References

1. Bradbury, P.J. et al. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23, 2633-2635 (2007).
2. Zhang, Z., Buckler, E.S., Casstevens, T.M. & Bradbury, P.J. Software engineering the mixed model for genome-wide association studies on large samples. Brief Bioinform 10, 664-75 (2009).
3. Kang, H.M. et al. Efficient Control of Population Structure in Model Organism Association Mapping. Genetics 178, 1709-1723 (2008).
4. Zhang, Z. et al. Mixed linear model approach adapted for genome-wide association studies. Nat Genet 42, 355-60 (2010).
5. Kang, H.M. et al. Variance component model to account for sample structure in genome-wide association studies. Nat Genet 42, 348-54 (2010).
6. Thornsberry, J.M. et al. Dwarf8 polymorphisms associate with variation in flowering time. Nature Genetics 28, 286-289 (2001).
7. Pritchard, J.K., Stephens, M., Rosenberg, N.A. & Donnelly, P. Association mapping in structured populations. American Journal of Human Genetics 67, 170-181 (2000).
8. Zhao, K. et al. An Arabidopsis example of association mapping in structured samples. PLoS Genet 3, e4 (2007).
9. Yu, J.M. et al. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics 38, 203-208 (2006).
10. Ware, D. et al. Gramene: a resource for comparative grass genomics. Nucleic Acids Research 30, 103-105 (2002).
11. Ware, D.H. et al. Gramene, a tool for grass Genomics. Plant Physiology 130, 1606-1613 (2002).
12. Jaiswal, P. et al. Gramene: development and integration of trait and gene ontologies for rice. Comparative and Functional Genomics 3, 132-136 (2002).
13. Yamazaki, Y. & Jaiswal, P. Biological ontologies in rice databases. An introduction to the activities in gramene and oryzabase. Plant and Cell Physiology 46, 63-68 (2005).
14. Zhao, W. et al. Panzea: a database and resource for molecular and functional diversity in the maize genome. Nucleic Acids Research 34, D752-D757 (2006).
15. Canaran, P., Stein, L. & Ware, D. Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support. Bioinformatics 22, 885-886 (2006).
16. Du, C.G., Buckler, E. & Muse, S. Development of a maize molecular evolutionary genomic database. Comparative and Functional Genomics 4, 246-249 (2003).
17. SAS, I.I. SAS. Statistical Analysis Software for Windows, 9.0 ed. Cary, NC. USA. ( 2002.).
18. Hardy, O.J. & Vekemans, X. SPAGEDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Molecular Ecology Notes 2, 618-620 (2002).
19. Cover, T. & Hart, P. Nearest neighbor pattern classification. Proc IEEE Trans Inform Theory 13(1967).
20. Weir. Genetic Data Analysis II. Sunderland, MA. (1996).
21. Farnir, F. et al. Extensive genome-wide linkage disequilibrium in cattle. Genome Res 10, 220-7 (2000).
22. Henderson, C.R. Best Linear Unbiased Estimation and Prediction under a Selection Model. Biometrics 31, 423-447 (1975).
23. Kang, H.M. et al. Efficient control of population structure in model organism association mapping. Genetics 178, 1709-23 (2008).
24. Laird, N.M. & Ware, J.H. Random-Effects Models for Longitudinal Data. Biometrics 38, 963-974 (1982).
25. Thornsberry, J.M. et al. Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28, 286-9 (2001).
26. Flint-Garcia, S.A. et al. Maize association population: a high-resolution platform for quantitative trait locus dissection. Plant J 44, 1054-64 (2005).
27. Anderson, M.J. & Ter Braak, C.J.F. Permutations tests for multi-factorial analysis of variance. Journal of Statistical Computation and Simulation 73, 85-113 (2003)
28. Shabalin, A.A. Matrix eQTL: ultra fast eQTL analysis via large matrix operations. Bioinformatics 28, 1353-1358 (2012).