017-0358-6
 
Szmatola T, Gurgul A, Ropka-Molik K, Jasielczuk I, Zabek T, Bugno-Poniewierska M. Characteristics of runs of homozygosity in selected cattle breeds maintained in Poland. Livest Sci. 2016 Jun 1;188:72-80. https://doi.org/10.1016/j.livsci.2016.04.006
 
Wright S. Size of population and breeding structure in relation to evolution. Science. 1938;87:430-1.
 
Zhang Q, Calus MPL, Guldbrandtsen B, Lund MS, Sahana G. Estimation of inbreeding using pedigree, 50k SNP chip genotypes and full sequence data in three cattle breeds. BMC Genet. 2015 Dec;16: 11 p. https://doi.org/10.1186/s12863-015-0227-7
 
Zhou Y, Connor EE, Bickhart DM, Li C, Baldwin RL, Schroeder SG, Rosen BD, Yang L, Van Tassell CP, Liu EL. Comparative whole genome DNA methylation profiling of cattle sperm and somatic tissues reveals striking hypomethylated patterns in sperm. GigaScience. 2018 May;7(5): 13 p. https://doi.org/10.1093/gigascience/giy039
 
download PDF

© 2022 Czech Academy of Agricultural Sciences | Prohlášení o přístupnosti