SNPs and their use in maize

Plant Genotyping II: SNP Technology

Volumn , Issue , 2008, Pages 30-43

  Rafalski, A ^a   Tingey, S ^a  

^a DUPONT COMPANY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77749264024     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (51)

1. Ananiev, E.V. et al. (1997) Oat-maize chromosome addition lines: a new system for mapping the maize genome. Proceedings of the National Academy of Sciences of the USA 94, 3524-3529.
2. Barker, G., Batley, J., O' Sullivan, H., Edwards, K.J. and Edwards, D. (2003) Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics 19, 421-422.
3. Batley, J., Barker, G., O'Sullivan, H., Edwards, K.J. and Edwards, D. (2003) Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiology 132, 84-91.
4. Bhattramakki, D., Dolan, M., Hanafey, M., Wineland, R., Vaske, D., Register III, J.C., Tingey, S.V. and Rafalski, A. (2002) Insertion-deletion polymorphisms in 3' regions of maize genes occur frequently and can be used as highly informative genetic markers. Plant Molecular Biology 48, 539-547.
5. Chen, X. and Sullivan, P.F. (2003) Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput. Journal of Pharmacogenomics 3, 77-96.
6. Chen, X., Cho, Y.G. and McCouch, S.R. (2002) Sequence divergence of rice microsatellites in Oryza and other plant species. Molecular Genetics and Genomics 268, 331-343.
7. Ching, A. and Rafalski, A. (2002) Rapid genetic mapping of ESTs using SNP pyrosequencing and indel analysis. Cellular and Molecular Biology Letters 7, 803-810.
8. Ching, A. and Rafalski, A. (2002) Rapid genetic mapping of ESTs using SNP pyrosequencing and indel analysis. Cellular and Molecular Biology Letters 7, 803-810.
9. Clark, A.G., Hubisz, M.J., Bustamante, C.D., Williamson, S.H. and Nielsen, R. (2005) Ascertainment bias in studies of human genome-wide polymorphism. Genome Research 15, 1496-1502.
10. Clark, R.M., Linton, E., Messing, J. and Doebley, J.F. (2004) Pattern of diversity in the genomic region near the maize domestication gene tb1. Proceedings of the National Academy of Sciences of the USA 101, 700-707.
11. Clark, R.M., Wagler, T.N., Quijada, P. and Doebley, J. (2006) A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nature Genetics 38, 594-597.
12. Coe, E., Cone, K., McMullen, M., Chen, S.S., Davis, G., Gardiner, J., Liscum, E., Polacco, M., Paterson, A., Sanchez-Villeda, H., Soderlund, C. and Wing, R. (2002) Access to the maize genome: an integrated physical and genetic map. Plant Physiology 128, 9-12.
13. Cone, K.C., McMullen, M.D., Bi, I.V., Davis, G.L., Yim, Y.S., Gardiner, J.M., Polacco, M.L., Sanchez-Villeda, H., Fang, Z., Schroeder, S.G., Havermann, S.A., Bowers, J.E., Paterson, A.H., Soderlund, C.A., Engler, F.W., Wing, R.A. and Coe, E.H.J. (2002) Genetic, physical, and informatics resources for maize. On the road to an integrated map. Plant Physiology 130, 1598-1605.
14. Doebley, J. and Lukens, L. (1998) Transcriptional regulators and the evolution of plant form. Plant Cell 10, 1075-1082.
15. Emrich, S., Li, L., Wen, T.J., Yandeau-Nelson, M.D., Fu, Y., Guo, L., Chou, H.H., Aluru, S., Ashlock, D.A. and Schnable, P.S. (2007) Nearly identical paralogs: implications for maize (Zea mays L.) Genome evolution. Genetics 175, 429-439.
16. Fan, J.B., Gunderson, K.L., Bibikova, M., Yeakley, J.M., Chen, J., Wickham Garcia, E., Lebruska, L.L., Laurent, M., Shen, R. and Barker, D. (2006) Illumina universal bead arrays. Methods in Enzymology 410, 57-73.
17. Flint-Garcia, S.A., Thornsberry, J.M. and Buckler, E.S.I. (2003) Structure of linkage disequilibrium in plants. Annual Review of Plant Biology 54, 357-374.
18. Gardiner, J., Schroeder, S., Polacco, M.L., Sanchez-Villeda, H., Fang, Z., Morgante, M., Landewe, T., Fengler, K., Useche, F., Hanafey, M., Tingey, S., Chou, H., Wing, R., Soderlund, C. and Coe, E.H., Jr (2004a) Anchoring 9,371 maize expressed sequence tagged unigenes to the bacterial artificial chromosome contig map by two-dimensional overgo hybridization. Plant Physiology 134, 1317-1326.
19. Gardiner, J., Schroeder, S., Polacco, M.L., Sanchez-Villeda, H., Fang, Z., Morgante, M., Landewe, T., Fengler, K., Useche, F., Hanafey, M., Tingey, S., Chou, H., Wing, R., Soderlund, C. and Coe, E.H.J. (2004b) Anchoring 9,371 maize expressed sequence tagged unigenes to the bacterial artificial chromosome contig map by two-dimensional overgo hybridization. Plant Physiology 134, 1317-1326.
20. Gaut, B.S. and Long, A.D. (2003) The lowdown on linkage disequilibrium. The Plant Cell 15, 1502-1506.
21. Gaut, B.S. and Long, A.D. (2003) The lowdown on linkage disequilibrium. The Plant Cell 15, 1502-1506.
22. Gray, I.C., Campbell, D.A. and Spurr, N.K. (2000) Single nucleotide polymorphisms as tools in human genetics. Human Molecular Genetics 9, 2403-2408.
23. Grotewold, E., Drummond, B.J., Bowen, B. and Peterson, T. (1994) The myb-homologous P gene controls phlobaphene pigmentation in maize floral organs by directly activating a flavonoid biosynthetic gene subset. Cell 76, 543-553.
24. Gut, I.G. (2001) Automation in genotyping single nucleotide polymorphisms. Human Mutation 17, 475-492.
25. Hsia, A.P., Wen, T.J., Chen, H.D., Liu, Z., Yandeau-Nelson, M.D., Wei, Y., Guo, L. and Schnable, P. (2005) Temperature gradient capillary electrophoresis (TGCE)-a tool for the high-throughput discovery and mapping of SNPs and IDPs. Theoretical and Applied Genetics 111, 218-225.
26. Huang, X., Barbee, K., Chen, Y.J. and Roller, E. (2006) Towards a $1000 human genome. Nanomedicine 2, 271-272.
27. Hyten, D.L., Choi, I.Y., Song, Q., Shoemaker, R.C., Nelson, R.L., Costa, J.M., Specht, J.E. and Cregan, P.B. (2007) Highly variable patterns of linkage disequilibrium in multiple soybean populations. Genetics 175, 1937-1944.
28. The International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437, 1299-1320.
29. Jung, M., Ching, A., Bhattramakki, D., Dolan, M., Tingey, S., Morgante, M. and Rafalski, A. (2004) Linkage disequilibrium and sequence diversity in a 500-kbp region around the adh1 locus in elite maize germplasm. Theoretical and Applied Genetics 109, 681-689.
30. Konieczny, A. and Ausubel, F.M. (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. The Plant Journal 4, 403-410.
31. Kwok, P.Y. (2001) Methods for genotyping single nucleotide polymorphisms. Annual Review of Genomics and Human Genetics 2, 235-258.
32. Kynast, R.G., Riera-Lizarazu, O., Vales, M.I., Okagaki, R.J., Maquieira, S.B., Chen, G., Ananiev, E.V., Odland, W.E., Russell, C.D., Stec, A.O., Livingston, S.M., Zaia, H.A., Rines, H.W. and Phillips, R.L. (2001) A complete set of maize individual chromosome additions to the oat genome. Plant Physiology 125, 1216-1227.
33. Marth, G.T., Korf, I., Yandell, M.D., Yeh, R.T., Gu, Z., Zakeri, H., Stitziel, N.O., Hillier, L., Kwok, P.Y. and Gish, W.R. (1999) A general approach to single-nucleotide polymorphism discovery. Nature Genetics 23, 452-456.
34. Nordborg, M., Borevitz, J.O., Bergelson, J., Berry, C.C., Chory, J., Hagenblad, J., Kreitman, M., Maloof, J.N., Noyes, T., Oefner, P.J., Stahl, E.A. and Weigel, D. (2002) The extent of linkage disequilibrium in Arabidopsis thaliana. Nature Genetics 30, 190-193.
35. Olivier, M. (2005) The invader assay for SNP genotyping. Mutation Research 573, 102-110.
36. Palaisa, K., Morgante, M., Williams, M. and Rafalski, A. (2003a) Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci. The Plant Cell 15, 1795-1806.
37. Palaisa, K.A., Morgante, M., Williams, M. and Rafalski, A. (2003b) Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci. Plant Cell 15, 1795-1806.
38. Palaisa, K., Morgante, M., Tingey, S. and Rafalski, A. (2004) Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an assymetric selective sweep. Proceedings of the National Academy of Sciences of the USA 101, 9885-9890.
39. Peakall, R., Gilmore, S., Keys, W., Morgante, M. and Rafalski, A. (1998) Cross-species amplification of soybean (Glycine max) simple sequence repeat (SSRs) within the genus and other legume genera: implications for the transferability of SSRs in plants. Molecular Biology and Evolution 15, 1275-1287.
40. Peleman, J. and van der Voort, J.R. (2003) Breeding by design. Trends in Plant Science 8, 330-334.
41. Powell, W., Morgante, M., Andre, C., Hanafey, M., Vogel, J., Tingey, S. and Rafalski, A. (1996) The comparison of RFLP, RAPD, AFLP and SSR (Microsatellite) markers for germplasm analysis. Molecular Breeding 2, 225-238.
42. Remington, D.L., Thornsberry, J.M., Matsuoka, Y., Wilson, L.M., Whitt, S.R., Doebley, J., Kresovich, S., Goodman, M.M. and Buckler, E.S.T. (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proceedings of the National Academy of Sciences of the USA 98, 11479-11484.
43. Ronaghi, M., Uhlen, M. and Nyren, P. (1998) A sequencing method based on real-time pyrophosphate. Science 281, 363-365.
44. Tenaillon, M.I., Sawkins, M.C., Long, A.D., Gaut, R.L., Doebley, J.F. and Gaut, B.S. (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proceedings of the National Academy of Sciences of the USA 98, 9161-9166.
45. Thornsberry, J.M., Goodman, M.M., Doebley, J., Kresovich, S., Nielsen, D. and Buckler, E.S.I. (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nature Genetics 28, 286-289.
46. Useche, F., Gao, G., Hanafey, M. and Rafalski, A. (2001) High-throughput identification, database storage and analysis of SNPs in EST sequences. Genome Informatics 12, 194-203.
47. Vigouroux, Y., Jaqueth, J.S., Matsuoka, Y., Smith, O.S., Beavis, W.D., Smith, J.S. and Doebley, J. (2002) Rate and pattern of mutation at microsatellite loci in maize. Molecular Biology and Evolution 19, 1251-1260.
48. Wang, H., Nussbaum-Wagler, T., Li, B., Zhao, Q., Vigouroux, Y., Faller, M., Bomblies, K., Lukens, L. and Doebley, J.F. (2005) The origin of the naked grains of maize. Nature 436, 714-719.
49. Wang, R.L., Stec, A., Hey, J., Lukens, L. and Doebley, J. (1999) The limits of selection during maize domestication. Nature 398, 236-239.
50. Yu, J., Pressoir, G., Briggs, W.H., Vroh, B.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. Nature Genetics 38, 203-208.
51. Zhang, W., Gianibelli, M.C., Ma, W., Rampling, L. and Gale, K.R. (2003) Identification of SNPs and development of allele-specific PCR markers for gamma-gliadin alleles in Triticum aestivum. Theoretical and Applied Genetics 107, 130-138.