JOURNAL BROWSE
Search
Advanced SearchSearch Tips
Simulation Study on Parentage Analysis with SNPs in the Japanese Black Cattle Population
facebook(new window)  Pirnt(new window) E-mail(new window) Excel Download
 Title & Authors
Simulation Study on Parentage Analysis with SNPs in the Japanese Black Cattle Population
Honda, Takeshi; Katsuta, Tomohiro; Mukai, Fumio;
  PDF(new window)
 Abstract
Parentage tests using polymorphic DNA marker are commonly performed to avoid incorrect recording of the parental information of livestock animals, and single-nucleotide polymorphisms (SNPs) are becoming the method of choice. In Japanese Black cattle, parentage tests based on the exclusion method using microsatellite markers are currently conducted; however, an alternative SNP system aimed at parentage tests has recently been developed. In the present study, two types of simulations were conducted using the pedigree data of two subpopulations in the breed (subpopulations of Hyogo and Shimane prefectures) in order to examine the effect of actual genetic and breeding structures. The first simulation (simulation 1) investigated the usefulness of SNPs for excluding a close relative of the true sire; the second one (simulation 2) investigated the accuracy of sire identification tests for multiple full-sib putative sires by a combined method of exclusion and paternity assignment based on the LOD score. The success rates of excluding a single fullsib and sire of the true sires were, respectively, 0.9915 and 0.9852 in Hyogo and 0.9848 and 0.9852 in Shimane, when 50 SNPs with minor allele frequency (MAF: q) of 0.25q0.35 were used in simulation 1. The success rates of sire identification tests based solely on the exclusion method were relatively low in simulation 2. However, assuming that 50 SNPs with MAF of 0.25q0.35 or 0.45q0.5 were available, the total success rates including achievements due to paternity assignment were, respectively, 0.9430 and 0.9681 in Hyogo and 0.8999 and 0.9399 for Shimane, even when each true sire was assumed to compete with 50 full-sibs.
 Keywords
Parentage Analysis;SNPs;Simulation;Japanese Black;Pedigree Analysis;
 Language
English
 Cited by
1.
국내산 돼지고기의 원산지 검증을 위한 SNP Marker Set 개발,김상욱;이소평;이윤미;김종주;김태헌;최봉환;김관석;

Journal of Animal Science and Technology, 2010. vol.52. 2, pp.91-96 crossref(new window)
 References
1.
Anderson, E. C. and J. C. Garza. 2006, The power of singlenucleotide polymorphisms for large-scale parentage inference, Genetics 172:2567-2582 crossref(new window)

2.
Baruch, E. and J. I. Weller. 2008, Estimation of the number of SNP genetic markers required for parentage verification, Anim. Genet. 39:474-479 crossref(new window)

3.
Caballero, A. and M. A. Toro. 2000, Interrelations between effective population size and other pedigree tools for management of conserved populations, Genet. Res. Camb. 75:331-343 crossref(new window)

4.
Chakraborty, R., T. R. Meagher and P. E. Smouse. 1988, Parentage analysis with genetic markers in natural populations. I. The expected proportion of offspring with unambiguous paternity, Genetics 118:527-536

5.
Dodds, K. G., M. L. Tate, J. C. McEwan and A. M. Crawford. 1996, Exclusion probabilities for pedigree testing farm animals, Theor. Appl. Genet. 92:966-975 crossref(new window)

6.
Dodds, K. G., M. L. Tate and J. A. Sise. 2005, Genetic evaluation using parentage information from genetic markers, J. Anim. Sci. 83:2271-2279

7.
Double, M. C., A. Cockburn, S. C. Barry and P. E. Smouse. 1997, Exclusion probabilities for single-locus paternity analysis when related males compete for matings, Mol. Ecol. 6:1155-1166 crossref(new window)

8.
Eenennaam, A. L. V., R. L. Weaber, D. J. Drake, M. C. T. Penedo, R. L. Quaas, D. J. Garrick and E. J. Pollak. 2007, DNA-based paternity analysis and genetic evaluation in a large, commercial cattle ranch setting, J. Anim. Sci. 85:3159-3169 crossref(new window)

9.
Frankham, R., J. D. Ballou and D. A. Briscoe. 2002. Introduction to Conservation Genetics. Cambridge University Press, Cambridge

10.
Gomez-Raya, L., K. Priest, W. M. Rauw, M. Okomo-Adhiambo, D. Thain, B. Bruce, A. Rink, R. Torell, L. Grellman, R. Narayanan and C. W. Beattie. 2008, The value of DNA paternity identification in beef cattle: Examples from Nevada's free-range ranches, J. Anim. Sci. 86:17-24

11.
Heaton, M. P., G. P. Harhay, G. L. Bennett, R. T. Stone, W. M. Grosse, E. Casas, J. W. Keele, T. P. L. Smith, C. G. Chitko- McKown and W. W. Laegreid. 2002, Selection and use of SNP markers for animal identification and paternity analysis in US beef cattle. Mamm, Genome 13:272-281

12.
Hill, W. G., B. A. Salisbury and A. J. Webb. 2008, Parentage identification using single nucleotide polymorphism genotypes: Application to product tracing, J. Anim. Sci. 86:2508-2517 crossref(new window)

13.
Honda, T., T. Nomura, Y. Yamaguchi and F. Mukai. 2002, Pedigree analysis of genetic subdivision in a population of Japanese Black cattle, Anim. Sci. J. 73:445-452 crossref(new window)

14.
Jones, A. and W. R. Ardren. 2003, Methods of parentage analysis in natural populations, Mol. Ecol. 12:2511-2523 crossref(new window)

15.
Kalinowski, S. T., M. L. Taper and T. C. Marshall. 2007, Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment, Mol. Ecol. 16:1099-1106 crossref(new window)

16.
MacCluer, J. W., J. L. VandeBerg, B. Read and O. A. Ryder. 1986, Pedigree analysis by computer simulation, Zoo. Biol. 5:147-160 crossref(new window)

17.
Marshall, T. C., J. Slate, L. E. B. Kruuk and J. M. Pemberton. 1998, Statistical confidence for likelihood-based paternity inference in natural populations, Mol. Ecol 7:639-655 crossref(new window)

18.
Meagher, T. R. 1986, Analysis of paternity within a natural population of Chamaelirium luteum. I. Identification of mostlikely male parents, Am. Nat. 128:199-215 crossref(new window)

19.
Nei, M. 1977, F-statistics and analysis of gene diversity in subdivided populations, Ann. Hum. Genet. 41:225-233 crossref(new window)

20.
Robertson, A. 1965, The interpretation of genotypic ratios in domestic animal populations, Anim. Prod. 7:319-324 crossref(new window)

21.
Rohrer, G. A., B. A. Freking and D. Nonneman. 2007, Single nucleotide polymorphisms for pig identification and parentage exclusion, Anim. Genet. 38:253-258 crossref(new window)

22.
Wang, J. 1996, Deviation from Hardy-Weinberg proportions in finite populations, Genet. Res., Camb. 68:249-257 crossref(new window)

23.
Werner, F. A. O., G. Durstewitz, F. A. Habermann, G. Thaller, W. Kr$\ddot{a}$mer, S. Kollers, J. Buitkamp, M. Georges, G. Brem, J. Mosner and R. Fries. 2004, Detection and characterization of SNPs useful for identity control and parentage testing in major European dairy breeds, Anim. Genet. 35:44-49 crossref(new window)