Simulation Appraisal of the Adequacy of Number of Background Markers for Relationship Estimation in Association Mapping

Plant Genome

Volumn 2, Issue 1, 2009, Pages

  Yu, Jianming ^a   Zhang, Zhiwu ^b   Zhu, Chengsong ^a   Tabanao, Dindo A ^c   Pressoir, Gael ^d   Tuinstra, Mitchell R ^e   Kresovich, Stephen ^b   Todhunter, Rory J ^f   Buckler, Edward S ^b  

^a KANSAS STATE UNIVERSITY   (United States)

^b Department of Obstetrics Gynecology   (United States)

^c PHILIPPINE RICE RESEARCH INSTITUTE   (Philippines)

^d Hispaniola Center for Biofuels and Sustainable Agriculture   (Haïti)

^e PURDUE UNIVERSITY   (United States)

^f Animal Health Diagnostic Center   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 70949095163     PISSN: None     EISSN: 19403372     Source Type: Journal    
DOI: 10.3835/plantgenome2008.09.0009     Document Type: Article

References (63)

1. Anderson, J.A., Churchill, G.A., Autrique, J.E., Tanksley, S.D., and Sorrells, M.E. 1993. Optimizing parental selection for genetic-linkage maps. Genome 36:181–186.10.1139/g93-024. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=A1993KP62300024&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
2. Aranzana, M.J., Kim, S., Zhao, K., Bakker, E., Horton, M., Jakob, K., Lister, C., Molitor, J., Shindo, C., Tang, C., Toomajian, C., Traw, B., Zheng, H., Bergelson, J., Dean, C., Marjoram, P., and Nordborg, M. 2005. Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet. 1:e60.
3. Blouin, M.S. 2003. DNA-based methods for pedigree reconstruction and kinship analysis in natural populations. Trends Ecol. Evol. 18:503–510.10.1016/S0169-5347(03)00225-8. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000185728100007&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
4. Breseghello, F., and Sorrells, M.E. 2006. Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177.10.1534/genetics.105.044586. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000236178800040&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
5. Camus-Kulandaivelu, L., Veyrieras, J., Gouesnard, B., Charcosset, A., and Manicacci, D. 2007. Evaluating the reliability of structure outputs in case of relatedness between individuals. Crop Sci. 47:887–890.10.2135/cropsci2006.06.0366N. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000245735800049&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
6. Camus-Kulandaivelu, L., Veyrieras, J.B., Madur, D., Combes, V., Fourmann, M., Barraud, S., Dubreuil, P., Gouesnard, B., Manicacci, D., and Charcosset, A. 2006. Maize adaptation to temperate climate: Relationship between population structure and polymorphism in the Dwarf8 gene. Genetics 172:2449–2463.10.1534/genetics.105.048603. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000237225800036&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
7. Casa, A.M., Pressoira, G., Brown, P.J., Mitchell, S.E., Rooney, W.L., Tuinstrac, M.R., Franks, C.D., and Kresovich, S. 2008. Community resources and strategies for association mapping in sorghum. Crop Sci. 48:30–40.10.2135/cropsci2007.02.0080. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000252971400004&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
8. Darvasi, A., and Shifman, S. 2005. The beauty of admixture. Nat. Genet. 37:118–119.10.1038/ng0205-118
9. Devlin, B., Bacanu, S.A., and Roeder, K. 2004. Genomic control to the extreme. Nat. Genet. 36:1129–1130.10.1038/ng1104-1129
10. Devlin, B., and Roeder, K. 1999. Genomic control for association studies. Biometrics 55:997–1004.10.1111/j.0006-341X.1999.00997.x. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000084218000001&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
11. Devlin, B., Roeder, K., and Wasserman, L. 2001. Genomic control, a new approach to genetic-based association studies. Theor. Popul. Biol. 60:155–166.10.1006/tpbi.2001.1542. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000174375600004&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
12. Doerge, R.W. 2002. Mapping and analysis of quantitative trait loci in experimental populations. Nat. Rev. Genet. 3:43–52.10.1038/nrg703. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000173267200016&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
13. Evanno, G., Regnaut, S., and Goudet, J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol. Ecol. 14:2611–2620.10.1111/j.1365-294X.2005.02553.x. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000229961500029&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
14. Falush, D., Stephens, M., and Pritchard, J.K. 2003. Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics 164:1567–1587.http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000185248000029&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
15. Flint-Garcia, S.A., Thornsberry, J.M., and Buckler, E.S. 2003. Structure of linkage disequilibrium in plants. Annu. Rev. Plant Biol. 54:357–374.10.1146/annurev.arplant.54.031902.134907. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000185094100014&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
16. Flint-Garcia, S.A., Thuillet, A.C., Yu, J., Pressoir, G., Romero, S.M., Mitchell, S.E., Doebley, J., Kresovich, S., Goodman, M.M., and Buckler, E.S. 2005. Maize association population: A high-resolution platform for quantitative trait locus dissection. Plant J. 44:1054–1064.10.1111/j.1365-313X.2005.02591.x. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000233776900014&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
17. Hallauer, A.R., and Miranda Filho, J.B. 1988. Quantitative genetics in maize breeding. 2nd ed. Iowa State Univ. Press, Ames.
18. Hardy, O.J., and Vekemans, X. 2002. SPAGeDi: A versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol. Ecol. Notes 2:618–620.10.1046/j.1471-8286.2002.00305.x
19. Henderson, C.R. 1975. Best linear unbiased estimation and prediction under a selection model. Biometrics 31:423–447.10.2307/2529430. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=A1975AF09900010&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
20. Henderson, C.R. 1984. Application of linear models in animal breeding. Univ. of Guelph, Guelph, ON.
21. Hey, J., and Machado, C.A. 2003. The study of structured populations: New hope for a difficult and divided science. Nat. Rev. Genet. 4:535–543.10.1038/nrg1112. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000183892300015&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
22. Hirschhorn, J.N., and Daly, M.J. 2005. Genome-wide association studies for common diseases and complex traits. Nat. Rev. Genet. 6:95–108.10.1038/nrn1622. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000226721300010&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
23. Lande, R., and Thompson, R. 1990. Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124:743–756.http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=A1990CQ97500027&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
24. Lander, E.S., and Schork, N.J. 1994. Genetic dissection of complex traits. Science 265:2037–2048.10.1126/science.8091226. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=A1994PJ91200021&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
25. Lee, S.H., and van der Werf, J.H. 2006. Using dominance relationship coefficients based on linkage disequilibrium and linkage with a general complex pedigree to increase mapping resolution. Genetics 174:1009–1016.10.1534/genetics.106.060806. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000241798700037&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
26. Lindblad-Toh, K., Wade, C.M., Mikkelsen, T.S., Karlsson, E.K., Jaffe, D.B., Kamal, M., Clamp, M., Chang, J.L., Kulbokas, E.J.III, Zody, M.C., Mauceli, E, Xie, X., Breen, M., Wayne, R.K., Ostrander, E.A., Ponting, C.P., Galibert, F., Smith, D.R., deJong, P.J., Kirkness, E., Alvarez, P., Biagi, T., Brockman, W., Butler, J., Chin, C.W., Cook, A., Cuff, J., Daly, M.J., deCaprio, D., Gnerre, S., Grabherr, M., Kellis, M., Kleber, M., Bardeleben, C., Goodstadt, L., Heger, A., Hitte, C., Kim, L., Koepfli, K.P., Parker, H.G., Pollinger, J.P., Searle, S.M., Sutter, N.B., Thomas, R., Webber, C., Baldwin, J., Abebe, A., Abouelleil, A., Aftuck, L., Ait-Zahra, M., Aldredge, T., Allen, N., An, P., Anderson, S., Antoine, C., Arachchi, H., Aslam, A., Ayotte, L., Bachantsang, P., Barry, A., Bayul, T., Benamara, M., Berlin, A., Bessette, D., Blitshteyn, B., Bloom, T., Blye, J., Boguslavskiy, L., Bonnet, C., Boukhgalter, B., Brown, A., Cahill, P., Calixte, N., Camarata, J., Cheshatsang, Y., Chu, J., Citroen, M., Collymore, A., Cooke, P., Dawoe, T., Daza, R., Decktor, K., deGray, S., Dhargay, N., Dooley, K., Dooley, K., Dorje, P., Dorjee, K., Dorris, L., Duffey, N., Dupes, A., Egbiremolen, O., Elong, R., Falk, J., Farina, A., Faro, S., Ferguson, D., Ferreira, P., Fisher, S., and FitzGerald, M. et al. 2005. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438:803–819.10.1038/nature04338. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000233777800043&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
27. Littell, R.C., Milliken, G.A., Stroup, W.W., Wolfinger, R.D., and Schabenberger, O. 2006. SAS for mixed models. 2nd ed. SAS Inst., Cary, NC.
28. Liu, K., Goodman, M., Muse, S., Smith, J.S., Buckler, E., and Doebley, J. 2003. Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165:2117–2128.http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000187805300038&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
29. Loiselle, B.A., Sork, V.L., Nason, J., and Graham, C. 1995. Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae). Am. J. Bot. 82:1420–1425.10.2307/2445869. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=A1995TF10800010&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
30. Lynch, M., and Ritland, K. 1999. Estimation of pairwise relatedness with molecular markers. Genetics 152:1753–1766.http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000081889600046&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
31. Lynch, M., and Walsh, J.B. 1998. Genetics and analysis of quantitative traits. Sinauer Associates, Sunderland, MA.
32. Mackay, T.F. 2001. The genetic architecture of quantitative traits. Annu. Rev. Genet. 35:303–339.10.1146/annurev.genet.35.102401.090633. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000172991500012&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
33. Mateescu, R.G., Zhang, Z., Tsai, K., Phavaphutanon, J., Burton-Wurster, N.I., Lust, G., Quaas, R., Murphy, K., Acland, G.M., and Todhunter, R.J. 2005. Analysis of allele fidelity, polymorphic information content, and density of microsatellites in a genome-wide screening for hip dysplasia in a crossbreed pedigree. J. Hered. 96:847–853.10.1093/jhered/esi109. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000233492400022&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
34. Milligan, B.G. 2003. Maximum-likelihood estimation of relatedness. Genetics 163:1153–1167.http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000182046900027&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
35. Neale, D.B., and Savolainen, O. 2004. Association genetics of complex traits in conifers. Trends Plant Sci. 9:325–330.10.1016/j.tplants.2004.05.006. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000223010600004&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
36. Price, A.L., Patterson, N.J., Plenge, R.M., Weinblatt, M.E., Shadick, N.A., and Reich, D. 2006. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38:904–909.10.1038/ng1847
37. Pritchard, J.K., and Rosenberg, N.A. 1999. Use of unlinked genetic markers to detect population stratification in association studies. Am. J. Hum. Genet. 65:220–228.10.1086/302449. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000081224300027&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
38. Pritchard, J.K., Stephens, M., and Donnelly, P. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945–959.http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000087475100039&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
39. Queller, D.C., and Goodnight, K.F. 1989. Estimating relatedness using genetic-markers. Evolution Int. J. Org. Evolution 43:258–275.
40. Risch, N., and Merikangas, K. 1996. The future of genetic studies of complex human diseases. Science 273:1516–1517.10.1126/science.273.5281.1516. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=A1996VG59700028&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
41. Ritland, K. 1996a. Estimators for pairwise relatedness and individual inbreeding coefficients. Genet. Res. 67:175–186.10.1017/S0016672300033620
42. Ritland, K. 1996b. Marker-based method for inferences about quantitative inheritance in natural populations. Evolution Int. J. Org. Evolution 50:1062–1073.
43. Rousset, F. 2002. Inbreeding and relatedness coefficients: What do they measure?. Heredity 88:371–380.10.1038/sj.hdy.6800065. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000176215800007&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
44. SAS Institute. 1999. SAS/STAT user's guide. Version 8. SAS Inst., Cary, NC.
45. Schwarz, G. 1978. Estimating dimension of a model. Ann. Stat. 6:461–464.10.1214/aos/1176344136. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=A1978EQ63300014&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
46. Senior, M.L., Chin, E.C.L., Lee, M., Smith, J.S.C., and Stuber, C.W. 1996. Simple sequence repeat markers developed from maize sequences found in the GENBANK database: Map construction. Crop Sci. 36:1676–1683.10.2135/cropsci1996.0011183X003600060043x. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=A1996VZ26100043&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
47. Shendure, J., Porreca, G.J., Reppas, N.B., Lin, X., McCutcheon, J.P., Rosenbaum, A.M., Wang, M.D., Zhang, K., Mitra, R.D., and Church, G.M. 2005. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309:1728–1732.10.1126/science.1117389. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000231836700046&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
48. Sillanpaa, M.J., and Corander, J. 2002. Model choice in gene mapping: What and why. Trends Genet. 18:301–307.10.1016/S0168-9525(02)02688-4. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000175854700012&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
49. Syvanen, A.C. 2005. Toward genome-wide SNP genotyping. Nat. Genet. 37(Suppl.):S5–S10.10.1038/ng1558
50. Tenaillon, M.I., Sawkins, M.C., Anderson, L.K., Stack, S.M., Doebley, J., and Gaut, B.S. 2002. Patterns of diversity and recombination along chromosome 1 of maize (Zea mays ssp. mays L.). Genetics 162:1401–1413.http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000179739900034&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
51. Thornsberry, J.M., Goodman, M.M., Doebley, J., Kresovich, S., Nielsen, D., and Buckler, E.S. 2001. Dwarf8 polymorphisms associate with variation in flowering time. Nat. Genet. 28:286–289.10.1038/90135
52. Todhunter, R.J., Bliss, S.P., Casella, G., Wu, R., Lust, G., Burton-Wurster, N.I., Williams, A.J., Gilbert, R.O., and Acland, G.M. 2003a. Genetic structure of susceptibility traits for hip dysplasia and microsatellite informativeness of an outcrossed canine pedigree. J. Hered. 94:39–48.10.1093/jhered/esg006. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000182413500007&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
53. Todhunter, R.J., Casella, G., Bliss, S.P., Lust, G., Williams, A.J., Hamilton, S., Dykes, N.L., Yeager, A.E., Gilbert, R.O., Burton-Wurster, N.I., Mellersh, C.C., and Acland, G.M. 2003b. Power of a Labrador Retriever–Greyhound pedigree for linkage analysis of hip dysplasia and osteoarthritis. Am. J. Vet. Res. 64:418–424.10.2460/ajvr.2003.64.418. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000181876000005&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
54. Todhunter, R.J., Mateescu, R., Lust, G., Burton-Wurster, N.I., Dykes, N.L., Bliss, S.P., Williams, A.J., Vernier-Singer, M., Corey, E., Harjes, C., Quaas, R.L., Zhang, Z., Gilbert, R.O., Volkman, D., Casella, G., Wu, R., and Acland, G.M. 2005. Quantitative trait loci for hip dysplasia in a cross-breed canine pedigree. Mamm. Genome 16:720–730.http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000232303800008&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
55. Voight, B.F., and Pritchard, J.K. 2005. Confounding from cryptic relatedness in case-control association studies. PLoS Genet. 1:e32.10.1371/journal.pgen.0010032
56. Wang, J. 2002. An estimator for pairwise relatedness using molecular markers. Genetics 160:1203–1215.http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000174790600032&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
57. Wang, W.Y., Barratt, B.J., Clayton, D.G., and Todd, J.A. 2005. Genome-wide association studies: Theoretical and practical concerns. Nat. Rev. Genet. 6:109–118.10.1038/nrg1522. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000226721300011&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
58. Wardyn, B.M., Edwards, J.W., and Lamkey, K.R. 2007. The genetic structure of a maize population: The role of dominance. Crop Sci. 47:467–476.10.2135/cropsci2006.05.0294. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000245735800001&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
59. Weir, B.S., Anderson, A.D., and Hepler, A.B. 2006. Genetic relatedness analysis: Modern data and new challenges. Nat. Rev. Genet. 7:771–780.10.1038/nrg1960. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000241158700013&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
60. Wilson, L.M., Whitt, S.R., Ibanez, A.M., Rocheford, T.R., Goodman, M.M., and Buckler, E.S. 2004. Dissection of maize kernel composition and starch production by candidate gene association. Plant Cell 16:2719–2733.10.1105/tpc.104.025700. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000224536200016&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
61. Yu, J., Arbelbide, M., and Bernardo, R. 2005. Power of in silico QTL mapping from phenotypic, pedigree, and marker data in a hybrid breeding program. Theor. Appl. Genet. 110:1061–1067.10.1007/s00122-005-1926-7. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000228642000009&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
62. Yu, J., Pressoir, G., Briggs, W.H., Vroh Bi, I., Yamasaki, M., Doebley, J.F., McMullen, M.D., Gaut, B.S., Nielsen, D.M., Holland, J.B., Kresovich, S., and Buckler, E.S. 2006. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet. 38:203–208.10.1038/ng1702
63. Zhao, K., Aranzana, M.J., Kim, S., Lister, C., Shindo, C., Tang, C., Toomajian, C., Zheng, H., Dean, C., Marjoram, P., and Nordborg, M. 2007. An Arabidopsis example of association mapping in structured samples. PLoS Genet. 3:e4.10.1371/journal.pgen.0030004