Development of novel SNP system for individual and pedigree control in a Japanese Black cattle population using whole-genome genotyping assay

Animal Science Journal

Volumn 81, Issue 4, 2010, Pages 506-512

  Hara, Kazuhiro ^a   Kon, Yukari ^a   Sasazaki, Shinji ^a   Mukai, Fumio ^a   Mannen, Hideyuki ^a  

^a KOBE UNIVERSITY   (Japan)

Author keywords

Individual identification; Japanese Black cattle; Parentage test; Single nucleotide polymorphism

Indexed keywords

ANIMAL; ARTICLE; CATTLE; FEMALE; GENETICS; GENOMICS; GENOTYPE; JAPAN; MALE; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; CATTLE; FEMALE; GENOMICS; GENOTYPE; JAPAN; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE;

BOS;

EID: 77955170068     PISSN: 13443941     EISSN: 17400929     Source Type: Journal    
DOI: 10.1111/j.1740-0929.2010.00766.x     Document Type: Article

References (20)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. Heredity 1990, 86:395-398.
2. Baruch E, Weller JI. Estimation of the number of SNP genetic markers required for parentage verification. Animal Genetics 2008, 39:474-479.
3. Excoffier L, Laval G, Schneider S. Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 2005, 1:47-50.
4. Hara K, Watabe H, Sasazaki S, Mukai F, Mannen H. Development of SNP markers for individual identification and parentage test in Japanese Black cattle population. Animal Science Journal 2010, 81:152-157.
5. Heaton MP, Harhay GP, Bennett GL, Stone RT, Grosse WM, Casas E, Keele JW, Smith TPL, Chitko-McKown CG, Laegreid WW. Selection and use of SNP markers for animal identification and paternity in U.S. beef cattle. Mammalian Genome 2002, 13:272-281.
6. Holland PM, Abramson RD, Watson R, Gelfand DH. Detection of specific polymerase chain reaction product by utilizing the 5′→3′ exonuclease activity of Thermus aquaticus DNA polymerase. Proceedings of the National Academy of Sciences of the United States of America 1991, 88:7276-7280.
7. Holt CL, Stauffer C, Wallin JM, Lazaruk KD, Nguyen T, Budowle B, Walsh PS. Practical applications of genotypic surveys for forensic STR testing. Forensic Science International 2000, 112:91-109.
8. Jamieson A, Taylor SC. Comparisons of three probability formulae for parentage exclusion. Animal Genetics 1997, 28:397-400.
9. Khatkar MS, Nicholas FW, Collins AR, Zenger KR, Cavanagh JA, Barris W, Schnabel RD, Taylor JF, Raadsma HW. Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel. BMC Genomics 2008, 9:187.
10. McKay SD, Schnabel RD, Murdoch BM, Matukumalli LK, Aerts J, Coppieters W, Crews D, Dias Neto E, Gill CA, Gao C, Mannen H, Wang Z, Van Tassell CP, Williams JL, Taylor JF, Moore SS. An assessment of population structure in eight breeds of cattle using a whole genome SNP panel. BMC Genetics 2008, 9:37-45.
11. Nijman IJ, Kuipers S, Verheul M, Guryev V, Cuppen E. A genome-wide SNP panel for mapping and association studies in the rat. BMC Genomics 2008, 9:95-103.
12. Nishida N, Tanabe T, Takasu M, Suyama A, Tokunaga K. Further development of multiplex single nucleotide polymorphism typing method, the DigiTag2 assay. Analytical Biochemistry 2007, 364:78-85.
13. Ross P, Hall L, Smirnov I, Haff L. High level multiplex genotyping by MALDI-TOF mass spectrometry. Nature Biotechnology 1998, 16:1347-1351.
14. Sambrook J, Russell D. Molecular Cloning 2001, A Laboratory Manual, Cold Spring Harbor Laboratory, New York
15. Schnabel RD, Ward TJ, Derr JN. Validation of 15 microsatellites for parentage testing in North American bison, Bison bison and domestic cattle. Animal Genetics 2000, 31:360-366.
16. Staaf J, Vallon-Christersson J, Lindgren D, Juliusson G, Rosenquist R, Höglund M, Borg A, Ringner M. Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios. BMC Bioinformatics 2008, 9:409.
17. Taylor JD, Briley D, Nguyen Q, Long K, Iannone MA, Li MS, Ye F, Afshari A, Lai E, Wagner M, Chen J, Weiner MP. Flow cytometric platform for high-throughput single nucleotide polymorphism analysis. Biotechniques 2001, 30:661-669.
18. Tobler AR, Short S, Andersen MR, Paner TM, Briggs JC, Lambert SM, Wu Wang Y, Spoonde AY, Koehler RT, Peyret N, Chen C, Broomer AJ, Ridzon DA, Zhou H, Hoo BS, Hayashibara KC, Leong LN, Ma CN, Rosenblum BB, Day JP, Ziegle JS, De, Vega FM, Rhodes MD, Hennessy KM, Wenz HM. The SNPlex genotyping system: a flexible and scalable platform for SNP genotyping. Biomolecular Techniques 2005, 16:398-406.
19. Werner FAO, Durstewitz G, Habermann FA, Thaller G, Kramer W, Kollers S, Buitkamp J, Georges M, Brem G, Mosner J, Fries R. Detection and characterization of SNPs useful for identity control and parentage testing in major European dairy breeds. Animal Genetics 2004, 35:44-49.
20. Wiggans GR, Sonstegard TS, VanRaden PM, Matukumalli LK, Schnabel RD, Taylor JF, Schenkel FS, Van Tassell CP. Selection of single-nucleotide polymorphisms and quality of genotypes used in genomic evaluation of dairy cattle in the United States and Canada. Dairy Science 2009, 92:3431-3436.