Browse > Article
http://dx.doi.org/10.5713/ajas.2010.r.03

Development and Application of High-density SNP Arrays in Genomic Studies of Domestic Animals  

Fan, Bin (Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University)
Du, Zhi-Qiang (Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University)
Gorbach, Danielle M. (Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University)
Rothschild, Max F. (Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University)
Publication Information
Asian-Australasian Journal of Animal Sciences / v.23, no.7, 2010 , pp. 833-847 More about this Journal
Abstract
In the past decade, there have been many advances in whole-genome sequencing in domestic animals, as well as the development of "next-generation" sequencing technologies and high-throughput genotyping platforms. Consequently, these advances have led to the creation of the high-density SNP array as a state-of-the-art tool for genetics and genomics analyses of domestic animals. The emergence and utilization of SNP arrays will have significant impacts not only on the scale, speed, and expense of SNP genotyping, but also on theoretical and applied studies of quantitative genetics, population genetics and molecular evolution. The most promising applications in agriculture could be genome-wide association studies (GWAS) and genomic selection for the improvement of economically important traits. However, some challenges still face these applications, such as incorporating linkage disequilibrium (LD) information from HapMap projects, data storage, and especially appropriate statistical analyses on the high-dimensional, structured genomics data. More efforts are still needed to make better use of the high-density SNP arrays in both academic studies and industrial applications.
Keywords
Whole-genome Sequencing; HapMap; SNP Array; Genomics; Domestic Animals;
Citations & Related Records

Times Cited By Web Of Science : 2  (Related Records In Web of Science)
Times Cited By SCOPUS : 2
연도 인용수 순위
1 vonHoldt, B. M., J. P. Pollinger, K. E. Lohmueller, E. Han, H. G. Parker et al. Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature 464:898-902.   DOI   ScienceOn
2 Wade, C. M., E. Giulotto, S. Sigurdsson, M. Zoli, S. Gnerre et al. 2009. Genome sequence, comparative analysis, and population genetics of the domestic horse. Science 326:865-867.   DOI   ScienceOn
3 Weller, J. I., G. Glick, Y. Zeron, E. Seroussi and M. Ron. 2010. Paternity validation and estimation of genotyping error rate for the BovineSNP50 BeadChip. Anim. Genet. Published online doi:10.1111/j.1365-2052.2010.02035.x   DOI   ScienceOn
4 Wernersson, R., M. H. Schierup, F. G. Jorgensen, J. Gorodkin, F. Panitz et al. 2005. Pigs in sequence space: A 0.66× coverage pig genome survey based on shotgun sequencing. BMC Genomics 6:70.   DOI   ScienceOn
5 Wiedmann, R. T., T. P. L. Smith and D. J. Nonneman. 2008. SNP discovery in swine by reduced representation and high throughput pryosequencing. BMC Genet. 9:81.
6 Wilbe, M., P. Jokinen, K. Truve, E. H. Seppala, E. K. Karlsson et al. 2010. Genome-wide association mapping identifies multiple loci for a canine SLE-related disease complex. Nat. Genet. 42: 250-254.   DOI   ScienceOn
7 Wood, S. H., X. Y. Ke, T. Nuttall, N. McEwan, W. E. Ollier et al. 2009. Genome-wide association analysis of canine atopic dermatitis and identification of disease related SNPs. Immunogenetics 61:765-772.   DOI
8 Zhao, X., H. T. Blair, S. Onteru, S. A. Piripi, M. F. Rothschild et al. 2010. A genome wide association study and fine mapping for Chondrodysplasia of Texel sheep. The International Plant & Animal Genome XVIII Conference. January 9-13, San Diego, California. P579.
9 Steemers, F. J. and K. L. Gunderson. 2007. Whole genome genotyping technologies on the $BeadArray^{TM}$ platform. Biotechnol. J. 2:41-49.   DOI   ScienceOn
10 Sved, J. A. 1971. Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theor. Popul. Biol. 2:125-141.   DOI   ScienceOn
11 The Bovine Genome Sequencing and Analysis Consortium. 2009. The genome sequence of Taurine cattle: A window to ruminant biology and evolution. Science 324:522-528.   DOI   ScienceOn
12 The Bovine HapMap Consortium. 2009. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324:528-532.   DOI   ScienceOn
13 VanRaden, P. M., C. P. Van Tassell, G. R. Wiggans, T. S. Sonstegard, R. D. Schnabel et al. 2009. Reliability of genomic prediction s for North American Holstein bulls. J. Dairy Sci. 92:16-24.   DOI   ScienceOn
14 Toosi, A., R. L. Fernando and J. C. M. Dekkers. 2010. Genomic selection in admixed and crossbred populations. J. Anim. Sci. 88:32-46.   DOI   ScienceOn
15 Van Tassell, C. P., T. P. L. Smith, L. K. Matukumalli, J. F. Taylor, R. D. Schnabel et al. 2008. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat. Methods 5:247-252.   DOI   ScienceOn
16 VanRaden, P. and P. G. Sullivan. 2010. International genomic evaluation methods for dairy cattle. Genet. Sel. Evol. 42:7.   DOI   ScienceOn
17 Verbyla, K. L., B. J. Hayes, P. J. Bowman and M. E. Goddard. 2009. Accuracy of genomic selection using stochastic variable selection in Australian Holstein Friesian dairy cattle. Genet. Res. Camb. 91:307-311.   DOI   ScienceOn
18 Villa-Angulo, R., L. K. Matukumalli, C. A. Gill, J. Choi, C. P. Van Tassell and J. J. Grefenstette. 2009. High-resolution haplotype block structure in the cattle genome. BMC Genet. 10:19.
19 Qanbari, S., E. C. G. Pimentel, J. Tetens, G. Thaller, P. Lichtner et al. 2010b. The pattern of linkage disequilibrium in German Holstein cattle. Anim. Genet. Published Online doi:10.1111/j.1365-2052.2009.02011.x   DOI   ScienceOn
20 Ramos, A. M., R. P. M. A. Crooijmans, N. A. Affara, A. J. Amaral, A. L. Archibald et al. 2009. Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS ONE 4: e6524.   DOI   ScienceOn
21 Rothschild, M. F., Z. L. Hu and Z. H. Jiang. 2007. Advances in QTL mapping in pigs. Int. J. Biol. Sci. 3:192-197.
22 Settles, M., R. Zanella, S. D. McKay, R. D. Schnabel, J. F. Taylor et al. 2009. A whole genome association analysis identifies loci associated with Mycobacterium avium subsp. paratuberculosis infection status in US Holstein cattle. Anim. Genet. 40:655-662.   DOI   ScienceOn
23 Rothschild, M. F., D. M. Gorbach, B. Fan, S. K. Onteru, Z. Q. Du et al. 2010. Applications of new porcine genomic tools to trait discovery and understanding genomic architecture. The International Plant & Animal Genome XVIII Conference. January 9-13, San Diego, California. W614.
24 Rubin, C. J., M. C. Zody, J. Eriksson, J. R. S. Meadows, E. Sherwood et al. 2010. Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464:587-591.   DOI   ScienceOn
25 Sabeti, P. C., P. Varilly, B. Fry, J. Lohmueller, E. Hostetter et al. 2007. Genome-wide detection and characterization of positive selection in human populations. Nature 449:913-918.   DOI   ScienceOn
26 Sherman, E. L., J. D. Nkrumah and S. S. Moore. 2010. Whole genome single nucleotide polymorphism associations with feed intake and feed efficiency in beef cattle. J. Anim. Sci. 88:16-22.   DOI   ScienceOn
27 Snelling, W. M., M. F. Allan, J. W. Keele, L. A. Kuehn, T. McDaneld, T. P. L. Smith, T. S. Sonstegard, R. M. Thallman and G. L. Bennett. 2010. Genome-wide association study of growth in crossbred beef cattle. J. Anim. Sci. 88:837-848.   DOI   ScienceOn
28 Muir, W. M., G. K. S. Wong, Y. Zhang, J. Wang, M. A. M. Groenen et al. 2008. Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds. Proc. Natl. Acad. Sci. USA 105:17312-17317.   DOI   ScienceOn
29 Murdoch, B. M., M. L. Clawson, W. W. Laegreid, P. Stothard, M. Settles et al. 2010. A 2cM genome-wide scan of European Holstein cattle affected by classical BSE. BMC Genet.11:20.
30 Ogorevc, J., A. Razpet and P. Dovc. 2009. Database of cattle candidate genes and genetic markers for milk production and mastitis. Anim. Genet. 40:832-851.   DOI   ScienceOn
31 Onteru, S. K., B. Fan, D. Garrick, K. J. Stalder and M. F. Rothschild. 2009. Whole genome analyses for pig reproductive traits using the PorcineSNP60 BeadChip. Pig Genome III Conference. November 2-4, 2009, Hinxton, Cambridge, UK. Abstract No. 5.
32 Pant, S. D., F. S. Schenkel, C. P. Verschoor, Q. You, D. F. Kelton et al.. 2010. A principal component regression based genome wide analysis approach reveals the presence of a novel QTL on BTA7 for MAP resistance in holstein cattle. Genomics 95:176-182.   DOI   ScienceOn
33 Parker, H. G., B. M. VonHoldt, P. Quignon, E. H. Margulies, S. Shao et al. 2009. An expressed fgf4 retrogene is associated with breed-defining chondrodysplasia in domestic dogs. Science 325:995-998.   DOI   ScienceOn
34 Perkel, J. 2008. SNP genotyping: six technologies that keyed a revolution. Nat. Methods 5:447-453.   DOI   ScienceOn
35 Pontius, J. U., J. C. Mullikin, D. R. Smith, Agencourt Sequencing Team, K. Lindblad-Tohet et al. 2007. Initial sequence and comparative analysis of the cat genome. Genome Res. 17:1675-1689.   DOI   ScienceOn
36 Qanbari, S., E. C. G. Pimentel, J. Tetens, G. Thaller, P. Lichtner et al. 2010a. A genome-wide scan for signatures of recent selection in Holstein cattle. Anim. Genet. Published Online doi:10.1111/j.1365-2052.2009.02016.x   DOI   ScienceOn
37 Karlsson, E. K., I. Baranowska, C. M. Wade, N. S. Hillbertz, M. C. Zody et al. 2007. Efficient mapping of mendelian traits in dogs through genome-wide association. Nat. Genet. 39:1321-1328.   DOI   ScienceOn
38 Kerstens, H. H. D., S. Kollers, A. Kommadath, M. del Rosario, B. Dibbits et al. 2009. Mining for single nucleotide polymorphism in pig genome sequence data. BMC Genomics 10:4.   DOI   ScienceOn
39 Kim, E. S. and B. W. Kirkpatrick. 2009. Linkage disequilibrium in the North American Holstein population. Anim. Genet. 40:279-288.   DOI   ScienceOn
40 Kijas, J. W., D. Townley, B. P. Dalrymple, M. P. Heaton, J. F. Maddox et al. 2009. A genome wide survey of SNP variation reveals the genetic structure of sheep breeds. PLoS ONE 4:e4668.   DOI   ScienceOn
41 Kirkness, E. F., V. Bafna, A. L. Halpern, S. Levy, K. Remington et al. 2003. The dog genome: Survey sequencing and comparative analysis. Science 301:1898-1903.   DOI   ScienceOn
42 Lindblad-Toh, K., C. M. Wade, T. S. Mikkelsen, E. K. Karlsson, D. B. Jaffe et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438:803-819.   DOI   ScienceOn
43 Manolio, T. A., F. S. Collins, N. J. Cox, D. B. Goldstein, L. A. Hindorff et al. 2009. Finding the missing heritability of complex disease. Nature 461:747-753.   DOI   ScienceOn
44 Matukumalli, L. K., C. T. Lawley, R. D. Schnabel, J. F. Taylor, M. F. Allan et al. 2009. Development and characterization of a high density SNP genotyping assay for cattle. PLoS ONE 4:e5350.   DOI   ScienceOn
45 Megens, H. J., R. P. M. A. Crooijmans, J. W. M. Bastiaansen, H. H. D. Kerstens, A. Coster et al. 2009. Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken. BMC Genet. 10:86.
46 Meuwissen, T. H. E., B. J. Hayes and M. E. Goddard. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819-1829.
47 Groenen, M. A. M., A. Amaral, H. J. Megens, G. Larson, A. L. Archibald et al. 2010a. The Porcine HapMap Project: genome-wide assessment of nucleotide diversity, haplotype diversity and footprints of selection in the pig. The International Plant & Animal Genome XVIII Conference. January 9-13, San Diego, California. W609.
48 Hayes, B. J., P. J. Bowman, A. J. Chamberlain and M. E. Goddard. 2009b. Genomic selection in dairy cattle: Progress and challenges. J. Dairy Sci. 92:433-443.   DOI   ScienceOn
49 Groenen, M. A. M., P. Wahlberg, M. Foglio, H. H. Cheng, H. J. Megens et al. 2010b. A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate. Genome Res. 19:510-519.
50 Hayes, B. J., P. J. Bowman, A. J. Chamberlain, K. Savin, C. P. van Tassell et al. 2009a. A validated genome wide association study to breed cattle adapted to an environment altered by climate change. PLoS ONE 4:e6676.   DOI   ScienceOn
51 Hindorff, L. A., P. Sethupathy, H. A. Junkins, E. M. Ramos, J. P. Mehta, F. S. Collins and T. A. Manolio. 2009. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. USA 106:9362-9367.   DOI   ScienceOn
52 Ibanez-Escriche, N., R. L. Fernando, A. Toosi and J. C. M. Dekkers. 2009. Genomic selection of purebred for crossbred performance. Genet. Sel. Evol. 41:12.   DOI   ScienceOn
53 International Chicken Genome Sequencing Consortium. 2004. Sequence and comparative analysis of the chicken genome provide unique perspective on vertebrate evolution. Nature 432:695-716.   DOI   ScienceOn
54 International Chicken Polymorphism Map Consortium. 2004. A Genetic variation map for chicken with 2.8 million single-nucleotide polymorphism. Nature 432:717-722.   DOI   ScienceOn
55 Iso-Touru, T., J. Kantanen, M. H. Li, Z. Gizejewski and J. Vilkki. 2009. Divergent evolution in the cytoplasmic domains of PRLR and GHR genes in Artiodactyla. BMC Evol. Biol. 9:172.   DOI   ScienceOn
56 Fernando, R. L. and D. J. Garrick. 2009. GenSel - User manual for a portfolio of genomic selection related analyses. Animal Breeding and Genetics, Iowa State University, Ames.
57 Georges, M. 2007. Mapping, fine mapping, and molecular dissection of quantitative trait loci in domestic animals. Annu. Rev. Genomics Hum. Genet. 8:131-162.   DOI   ScienceOn
58 Feugang, J. M., A. Kaya, G. P. Page, L. Chen, T. Mehta et al. 2009. Two-stage genome-wide association study identifies integrin beta 5 as having potential role in bull fertility. BMC Genomics 10:176.   DOI   ScienceOn
59 Fisher, P. J., B. Malthus, M. C. Walker, G. Corbett and R. J. Spelman. 2009. The number of single nucleotide polymorphisms and on-farm data required for whole-herd parentage testing in dairy cattle herds. J. Dairy Sci. 92:369-374.   DOI   ScienceOn
60 Flori, L., S. Fritz, F. Jaffrézic, M. Boussaha, I. Gu et al. 2009. The genome response to artificial selection: A case study in dairy cattle. PLoS ONE 4:e6595.   DOI   ScienceOn
61 Gianola, D., R. L. Fernando and A. Stella. 2006. Genomic-assisted prediction of genetic value with semiparametric procedures. Genetics 173:1761-1776.   DOI   ScienceOn
62 Goddard, M. E. 2009. Genomic selection: prediction of accuracy and maximisation of long term response. Genetica 136:245-257.   DOI
63 Goddard, M. E. and B. J. Hayes. 2009. Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nat. Rev. Genet. 10:381-391.   DOI   ScienceOn
64 Gorbach, D. M., W. Cai, J. C. M. Dekkers, J. M. Young, D. J. Garrick et al. 2009. Whole-genome analyses for genes associated with residual feed intake and related traits utilizing the PorcineSNP60 BeadChip. Pig Genome III Conference. November 2-4. Hinxton, UK. Abstract No. 11.
65 Green, E. D. 2001. Strategies for the systematic sequencing of complex genomes. Nat. Rev. Genet. 2: 573-583.
66 Dalrymple, B. P., E. F. Kirkness, M. Nefedov, S. McWilliam, A. Ratnakumar et al. 2007. Using comparative genomics to reorder the human genome sequence into a virtual sheep genome. Genome Biol. 8:R152.   DOI
67 Cadieu, E., M. W. Neff, P. Quignon, K. Walsh, K. Chase et al. 2009. Coat variation in the domestic dog is governed by variants in three genes. Science 326:150-153.   DOI   ScienceOn
68 Calus, M. P. L. 2009. Genomic breeding value prediction: methods and procedures. Animal 4:157-164.
69 Charlier, C., W. Coppieters, H. Rollin, D. Desmecht, J. S. Agerholm et al. 2008. Highly effective SNP-based association mapping and management of recessive defects in livestock. Nat. Genet. 40:449-454.   DOI   ScienceOn
70 de Roos, A. P., B. J. Hayes, R. J. Spelman and M. E. Goddard. 2008. Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle. Genetics 179:1503-1512.   DOI   ScienceOn
71 Decker, J. E., J. C. Pires., G. C. Conant, S. D. McKay, M. P. Heaton et al. 2009. Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics. Proc. Natl. Acad. Sci. USA 106:18644-18649.   DOI   ScienceOn
72 Drogemuller, C., E. K. Karlsson, M. K. Hytonen, M. Perloski, G. Dolf et al. 2008. A mutation in hairless dogs implicates FOXI3 in ectodermal development. Science 321:1462.   DOI   ScienceOn
73 Eck, S. H., A. Benet-Pages, K. Flisikowski, T. Meitinger, R. Fries and T. Storm. 2009. Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery. Genome Biol. 10:R82.   DOI   ScienceOn
74 Fan, B., S. K. Onteru, D. Garrick, K. J. Stalder and M. F. Rothschild. 2009. A genome-wide association study for pig production and feet and leg structure traits using the PorcineSNP60 BeadChip. Pig Genome III Conference, November 2-4, 2009, Hinxton, Cambridge, UK. Abstract No. 6.
75 Awano, T., G. S. Johnson, C. M. Wade, M. L. Katz, G. C. Johnson et al. 2009. Genome-wide association analysis reveals a SOD1 mutation in canine degenerative myelopathy that resembles amyotrophic lateral sclerosis. Proc. Natl. Acad. Sci. USA 106:2794-2799.   DOI   ScienceOn
76 Andersson, L. 2009. Genome-wide association analysis in domestic animals: a powerful approach for genetic dissection of trait loci. Genetica 136:341-349.   DOI
77 Arias, J. A., M. Keehan, P. Fisher, W. Coppieters and R. Spelman. 2009. A high density linkage map of the bovine genome BMC Genet. 10:18.
78 Aulchenko, Y. S., D. J. de Koning and C. Haley. 2007. Genomewide rapid association using mixed model and regression: a fast and simple method for genomewide pedigree-based quantitative trait loci association analysis. Genetics 177:577-585.   DOI   ScienceOn
79 Bannasch, D., A. Young, J. Myers, K. Truve, P. Dickinson et al. 2009. Localization of canine Brachycephaly using an across breed mapping approach. PLoS ONE 5:e9632.
80 Barendse, W., B. E. Harrison, R. J. Bunch, M. B. Thomas and L. B. Turner. 2009. Genome wide signatures of positive selection: The comparison of independent samples and the identification of regions associated to traits. BMC Genomics 10:178.   DOI   ScienceOn
81 Barendse, W., A. Reverter, R. J. Bunch, B. E. Harrison, W. Barris and M. B. Thomas. 2007. A validated whole-genome association study of efficient food conversion in cattle. Genetics 176:1893-1905.   DOI   ScienceOn
82 Becker, D., J. Tetens, A. Brunner, D. Burstel, M. Ganter et al. 2010. Microphthalmia in Texel sheep is associated with a missense mutation in the paired-like homeodomain 3 (PITX3) gene. PLoS ONE 5:8689.   DOI   ScienceOn
83 Amaral, A. J., H. J. Megens, H. H. D. Kerstens, H. C. M. Heuven, B. Dibbits et al. 2009. Application of massive parallel sequencing to whole genome SNP discovery in the porcine genome. BMC Genomics 10:374.   DOI   ScienceOn
84 Brooks, S. A., N. Gabreski, D. Miller, A. Brisbin, H. E. Brown et al. 2010. Whole-genome SNP association in the horse: Identification of a deletion in Myosin Va responsible for Lavender Foal Syndrome. PLoS Genet. 6:e1000909.   DOI   ScienceOn
85 Abasht, B., E. Sandford, J. Arango, P. Settar, J. E. Fulton et al. 2009. Extent and consistency of linkage disequilibrium and identification of DNA markers for production and egg quality traits in commercial layer chicken populations. BMC Genomics 10 (Suppl 2):S2.   DOI
86 Altshuler, D., V. J. Pollara, C. R. Cowles, W. J. Van Ettern, J. Baldwin et al. 2000. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407: 513-516.   DOI   ScienceOn
87 Andersson, L. and M. Georges. 2004. Domestic-animal genomics: Deciphering the genetics of complex traits. Nat. Rev. Genet. 5: 202-212.   DOI   ScienceOn
88 Amaral, A. J., H. J. Megens, R. P. M. A. Crooijmans, H. C. M. Heuven and M. A. M. Groenen. 2008. Linkage disequilibrium decay and haplotype block structure in the pig. Genetics 179: 569-579.   DOI   ScienceOn