Genetic diversity, linkage disequilibrium and association mapping

Handbook of Maize: Genetics and Genomics

Volumn , Issue , 2009, Pages 201-219

  Rafalski, Antoni ^a   Ananiev, Evgueni ^b  

^a DUPONT COMPANY   (United States)

^b Pioneer Hibred Int'l   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84919845684     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-0-387-77863-1_10     Document Type: Chapter

References (100)

1. Alfenito, M. R., and Birchler, J. A. (1993). Molecular characterization of a maize B chromosome centric sequence. Genetics 135, 589-597.
2. Ananiev, E. V., Phillips, R. L., and Rines, H. W. (1998a). Chromosome-specific molecular organization of maize (Zea mays L.) centromeric regions. Proc Natl Acad Sci U S A. 95, 13073-13078.
3. Ananiev, E. V., Phillips, R. L., and Rines, H. W. (1998b). Complex structure of knob DNA on maize chromosome 9. Retrotransposon invasion into heterochromatin. Genetics 149, 2025-2037.
4. Ananiev, E. V., Phillips, R. L., and Rines, H. W. (1998c). A knob-associated tandem repeat in maize capable of forming fold-back DNA segments: are chromosome knobs megatransposons?. Proc Natl Acad Sci U S A 95, 10785-10790.
5. Ananiev, E. V., Chamberlin, M. A., Klaiber, J., and Svitashev, S. (2005a). Microsatellite megatracts in the maize (Zea mays L.) genome. Genome 48, 1061-1069.
6. Ananiev, E. V., Chamberlin, M. A., Klaiber, J., and Svitashev, S. (2005b). Microsatellite megatracts in the maize (Zea mays L.) genome. Genome 48, 1061-1069.
7. Anderson, L. K., Salameh, N., Bass, H. W., Harper, L. C., Cande, W. Z., Weber, G., and Stack, S. M. (2004). Integrating genetic linkage maps with pachytene chromosome structure in maize. Genetics 166, 1923-1933.
8. Banks, J., Kingsbury, J., Raboy, V. Schiefelbein, J. W., Nelson, O., and Fedoroff, N. (1985). The Ac and Spm controlling element families in maize. Cold Spring Harb Symp Quant Biol. 50, 307-311.
9. Beló, A., Zheng, P., Luck, S., Shen, B., Meyer, D. J., Li, B., Tingey, S., and Rafalski, A. (2007). Whole genome scan detects an allelic variant of fad2 associated with increased oleic acid levels in maize. Mol Genet Genomics 279, 1-10.
10. Bennetzen, J. L. (2000). Transposable element contributions to plant gene and genome evolution. Plant Mol Biol. 42, 251-269.
11. Bruggmann, R., Bharti, A., Gundlach, H., Lai, J., Young, S., Pontaroli, A., Wei, F., Haberer, G., Fuks, G., Du, C., Raymond, C., Estep, M., Liu, R., Bennetzen, J., Chan, A., Rabinowicz, P., Quackenbush, J., Barbazuk, W., Wing, R., Birren, B., Nusbaum, C., Rounsley, S., Mayer, K., and Messing, J. (2006). Uneven chromosome contraction and expansion in the maize genome. Genome Res. 16, 1241-1251.
12. Brunner, S., Pea, G., and Rafalski, A. (2005a). Origins, genetic organization and transcription of a family of non-autonomous helitron elements in maize. The Plant Journal 43, 799-810.
13. Brunner, S., Fengler, K., Morgante, M., Tingey, S., and Rafalski, A. (2005b). Evolution of DNA sequence nonhomologies among maize inbreds. Plant Cell 17, 343-360.
14. Buckler, E. S., Gaut, B. S., and McMullen, M. D. (2006). Molecular and functional diversity of maize. Curr Opin Plant Biol. 9, 172-176.
15. Buckner, B., Kelson, T. L., and Robertson, D. S. (1990). Cloning of the y1 Locus of Maize, a Gene involved in the Biosynthesis of Carotenoids. The Plant Cell 2, 867-876.
16. Buckner, B., San Miguel, P., Janick-Buckner, D., and Bennetzen, J. L. (1998). The y1 Gene of Maize codes for Phytoene Synthase. Genetics 143, 479-488.
17. Bureau, T. E., and Wessler, S. R. (1994). Mobile inverted-repeat elements of the Tourist family are associated with the genes of many cereal grasses. Proc. Natl. Acad. Sci. USA 91, 1411-1415.
18. Burr, B., Burr, F. A., Matz, E. C., and Romero-Severson, J. (1992). Pinning down loose ends: mapping telomeres and factors affecting their length. Plant Cell 4, 953-960.
19. Cardon, L. R., and Bell, J. I. (2001). Association Study Designs for Complex Diseases. Nature Reviews Genetics 2, 91-99.
20. Cardon, L. R., and Abecasis, G. R. (2003). Using haplotype blocks to map human complex trait loci. Trends Genet 19, 135-140.
21. Chen, C., Yan, H., Zhai, W., Zhu, L., and Sun, J. (2000). Identification and chromosomal location of a new tandemly repeated DNA in maize. Genome 43, 181-184.
22. Cheng, Y. M., and Lin, B. Y. (2003). Cloning and characterization of maize B chromosome sequences derived from microdissection. Genetics 164, 299-310.
23. 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.
24. 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. Nat Genet. 38, 594-597.
25. Cooper, M., Smith, O. S., Graham, G., Arthur, L., Feng, L., and Podlich, D. W. (2004). Genomics, Genetics and Plant Breeding: A Private Sector Perspective. Crop Sci. 44, 1907-1913.
26. Curtis, D., Vine, A., and Knight, J. (2007). A pragmatic suggestion for dealing with results for candidate genes obtained from genome wide association studies BMC Genetics 8, 20.
27. Dennis, E. S., and Peacock, W. J. (1984). Knob heterochromatin homology in maize and its relatives. J. Mol. Evol. 20, 341-350.
28. Doebley, J., and Lukens, L. (1998). Transcriptional regulators and the evolution of plant form. Plant Cell 10, 1075-1082.
29. Doebley, J., Goodman, M. M., and Stuber, C. W. (1984). Isoenzymatic variation in Zea (Gramineae). Systematic Botany 9, 203-218.
30. Dooner, H. K., and Martinez-Ferez, I. M. (1997). Recombination occurs uniformly within the bronze gene, a meiotic recombination hotspot in the maize genome. Plant Cell 9, 1633-1646.
31. Fedoroff, N. (2000). Transposons and genome evolution in plants. Proc Natl Acad Sci U S A 97, 7002-7007.
32. Fengler, K., Allen, S. M., Li, B., and Rafalski, A. (2007). Distribution of genes, recombination, and repetitive elements in the maize genome. The Plant Genome [A Supplement to Crop Science], 83-95.
33. Flint-Garcia, S. A., Thornsberry, J. M., and Buckler IV, E. S. (2003). Structure of linkage disequilibrium in plants. Annu. Rev. Plant Biol. 54, 357-374.
34. Frary, A., Fulton, T. M., Zamir, D., and Tanksley, S. D. (2004). Advanced backcross QTL analysis of a Lycopersicon esculentum x L.pennellii cross and identification of possible orthologs in the Solanaceae. Theor Appl Genet. 108, 485-496.
35. Fu, H., and Dooner, H. K. (2002). Intraspecific violation of genetic colinearity and its implications in maize. Proc Natl Acad Sci U S A 99, 9573-9578.
36. Gardiner, J. M., Coe, E. H., and Chao, S. (1996). Cloning maize telomeres by complementation in Saccharomyces cerevisiae. Genome 39, 736-748.
37. Gaut, B. S., and Clegg, M. T. (1993). Molecular evolution of the Adh1 locus in the genus Zea. Proc. Natl. Acad. Sci. USA 90, 5095-5099.
38. Gaut, B. S., and Long, A. D. (2003). The Lowdown on Linkage Disequilibrium. The Plant Cell 15, 1502-1506.
39. 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.
40. Gupta, S., Gallavotti, A., Stryker, G. A., Schmidt, R. J., and Lal, S. K. (2005). A novel class of Helitron-related transposable elements in maize contain portions of multiple pseudogenes. Plant Mol Biol 57, 115-127.
41. Hanson, M. A., Gaut, B. S., Stec, A. O., Fuerstenberg, S. I., Goodman, M. M., Coe, E. H., and Doebley, J. F. (1996). Evolution of anthocyanin biosynthesis in maize kernels: the role of regulatory and enzymatic loci. Genetics 143, 1395-1407.
42. Hartl, D. (2000). A Primer of Population Genetics. (Sunderland, MA, USA.: Sinauer Associates).
43. Hoisington, D., Khairallah, M., Reeves, T., Ribaut, J. M., Skovmand, B., Taba, S., and Warburton, M. (1999). Plant genetic resources: what can they contribute toward increased crop productivity? Proc. Natl. Acad. Sci. U. S. A. 96, 5937-5943.
44. Hudson, R. R., and Kaplan, N. L. (1995). Deleterious background selection with recombination. Genetics 141, 1605-1617.
45. Jiang, N., Bao, Z., Zhang, X., Eddy, S. R., and Wessler, S. R. (2004). Pack-MULE transposable elements mediate gene evolution in plants. Nature 431, 569-573.
46. 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.
47. Kapitonov, V. V., and Jurka, J. (2001). Rolling-circle transposons in eukaryotes. Proc Natl Acad Sci U S A 98, 8714-8719.
48. Kato, A., Lamb, J. C., and Birchler, J. A. (2004). Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize. Proc Natl Acad Sci U S A. 101, 13554-13559.
49. Kumar, A., and Bennetzen, J. L. (2000). Retrotransposons: central players in the structure, evolution and function of plant genomes. Trends Plant Sci 5, 509-510.
50. Lai, J., Li, Y., Messing, J., and Dooner, H. K. (2005). Gene movement by Helitron transposons contributes to the haplotype variability of maize. Proc Natl Acad Sci U S A 102, 9068-9073.
51. Lal, S. K., Giroux, M. J., Brendel, V., Vallejos, C. E., and Hannah, L. C. (2003). The maize genome contains a helitron insertion. Plant Cell 15, 381-391.
52. Li, L., and Arumuganathan, K. (2001). Physical mapping of 45S and 5S rDNA on maize metaphase and sorted chromosomes by FISH. Hereditas 134, 141-145.
53. Lijavetzky, D., Cabezas, J. A., Ibanez, A., Rodriguez, V., and Martinez-Zapater, J. M. (2007). High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology. BMC Genomics 8, 424.
54. Lippman, Z., and Tanksley, S. D. (2001). Dissecting the genetic pathway to extreme fruit size in tomato using a cross between the small-fruited wild species Lycopersicon pimpinellifolium and L. esculentum var. Giant Heirloom. Genetics. 158, 413-422.
55. 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.
56. Liu, R., Vitte, C., Ma, J., Mahama, A. A., Dhliwayo, T., Lee, M., and Bennetzen, J. L. (2007). A GeneTrek analysis of the maize genome. Proc Natl Acad Sci U S A 104, 11844-11849.
57. Longley, A. E. (1939). Knob positions on corn chromosomes. J. Agric. Res. 59, 475-490.
58. Mackay, I., and Powell, W. (2007). Methods for linkage disequilibrium mapping in crops. Trends Plant Sci. 12, 57-63.
59. Mascia, P. N., Rubenstein, I., Phillips, R. L., Wang, A. S., and Xiang, L. Z. (1981). Localization of the 5S rRNA genes and evidence for diversity in the 5S rDNA region of maize. Gene 15, 7-20.
60. McClintock, B. (1931). The Order of the Genes C, Sh, and Wx in Zea Mays with Reference to a Cytologically Known Point in the Chromosome. Proc Natl Acad Sci U S A 17, 485-491.
61. McClintock, B. (1978). Significance of chromosome constitutions in tracing the origin and migration of races of maize in the Americas. In: Maize Breeding and Genetics. Walden, D. B., ed., 159-184. In in: Maize Breeding and Genetics, D. B. Walden, ed (New York: Wiley), pp. 159-184.
62. Meyers, B. C., Tingey, S. V., and Morgante, M. (2001). Abundance, distribution and transcriptional activity of repetitive elements in the maize genome. Genome Res. 11, 1660-1676.
63. Mikkilineni, V., and Rocheford, T. (2003). Sequence variation and genomic organization of fatty acid desaturase-2 (fad2 and fatty acid desaturase-6 (fad6) cDNAs in maize. Theor Appl Genet 106, 1326-1332.
64. Morgante, M., Brunner, S., Pea, G., Fengler, K., Zuccolo, A., and Rafalski, A. (2005). Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat Genet 37, 997-1002.
65. Mroczek, R. J., and Dawe, R. K. (2003). Distribution of retroelements in centromeres and neocentromeres of maize. Genetics 165, 809-819.
66. Nagaki, K., Song, J., Stupar, R. M., Parokonny, A. S., Yuan, Q., Ouyang, S., Liu, J., Hsiao, J., Jones, K. M., Dawe, R. K., Buell, C. R., and Jiang, J. (2003). Molecular and cytological analyses of large tracks of centromeric DNA reveal the structure and evolutionary dynamics of maize centromeres. Genetics 163, 759-770.
67. Nobuta, K., Venu, R. C., Lu, C., Belo, A., Vemaraju, K., Kulkarni, K., Wang, W., Pillay, M., Green, P. J., Wang, G. L., and Meyers, B. C. (2007). An expression atlas of rice mRNAs and small RNAs. Nat Biotechnol. 25, 473-477.
68. Page, B. T., Wanous, M. K., and Birchler, J. A. (2001). Characterization of a maize chromosome 4 centromeric sequence: evidence for an evolutionary relationship with the B chromosome centromere. Genetics 159, 291-302.
69. Palaisa, K., Morgante, M., Williams, M., and Rafalski, A. (2003). Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci. The Plant Cell 15, 1795-1806.
70. 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. Proc Natl Acad Sci U S A 101, 9885-9890.
71. Pritchard, J. K. (2001). Denconstructing maize population structure. Nature Genetics 28, 203-204.
72. 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.
73. Rafalski, A. (2002). Applications of single nucleotide polymorphisms in crop genetics. Current Opinion in Plant Biology 5, 94-100.
74. Rafalski, A. (2007). Tagging the rice transcriptome. Nat Biotechnol. 25, 430-431.
75. 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. Proc Natl Acad Sci U S A 98, 11479-11484.
76. Rose, L. E., Bittner-Eddy, P. D., Langley, C. H., Holub, E. B., Michelmore, R. W., and Beynon, J. L. (2004). The maintenance of extreme amino acid diversity at the disease resistance gene, RPP13, in Arabidopsis thaliana. Genetics 166, 1517-1527.
77. San Miguel, P., Gaut, B. S., Tikhonov, A., Nakajima, Y., and Bennetzen, J. L. (1998). The paleontology of intergene retrotransposons of maize. Nat. Genet. 20, 43-45.
78. San Miguel, P., Tikhonov, A., Jin, Y. K., Motchoulskaia, N., Zakharov, D., Melake-Berhan, A., Springer, P. S., Edwards, K. J., Lee, M., Avramova, Z., and Bennetzen, J. L. (1996). Nested retrotransposons in the intergenic regions of the maize genome. Science 274, 765-768.
79. Song, R., and Messing, J. (2003). Gene expression of a gene family in maize based on noncollinear haplotypes. Proc Natl Acad Sci U S A 100, 9055-9060.
80. Stam, M., Belele, C., Ramakrishna, W., Dorweiler, J. E., Bennetzen, J. L., and Chandler, V. L. (2002). The regulatory regions required for B' paramutation and expression are located far upstream of the maize b1 transcribed sequences. Genetics 162, 917-930.
81. Tajima, F. (1983). Evolutionary relationship of DNA sequences in finite populations. Genetics 105, 437-460.
82. Tanksley, S. D., and McCouch, S. R. (1997). Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277, 1063-1066.
83. Tenaillon, M. I., Sawkins, M. C., Long, A. D., Gaut, R. L., Doebley, J. F., and Gaut, B. S. (2001). Patterns of DNA sequence polym orphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc. Natl. Acad. Sci. USA 98, 9161-9166.
84. 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.
85. Tiffin, P., Hacker, R., and Gaut, B. S. (2004). Population genetic evidence for rapid changes in intraspecific diversity and allelic cycling of a specialist defense gene in Zea. Genetics 168, 425-434.
86. Tochtrop, C., and Buckner, B. (2000). Sequence analysis of a recessive allele of the y1 gene of maize. In Maize Genetics Conference Abstracts, pp. P96.
87. 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. Mol Biol Evol. 19, 1251-1260.
88. Vigouroux, Y. Mitchell, S., Matsuoka, Y. Hamblin, M., Kresovich, S., Smith, J. S., Jaqueth, J., Smith, O. S., and Doebley, J. (2005). An analysis of genetic diversity across the maize genome using microsatellites. Genetics 169, 1617-1630.
89. Wang, Q., and Dooner, H. K. (2006). Remarkable variation in maize genome structure inferred from haplotype diversity at the bz locus Proc Natl Acad Sci U S A 103, 17644-17649.
90. Wang, R. L., Stec, A., Hey, J., Lukens, L., and Doebley, J. (1999). The limits of selection during maize domestication. Nature 398, 236-239.
91. Wessler, S. R. (2006). Transposable elements and the evolution of eukaryotic genomes Proc Natl Acad Sci U S A 103, 17600-17601.
92. Whitt, S. R., Wilson, L. M., Tenaillon, M. I., Gaut, B. S., and Buckler, E. S.t. (2002). Genetic diversity and selection in the maize starch pathway. Proc Natl Acad Sci U S A 99, 12959-12962.
93. Wright, S. I., Bi, I. V., Schroeder, S. G., Yamasaki, M., Doebley, J. F., McMullen, M. D., and Gaut, B. S. (2005). The Effects of Artificial Selection on the Maize Genome. Science 308, 1310-1314.
94. Xiao, J., Li, J., Grandillo, S., Ahn S, N., Yuan, L., Tanksley, S. D., and McCouch, S. R. (1998). Identification of trait-improving quantitative trait loci alleles from a wild rice relative, Oryza rufipogon. Genetics 150, 899-909.
95. Xu, J. H., and Messing, J. (2006). Maize haplotype with a helitron-amplified cytidine deaminase gene copy. BMC Genet 7, 52.
96. Yamasaki, M., Tenaillon, M. I., Bi, I. V., Schroeder, S. G., Sanchez-Villeda, H., Doebley, J. F., Gaut, B. S., and McMullen, M. D. (2005). A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement. Plant Cell 17, 2859-2872.
97. 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 mixedmodel method for association mapping that accounts for multiple levels of relatedness. Nat Genet. 38, 203-208.
98. Zhang, Q., Arbuckle, J., and Wessler, S. R. (2000). Recent, extensive, and preferential insertion of memebers of the miniature inverted-repeat transposable element family Heartbreaker into genic regions of maize. PNAS 97, 1160-1165.
99. Zhu, Y. L., Song, Q. J., Hyten, D. L., Van Tassell, C. P., Matukumalli, L. K., Grimm, D. R., Hyatt, S. M., Fickus, E. W., Young, N. D., and Cregan, P. B. (2003). Single-nucleotide polymorphisms in soybean. Genetics 163, 1123-1134.
100. Zimmer, E. A., Jupe, E. R., and Walbot, V. (1988). Ribosomal gene structure, variation and inheritance in maize and its ancestors. Genetics 120, 1125-1136.