Association Mapping for the Exploration of Genetic Diversity and Identification of Useful Loci for Plant Breeding

The Handbook of Plant Mutation Screening: Mining of Natural and Induced Alleles

Volumn , Issue , 2010, Pages 231-246

  Beló, André ^a   Luck, Stanley D ^a  

^a UNIVERSITY OF DELAWARE   (United States)

Author keywords

Association mapping; Genetic diversity; Linkage disequilibrium; Plant breeding; Population statistics; Quantitative trait loci

Indexed keywords

EID: 84887555661     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527629398.ch14     Document Type: Chapter

References (71)

1. Fu, Y. (2007) Impact of plant breeding on genetic diversity of agricultural crops: searching for molecular evidence. Plant Genet. Resour., 4, 71-78.
2. Zamir, D. (2001) Improving plant breeding with exotic genetic libraries. Nat. Rev. Genet., 2, 983-989.
3. Tanksley, S. and McCouch, S. (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science, 277, 1063-1066.
4. Martin, G.B., Brommonschenkel, S.H., Chunwongse, J., Frary, A., Ganal, M.W., Spivey, R., Wu, T., Earle, E.D., and Tanksley, S.D. (1993) Map-based cloning of a protein kinase gene conferring disease resistance in tomato. Science, 262, 1432-1436.
5. Lander, E.S. and Schork, N.J. (1994) Genetic dissection of complex traits. Science, 265, 2037-2048.
6. Holland, J.B. (2007) Genetic architecture of complex traits in plants. Curr. Opin. Plant Biol., 10, 156-161.
7. Salvi, S. and Tuberosa, R. (2005) To clone or not to clone plant QTLs: present and future challenges. Trends Plant Sci., 10, 297-304.
8. Morgante, M. and Salamini, F. (2003) From plant genomics to breeding practice. Curr. Opin. Biotechnol., 14, 214-219.
9. Bortiri, E., Jackson, D., andHake, S. (2006) Advances in maize genomics: the emergence of positional cloning. Curr. Opin. Plant Biol., 9, 164-171.
10. Altshuler, D., Daly, M.J., and Lander, E.S. (2008) Genetic mapping in human disease. Science, 322, 881-888.
11. McCarthy, M., Abecasis, G., Cardon, L., Goldstein, D., Little, J., Ioannidis, J., and Hirschhorn, J. (2008) Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat. Rev. Genet., 9, 356-369.
12. Flint-Garcia, S.A., Thornsberry, J.M., and Buckler, E.S.4. (2003) Structure of linkage disequilibrium in plants. Annu. Rev. Plant Biol., 54, 357-374.
13. Yu, J. and Buckler, E.S. (2006) Genetic association mapping and genome organization of maize. Curr. Opin. Biotechnol., 17, 155-160.
14. Rafalski, A. (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr. Opin. Plant Biol., 5, 94-100.
15. Balding, D.J. (2006) A tutorial on statistical methods for population association studies. Nat. Rev. Genet., 7, 781-791.
16. Kruglyak, L. (2008) The road to genomewide association studies. Nat. Rev. Genet., 9, 314-318.
17. Abdurakhmonov, I.Y. and Abdukarimov, A. (2008) Application of association mapping to understanding the genetic diversity of plant germplasm resources. Int. J. Plant Genomics, 2008, 1574927.
18. Nordborg, M., Hu, T.T., Ishino, Y., Jhaveri, J., Toomajian, C., Zheng, H., Bakker, E., Calabrese, P., Gladstone, J., Goyal, R., Jakobsson, M., Kim, S., Morozov, Y., Padhukasahasram, B., Plagnol, V., Rosenberg, N.A., Shah, C., Wall, J.D., Wang, J., Zhao, K., Kalbfleisch, T., Schulz, V., Kreitman, M., and Bergelson, J. (2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol., 3, e196.
19. 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.
20. 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.
21. Flint-Garcia, S.A., Thuillet, A., 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.
22. Zhao, W., Canaran, P., Jurkuta, R., Fulton, T., Glaubitz, J., Buckler, E., Doebley, J., Gaut, B., Goodman, M., Holland, J., Kresovich, S., McMullen, M., Stein, L., and Ware, D. (2006) Panzea: a database and resource for molecular and functional diversity in the maize genome. Nucleic Acids Res., 34, 752-757.
23. Casa, A., Pressoir, G., Brown, P., Mitchell, S., Rooney, W., Tuinstra, M., Franks, C., and Kresovich, S. (2008) Community resources and strategies for association mapping in sorghum. Crop Sci., 48, 30.
24. Rafalski, J. (2002) Novel genetic mapping tools in plants: SNPs and LD-based approaches. Plant Sci., 162, 329-333.
25. Nguyen, H. and Wu, X. (2005) Molecular marker systems for genetic mapping, in The Handbook of Plant Genome Mapping: Genetic and Physical Mapping (eds K. Meksem and G. Kahl), Wiley-VCH, Weiheim.
26. Kahl, G., Mast, A., Tooke, N., Shen, R., and van den Boom, D. (2005) Single nucleotide polymorphisms: detection techniques and their potential for genotyping and genome mapping, in The Handbook of PlantGenome Mapping: Genetic and Physical Mapping (eds K.Meksem and G. Kahl), Wiley-VCH, Weiheim.
27. Abo, R., Knight, S., Wong, J., Cox, A., and Camp, N.J. (2008) hapConstructor: automatic construction and testing of haplotypes in a Monte Carlo framework. Bioinformatics, 24, 2105-2107.
28. Gupta, P.K., Rustgi, S., and Kulwal, P.L. (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol. Biol., 57, 461-485.
29. Ching, A., Caldwell, K.S., Jung, M., Dolan, M., Smith, O.S., Tingey, S., Morgante, M., and Rafalski, A.J. (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet., 3, 19.
30. 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. Theor. Appl. Genet., 109, 681-689.
31. Palaisa, K.A., Morgante, M., Williams, M., and Rafalski, A. (2003) Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci. Plant Cell, 15, 1795-1806.
32. 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 asymmetric selective sweep. Proc. Natl. Acad. Sci. USA, 101, 9885-9890.
33. Rafalski, A. and Morgante, M. (2004) Corn and humans: recombination and linkage disequilibrium in two genomes of similar size. Trends Genet., 20, 103-111.
34. Thornsberry, J.M., Goodman, M.M., Doebley, J., Kresovich, S., Nielsen, D., and Buckler, E.S.4. (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat. Genet., 28, 286-289.
35. 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.
36. Matthies, I., Weise, S., and Röder, M. (2009) Association of haplotype diversity in the α-amylase gene amy1 with malting quality parameters in barley. Mol. Breeding, 23, 139-152.
37. Piepho, H., Buchse, A., and Emrich, K. (2003) A hitchhiker's guide to mixed models for randomized experiments. J. Agron. Crop. Sci., 189, 310-322.
38. Ewens, W.J., Li, M., and Spielman, R.S. (2008) A review of family-based tests for linkage disequilibrium between a quantitative trait and a genetic marker. PLoS Genet., 4, e1000180.
39. 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.
40. Zhu, C., Gore, M., Buckler, E.S., and Yu, J. (2008) Status and prospects of association mapping in plants. Plant Genome, 1, 5-20.
41. Lynch, M. and Walsh, B. (1998) Genetics and Analysis of Quantitative Traits, Sinauer, Sunderland, MA.
42. Casella, G. and Berger, R. (2001) Statistical Inference, Duxbury Press, Pacific Grove, CA.
43. Schaid, D.J. (2004) Evaluating associations of haplotypes with traits. Genet. Epidemiol., 27, 348-364.
44. Becker, T. and Knapp, M. (2004) A powerful strategy to account for multiple testing in the context of haplotype analysis. Am. J. Hum. Genet., 75, 561-570.
45. Barnett, V. and Lewis, T. (1994) Outliers in Statistical Data, John Wiley & Sons Ltd, Chichester.
46. 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.
47. Excofier, L. (2001) Analysis of population subdivision, in Handbook of Statistical Genetics (eds D. Balding, M. Bishop, and C. Cannings), John Wiley & Sons Ltd, Chichester.
48. Weir, B., (1996) Genetic Data Analysis II, Sinauer, Sunderland, MA.
49. Devlin, B. and Roeder, K. (1999) Genomic control for association studies. Biometrics, 55, 997-1004.
50. Pritchard, J.K., Stephens, M., Rosenberg, N.A., and Donnelly, P. (2000) Association mapping in structured populations. Am. J. Hum. Genet., 67, 170-181.
51. Duda, R.O., Hart, P.E., and Stork, D.G. (2000) Pattern Classification, Wiley-Interscience, New York.
52. Rosenberg, N.A. (2004) DISTRUCT: a program for the graphical display of population structure. Mol. Ecol. Notes, 4, 137-138.
53. 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.
54. Kang, H.M., Zaitlen, N.A., Wade, C.M., Kirby, A., Heckerman, D., Daly, M.J., and Eskin, E. (2008) Efficient control of population structure in model organism association mapping. Genetics, 178, 1709-1723.
55. Lou, X., Casella, G., Littell, R.C., Yang, M.C.K., Johnson, J.A., and Wu, R. (2003) A haplotype-based algorithm for multilocus linkage disequilibrium mapping of quantitative trait loci with epistasis. Genetics, 163, 1533-1548.
56. Marchini, J., Donnelly, P., and Cardon, L.R. (2005) Genome-wide strategies for detecting multiple loci that influence complex diseases. Nat. Genet., 37, 413-417.
57. Alvarez-Castro, J.M. and Carlborg, O. (2007) A unified model for functional and statistical epistasis and its application in quantitative trait loci analysis. Genetics, 176, 1151-1167.
58. Churchill, G.A. and Doerge, R.W. (1994) Empirical threshold values for quantitative trait mapping. Genetics, 138, 963-971.
59. Farcomeni, A. (2008) A review of modern multiple hypothesis testing, with particular attention to the false discovery proportion. Stat. Methods Med. Res., 17, 347-388.
60. Sabatti, C., Service, S., and Freimer, N. (2003) False discovery rate in linkage and association genome screens for complex disorders. Genetics, 164, 829-833.
61. Storey, J.D. and Tibshirani, R. (2003) Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA, 100, 9440-9445.
62. Churchill, G.A. and Doerge, R.W. (2008) Naive application of permutation testing leads to inflated type I error rates. Genetics, 178, 609-610.
63. Mackay, I. and Powell, W. (2007) Methods for linkage disequilibrium mapping in crops. Trends Plant Sci., 12, 57-63.
64. Sorkheh, K., Malysheva, L., and Wirthensohn, M. (2008) Linkage disequilibrium, genetic association mapping and gene localization in crop plants. Genet. Mol. Biol., 31, 1415-4757.
65. Zhu, C., Gore, M., Buckler, E., and Yu, J. (2008) Status and prospects of association mapping in plants. Plant Genome, 1, 5.
66. Beló, A., Zheng, P., Luck, S., Shen, B., Meyer, D.J., Li, B., Tingey, S., and Rafalski, A. (2008) Whole genome scan detects an allelic variant of fad2 associated with increased oleic acid levels in maize. Mol. Genet. Genomics, 279, 1-10.
67. Hedrick, P. (1987) Gametic disequilibrium measures: proceed with caution. Genetics, 117, 331-341.
68. Lewontin, R. (1988) On measures of gametic disequilibrium. Genetics, 120, 849-852.
69. Hirschhorn, J.N. and Daly, M.J. (2005) Genome-wide association studies for common diseases and complex traits. Nat. Rev. Genet., 6, 95-108.
70. Zheng, P., Allen, W.B., Roesler, K., Williams, M.E., Zhang, S., Li, J., Glassman, K., Ranch, J., Nubel, D., Solawetz, W., Bhattramakki, D., Llaca, V., Deschamps, S., Zhong, G., Tarczynski, M.C., and Shen, B. (2008) Aphenylalanine in DGAT is a key determinant of oil content and composition in maize. Nat. Genet., 40, 367-372.
71. Wilson, L.M., Whitt, S.R., Ibanez, A.M., Rocheford, T.R., Goodman, M.M., and Buckler, E.S.4. (2004) Dissection of maize kernel composition and starch production by candidate gene association. Plant Cell, 16, 2719-2733.