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Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Behavior in Sapsaree Dog (Canis familiaris)

  • Ha, J.H. ;
  • Alama, M. ;
  • Lee, D.H. ;
  • Kim, J.J.
  • Received : 2014.12.15
  • Accepted : 2015.04.01
  • Published : 2015.07.01

Abstract

The purpose of this study was to characterize genetic architecture of behavior patterns in Sapsaree dogs. The breed population (n=8,256) has been constructed since 1990 over 12 generations and managed at the Sapsaree Breeding Research Institute, Gyeongsan, Korea. Seven behavioral traits were investigated for 882 individuals. The traits were classified as a quantitative or a categorical group, and heritabilities ($h^2$) and variance components were estimated under the Animal model using ASREML 2.0 software program. In general, the $h^2$ estimates of the traits ranged between 0.00 and 0.16. Strong genetic ($r_G$) and phenotypic ($r_P$) correlations were observed between nerve stability, affability and adaptability, i.e. 0.9 to 0.94 and 0.46 to 0.68, respectively. To detect significant single nucleotide polymorphism (SNP) for the behavioral traits, a total of 134 and 60 samples were genotyped using the Illumina 22K CanineSNP20 and 170K CanineHD bead chips, respectively. Two datasets comprising 60 (Sap60) and 183 (Sap183) samples were analyzed, respectively, of which the latter was based on the SNPs that were embedded on both the 22K and 170K chips. To perform genome-wide association analysis, each SNP was considered with the residuals of each phenotype that were adjusted for sex and year of birth as fixed effects. A least squares based single marker regression analysis was followed by a stepwise regression procedure for the significant SNPs (p<0.01), to determine a best set of SNPs for each trait. A total of 41 SNPs were detected with the Sap183 samples for the behavior traits. The significant SNPs need to be verified using other samples, so as to be utilized to improve behavior traits via marker-assisted selection in the Sapsaree population.

Keywords

Sapsaree;Single Nucleotide Polymorphism;Behavior;Heritability;Genome-wide Association

References

  1. Bartlett, C. R. 1976. Heritabilities and Genetic Correlations between Hip Dysplasia and Temperament Traits of Seeingeyedogs. Mastersthesis, Rutgers University, NewBrunswick, NJ, USA.
  2. Eggen, A. 2012. The development and application of genomic selection as a new breeding paradigm. Anim. Front. 2:10-15.
  3. Falconer, D. S. and T. F. C. Mackay. 1996. Introduction to Quantitative Genetics. 4th edn. Longman Group Ltd., Essex, England.
  4. Famular, T. R. 2001. Genetics of quantitative traits and improvement of dog breeds. In: The Genetics of the Dog (Eds. A. Ruvinsky and J. Sampson). CABI Publishing, CAB International, Wallingford, Oxon, UK, pp. 487-503.
  5. Ferrell, R. E., D. C. Morizot, J. Horn, and C. J. Carley. 1980. Biochemical markers in species endangered by introgression: The red wolf. Biochem. Genet. 18:39-49. https://doi.org/10.1007/BF00504358
  6. Fredholm, M. and A. K. Wintero. 1995. Variation of short tandem repeats within and between species belonging to the Canidae family. Mamm. Genome 6:11-18. https://doi.org/10.1007/BF00350887
  7. Galibert, F., C. Andre, A. Cheron, J. C. Chuat, C. Hitte, Z. Jiang, S. Jouquand, C. Priat, C. Renier, and F. Vignaux. 1998. The importance of the canine model in medical genetics. Bull. Acad. Natl. Med. 182:811-821.
  8. Gilmour, A. R., B. R. Cullis, S. J. Welham, and R. Thompson. 2001. ASREML Reference Manual. NSW Agriculture, Orange, Australia.
  9. Goddard, M. E. and R. G. Beilharz. 1982. Genetics of traits which determine the suitability of dogs as guide-dogs for the blind. Appl. Anim. Ethol. 9:299-315.
  10. Han, K. I., M. Alam., Y. M. Lee., D. H. Lee., J. H. Ha, and J. J. Kim. 2010. A study on t he morphology and Behavior of the Sapsaree: A Korean native dog (Canis familiaris). J. Anim. Sci. Technol. 52:481-490. https://doi.org/10.5187/JAST.2010.52.6.481
  11. Karlsson, E. K., I. Baranowska, C. M. Wade, N. H. Salmon Hillbertz, M. C. Zody, N. Anderson, T. M. Biagi, N. Patterson, G. R. Pielberg, E. J. Kulbokas 3rd et al. 2007. Efficient mapping of mendelian traits in dogs through genome-wide association. Nat. Genet. 39:1321-1328. https://doi.org/10.1038/ng.2007.10
  12. Karlsson, E. K. and K. Lindblad-Toh. 2008. Leader of the pack: gene mapping in dogs and other model organisms. Nat. Rev. Genet. 9:713-725.
  13. Kim, K. S., H. W. Jeong, C. K. Park, and J. H. Ha. 2001. Suitability of AFLP markers for the study of Genetic relationships among Korean native dogs. Genes Genet. Syst. 76:243-250. https://doi.org/10.1266/ggs.76.243
  14. Lynch, M. and B. Walsh. 1998. Genetics and analysis of quantitative traits. Sinauer, Sunderland, MA, USA.
  15. Neter, J., W. Wasserman, and M. H. Kutner. 1990. Applied Linear Statistical Models. 3rd ed. McGraw-Hill/Irwin, Boston, MA, USA.
  16. Ostrander, E. A. and E. Giniger. 1997. Semper fidelis: What man's best friend can teach us about human biology and disease. Am. J. Hum. Genet. 61:475-480. https://doi.org/10.1086/515522
  17. Patterson, D. F., M. E. Haskins, and P. F. Jezyk. 1982. Models of human genetic disease in domestic animals. Adv. Hum. Genet. 12:263-339.
  18. Reuterwall, C. and N. Ryman. 1973. An estimate of the magnitude of additive genetic variation of some mental characters in Alsatian dogs. Hereditas 73:277-283.
  19. Ruefenacht, S., S. Gebhardt-henrich, T. Miyake, and C. Gaillard. 2002. A behavior test of German Shepherd dogs: heritability of seven different traits. Appl. Anim. Behav. Sci. 79:113-132. https://doi.org/10.1016/S0168-1591(02)00134-X
  20. Spaady, T. C. and E. A. Ostrander. 2008. Canine behavioral genetics: Pointing out the phenotypes and herding up the genes. Am. J. Hum. Genet. 82:10-18. https://doi.org/10.1016/j.ajhg.2007.12.001
  21. Sutter, N. B., C. D. Bustamante, K. Chase, M. M. Gray, K. Zhao, L. Zhu, B. Padhukasahasram, E. Karlins, S. Davis, P. G. Jones, P. Quignon, G. S. Johnson, H. G. Parker, N. Fretwell, D. S. Mosher, D. F. Lawler, E. Satyaraj, M. Nordborg, K. G. Lark, R. K. Wayne, and E. A. Ostrander. 2007. A single IGFI allele is a major determinant of small size in dogs. Science 316(5821):112-115. https://doi.org/10.1126/science.1137045
  22. Sutter, N. B. and E. A. Ostrander. 2004. Dog star rising: The canine genetic system. Nat. Rev. Genet. 5:900-910. https://doi.org/10.1038/nrg1492
  23. Vila, C., P. Savolainen, J. E. Maldonado, I. R. Amorim, J. E. Rice, R. L. Honeycut, K. A. Crandall, J. Lundeberg, and R. K. Wayne. 1997. Multiple and ancient origins of the domestic dog. Science 276(5319):1687-1689. https://doi.org/10.1126/science.276.5319.1687
  24. Wayne, R. K. and E. A. Ostrander. 1999. Origin, genetic diversity, and genome structure of the domestic dog. BioEssays 21:247-257. https://doi.org/10.1002/(SICI)1521-1878(199903)21:3<247::AID-BIES9>3.0.CO;2-Z
  25. Wilsson, E. and P.-E. Sundgren. 1997. The use of a behavior test for selection of dogs for service and breeding. II: Heritability for tested parameters and effect of selection based on service dog characteristics. Appl. Anim. Behav. Sci. 54:235-241. https://doi.org/10.1016/S0168-1591(96)01175-6

Cited by

  1. Genetic mapping of canine fear and aggression vol.17, pp.1, 2016, https://doi.org/10.1186/s12864-016-2936-3
  2. Whole-transcriptome analyses of the Sapsaree, a Korean natural monument, before and after exercise-induced stress vol.58, pp.1, 2016, https://doi.org/10.1186/s40781-016-0097-1

Acknowledgement

Supported by : KNU