Homologous Recombination in Maize

  • Hugo K. Dooner
  • An-Ping Hsia
  • Patrick S. Schnable

We have divided this chapter into two major sections: somatic and meiotic recombination. Somatic recombination in plants has been mostly monitored with artificial recombination substrates in transgenic systems. Although, in this area, maize has lagged behind other plants that can be more easily transformed, excellent progress has been achieved recently, as detailed in the first section. Specific topics discussed in this section are site-specific and targeted recombination. Research on meiotic recombination, particularly intragenic recombination, has been historically strong in maize relative to other plants, principally because the maize endosperm provides distinct advantages as an experimental unit of observation for recombination studies. It is, at the same time, large enough so that many traits can be scored and small enough so that many kernels can be screened. Many of the genes utilized in meiotic recombi-national analyses affect anthocyanin pigmentation in the aleurone layer of the endosperm, as will be evident in the second section. In this section we discuss the distribution of recombination junctions at the genomic, regional, and genic levels, as well as modifiers that affect that distribution. We consider the special case of tandem duplications and gene families as recombination substrates and discuss how recombination has been used as a tool in the genetic analysis of paramutation and disease resistance.


Meiotic Recombination Maize Genome Intragenic Recombination Recombination Nodule Conversion Tract 
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  1. Albert, H., Dale, E.C., Lee, E., and Ow, D.W. (1995). Site-specific integration of DNA into wild-type and mutant lox sites placed in the plant genome. Plant J. 7, 649–659.PubMedGoogle Scholar
  2. 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.PubMedGoogle Scholar
  3. Anderson, L.K., Doyle, G.G., Brigham, B., Carter, J., Hooker, K.D., Lai, A., Rice, M., and Stack, S.M. (2003). High-resolution crossover maps for each bivalent of Zea mays using recombination nodules. Genetics 165, 849–865.PubMedGoogle Scholar
  4. Araki, H., Jearnpipatkul, A., Tatsumi, H., Sakurai, T., Ushio, K., Muta, T., and Oshima, Y. (1985). Molecular and functional organization of yeast plasmid pSR1. J. Mol. Biol. 182, 191–203.PubMedGoogle Scholar
  5. Athma, P., and Peterson, T. (1991). Ac induces homologous recombination at the maize P locus. Genetics 128, 163–173.PubMedGoogle Scholar
  6. Bass, H.W., Bordoli, S.J., and Foss, E.M. (2003). The desynaptic (dy) and desynaptic1 (dsy1) mutations in maize (Zea mays L) cause distinct telomere-misplacement phenotypes during meiotic prophase. J. Exp. Bot. 54, 39–46.PubMedGoogle Scholar
  7. Beavis, W.D., and Grant, D. (1991). A linkage map based on information from four F2 populations of maize (Zea mays L.). Theor. Appl. Genet. 82.Google Scholar
  8. Beckett, E.B., Burnham, C.R., Coe, E.H., Maguire, M.P., Patterson, E.B., and Phillips, R.L. (1978). Cytogenetic working map. Maize Genet. Newslet. 52, 129–145.Google Scholar
  9. Beetham, P.R., Kipp, P.B., Sawycky, X.L., Arntzen, C.J., and May, G.D. (1999). A tool for functional plant genomics: chimeric RNA/DNA oligonucleotides cause in vivo gene-specific mutations. Proc. Natl. Acad. Sci. USA 96, 8774–8778.PubMedGoogle Scholar
  10. Broach, J.R., Guarascio, V.R., and Jayaram, M. (1982). Recombination within the yeast plasmid 2um circle is site-specific. Cell 29, 227–234.PubMedGoogle Scholar
  11. Brown, J., and Sundaressan, V. (1991). A recombinational hotspot in the maize A1 intragenic region. Theor. Appl. Genet. 81, 185–188.Google Scholar
  12. Chawla, R., Ariza-Nieto, M., Wilson, A.J., Moore, S.K., and Srivastava, V. (2006). Transgene expression produced by biolistic-mediated, site-specific gene integration is consistently inherited by the subsequent generations. Plant Biotechnol. J. 4, 209–218.PubMedGoogle Scholar
  13. Civardi, L., Xia, Y., Edwards, K.J., Schnable, P.S., and Nikolau, B.J. (1994). The relationship between genetic and physical distances in the cloned a1-sh2 interval of the Zea mays L. genome. Proc. Natl. Acad. Sci. USA 91, 8268–8272.Google Scholar
  14. Collins, N., Drake, J., Ayliffe, M., Sun, Q., Ellis, J., Hulbert, S., and Pryor, T. (1999). Molecular charac- terization of the maize Rp1-D rust resistance haplotype and its mutants. Plant Cell 11, 1365–1376.PubMedGoogle Scholar
  15. Copenhaver, G.P., Keith, K.C., and Preuss, D. (2000). Tetrad analysis in higher plants. A budding technology. Plant Physiol 124, 7–16.PubMedGoogle Scholar
  16. Coppoolse, E.R., de Vroomen, M.J., van Gennip, F., Hersmus, B.J., and van Haaren, M.J. (2005). Size does matter: cre-mediated somatic deletion efficiency depends on the distance between the target lox-sites. Plant Mol. Biol. 58, 687–698.PubMedGoogle Scholar
  17. Coppoolse, E.R., de Vroomen, M.J., Roelofs, D., Smit, J., van Gennip, F., Hersmus, B.J., Nijkamp, H.J., and van Haaren, M.J. (2003). Cre recombinase expression can result in pheno- typic aberrations in plants. Plant Mol. Biol. 51, 263–279.PubMedGoogle Scholar
  18. Darbani, B., Eimanifar, A., Stewart, C.N., Jr., and Camargo, W.N. (2007). Methods to produce marker-free transgenic plants. Biotechnol. J. 2, 83–90.PubMedGoogle Scholar
  19. Das, O.P., Poliak, E., Ward, K., and Messing, J. (1991). A new allele of the duplicated 27kD zein locus of maize generated by homologous recombination. Nucleic Acids Res. 19, 3325–3330.PubMedGoogle Scholar
  20. Davis, G.L., McMullen, M.D., Baysdorfer, C., Musket, T., Grant, D., Staebell, M., Xu, G., Polacco, M., Koster, L., Melia-Hancock, S., Houchins, K., Chao, S., and Coe, E.H., Jr. (1999). A maize map standard with sequenced core markers, grass genome reference points and 932 expressed sequence tagged sites (ESTs) in a 1736-locus map. Genetics 152, 1137–1172.PubMedGoogle Scholar
  21. Djukanovic, V., Orczyk, W., Gao, H., Sun, X., Garrett, N., Zhen, S., Gordon-Kamm, W., Barton, J., and Lyznik, L.A. (2006). Gene conversion in transgenic maize plants expressing FLP/FRT and Cre/loxP site-specific recombination systems. Plant Biotechnol. J. 4, 345–357.PubMedGoogle Scholar
  22. Dooner, H.K. (1986). Genetic fine structure of the bronze locus in maize. Genetics 113, 1021–1036.PubMedGoogle Scholar
  23. Dooner, H.K. (2002). Extensive interallelic polymorphisms drive meiotic recombination into a crossover pathway. Plant Cell 14, 1173–1183.PubMedGoogle Scholar
  24. Dooner, H.K., and Kermicle, J.L. (1971). Structure of the R-r tandem duplication in maize. Genetics 67, 437–454.PubMedGoogle Scholar
  25. Dooner, H.K., and Kermicle, J.L. (1974). Reconstitution of the R-r compound allele in maize. Genetics 78, 691–701.PubMedGoogle Scholar
  26. Dooner, H.K., and Kermicle, J.L. (1986). The transposable element Ds affects the pattern of intra- genic recombination at the bz and R loci in maize. Genetics 113, 135–143.PubMedGoogle Scholar
  27. Dooner, H.K., and Ralston, E. (1990). Effect of the Mu1 insertion on intragenic recombination at the bz locus in maize. Maydica 35, 333–337.Google Scholar
  28. Dooner, H.K., and Martínez-Férez, I.M. (1997a). Recombination occurs uniformly within the bronze gene, a meiotic recombination hotspot in the maize genome. Plant Cell 9, 1633–1646.Google Scholar
  29. Dooner, H.K., and Martínez-Férez, I.M. (1997b). Germinal excisions of the maize transposon activator do not stimulate meiotic recombination or homology-dependent repair at the bz locus. Genetics 147, 1923–1932.Google Scholar
  30. Dooner, H.K., Weck, E., Adams, S., Ralston, E., Favreau, M., and English, J. (1985). A molecular genetic analysis of insertion mutations in the bronze locus in maize. Mol. Gen. Genet. 200, 240–246.Google Scholar
  31. Durai, S., Mani, M., Kandavelou, K., Wu, J., Porteus, M.H., and Chandrasegaran, S. (2005). Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells. Nucleic Acids Res 33, 5978–5990.PubMedGoogle Scholar
  32. Eggleston, W.B., Alleman, M., and Kermicle, J.L. (1995). Molecular organization and germinal instability of R-stippled maize. Genetics 141, 347–360.PubMedGoogle Scholar
  33. Emrich, S.J., 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.PubMedGoogle Scholar
  34. Esch, E., Szymaniak, J.M., Yates, H., Pawlowski, W.P., and Buckler, E.S. (2007). Using crossover breakpoints in recombinant inbred lines to identify quantitative trait loci controlling the global recombination frequency. Genetics, 177, 1851–1858.PubMedGoogle Scholar
  35. Fatmi, A., Poneleit, C.G., and Pfeiffer, T.W. (1993). Variability of recombination frequencies in the Iowa Stiff Stalk Synthetic (Zea mays L.). Theor Appl. Genet. 86, 859–866.Google Scholar
  36. Franklin, A.E., Golubovskaya, I.N., Bass, H.W., and Cande, W.Z. (2003). Improper chromosome synapsis is associated with elongated RAD51 structures in the maize desynaptic2 mutant. Chromosoma 112, 17–25.PubMedGoogle Scholar
  37. Freeling, M. (1976). Intragenic recombination in maize: pollen analysis methods and the effect of parental Adh1 alleles. Genetics 83, 707–719.Google Scholar
  38. Freeling, M. (1977). Allelic variation at the level of intragenic recombination. Genetics 89, 505–509.Google Scholar
  39. Freeling, M., and Bennett, D.C. (1985). Maize Adh1. Annu. Rev. Genet. 19, 297–323.PubMedGoogle Scholar
  40. Fu, H., and Dooner, H.K. (2002). Intraspecific violation of genetic colinearity and its implications in maize. Proc. Natl. Acad. Sci. USA 99, 9573–9578.PubMedGoogle Scholar
  41. Fu, H., Zheng, Z., and Dooner, H.K. (2002). Recombination rates between adjacent genic and retrotransposon regions in maize vary by 2 orders of magnitude. Proc. Natl. Acad. Sci. USA 99, 1082–1087.PubMedGoogle Scholar
  42. Hanin, M., and Paszkowski, J. (2003). Plant genome modification by homologous recombination. Curr. Opin. Plant Biol. 6, 157–162.PubMedGoogle Scholar
  43. Harper, L.C., and Cande, W.Z. (2000). Mapping a new frontier; development of integrated cytoge- netic maps in plants. Funct. Integr. Genomics 1, 89–98.PubMedGoogle Scholar
  44. He, L., and Dooner, H.K. (2007). Recombination in a 100-kb genic interval containing Helitrons and retrotransposons. In 49th Annual Maize Genet. Conf. Abstracts (St. Charles, IL), pp. 99.Google Scholar
  45. Hulbert, S.H., and Bennetzen, J.L. (1991). Recombination at the Rp1 locus of maize. Mol. Gen. Genet. 226, 377–382.PubMedGoogle Scholar
  46. Hulbert, S.H., Sudupak, M.A., and Hong, K.S. (1993). Genetic relationships between alleles of the Rp1 rust resistance locus in maize. Mol. Plant-Microbe Int. 6, 387–392.Google Scholar
  47. Igoucheva, O., Alexeev, V., and Yoon, K. (2004). Oligonucleotide-directed mutagenesis and tar- geted gene correction: a mechanistic point of view. Curr Mol Med 4, 445–463.PubMedGoogle Scholar
  48. Iida, S., and Terada, R. (2005). Modification of endogenous natural genes by gene targeting in rice and other higher plants. Plant Mol. Biol. 59, 205–219.PubMedGoogle Scholar
  49. Ji, Y., Stelly, D.M., De Donato, M., Goodman, M.M., and Williams, C.G. (1999). A candidate recombination modifier gene for Zea mays L. Genetics 151, 821–830.PubMedGoogle Scholar
  50. Kerbach, S., Lorz, H., and Becker, D. (2005). Site-specific recombination in Zea mays. Theor. Appl. Genet. 111, 1608–1616.PubMedGoogle Scholar
  51. Kermicle, J.L. (1970). Somatic and meiotic Instability of R-stippled, an aleurone spotting factor in maize. Genetics 64, 247–258.PubMedGoogle Scholar
  52. Kermicle, J.L. (1984). Recombination between Components of a Mutable Gene System in Maize. Genetics 107, 489–500.PubMedGoogle Scholar
  53. Kermicle, J.L., Eggleston, W.B., and Alleman, M. (1995). Organization of paramutagenicity in R-stippled maize. Genetics 141, 361–372.PubMedGoogle Scholar
  54. Kochevenko, A., and Willmitzer, L. (2003). Chimeric RNA/DNA oligonucleotide-based site- specific modification of the tobacco acetolactate syntase gene. Plant Physiol 132, 174–184.PubMedGoogle Scholar
  55. Kotani, H., Germann, M.W., Andrus, A., Vinayak, R., Mullah, B., and Kmiec, E.B. (1996). RNA facilitates RecA-mediated DNA pairing and strand transfer between molecules bearing limited regions of homology. Mol. Gen. Genet. 250, 626–634.PubMedGoogle Scholar
  56. Koumbaris, G.L., and Bass, H.W. (2003). A new single-locus cytogenetic mapping system for maize (Zea mays L.): overcoming FISH detection limits with marker-selected sorghum (S. propinquum L.) BAC clones. Plant J. 35, 647–659.PubMedGoogle Scholar
  57. Laughnan, J.R. (1952). The action of allelic forms of the gene A in maize. IV. On the compound nature of A and the occurrence and action of Its a derivatives. Genetics 37, 375–395.Google Scholar
  58. Lawrence, C.J., Seigfried, T.E., Bass, H.W., and Anderson, L.K. (2006). Predicting chromosomal locations of genetically mapped loci in maize using the Morgan2McClintock Translator. Genetics 172, 2007–2009.PubMedGoogle Scholar
  59. Li, J., Wen, T.J., and Schnable, P.S. (2007a). The role of RAD51 in the repair of MuDR-induced DSBs in Zea mays L. Genetics, 178, 57–66.Google Scholar
  60. Li, J., Harper, L.C., Golubovskaya, I., Wang, C.R., Weber, D., Meeley, R.B., McElver, J., Bowen, B., Cande, W.Z., and Schnable, P.S. (2007b). Functional analysis of maize RAD51 in meiosis and double-strand break repair. Genetics 176, 1469–1482.Google Scholar
  61. Li, Y., Bernot, J.P., Illingworth, C., Lison, W., Bernot, K.M., Eggleston, W.B., Fogle, K.J., DiPaola, J.E., Kermicle, J., and Alleman, M. (2001). Gene conversion within regulatory sequences generates maize r alleles with altered gene expression. Genetics 159, 1727–1740.PubMedGoogle Scholar
  62. Lloyd, A., Plaisier, C.L., Carroll, D., and Drews, G.N. (2005). Targeted mutagenesis using zinc- finger nucleases in Arabidopsis. Proc Natl Acad Sci USA 102, 2232–2237.PubMedGoogle Scholar
  63. Lowe, B., Mathern, J., and Hake, S. (1992). Active Mutator elements suppress the knotted pheno- type and increase recombination at the Kn1-O tandem duplication. Genetics 132, 813–822.PubMedGoogle Scholar
  64. Lyznik, L.A., Rao, K.V., and Hodges, T.K. (1996). FLP-mediated recombination of FRT sites in the maize genome. Nucleic Acids Res. 24, 3784–3789.PubMedGoogle Scholar
  65. Lyznik, L.A., Gordon-Kamm, W.J., and Tao, Y. (2003). Site-specific recombination for genetic engineering in plants. Plant Cell Rep. 21, 925–932.PubMedGoogle Scholar
  66. Lyznik, L.A., Mitchell, J.C., Hirayama, L., and Hodges, T.K. (1993). Activity of yeast FLP recom- binase in maize and rice protoplasts. Nucleic Acids Res. 21, 969–975.PubMedGoogle Scholar
  67. Lyznik, L.A., Hirayama, L., Rao, K.V., Abad, A., and Hodges, T.K. (1995). Heat-inducible expression of FLP gene in maize cells. Plant J. 8, 177–186.PubMedGoogle Scholar
  68. Mani, M., Smith, J., Kandavelou, K., Berg, J.M., and Chandrasegaran, S. (2005). Binding of two zinc finger nuclease monomers to two specific sites is required for effective double-strand DNA cleavage. Biochem. Biophys. Res. Commun. 334, 1191–1197.PubMedGoogle Scholar
  69. Matzke, A.J., and Matzke, M.A. (1998). Position effects and epigenetic silencing of plant trans- genes. Curr. Opin. Plant Biol. 1, 142–148.PubMedGoogle Scholar
  70. Messing, J., and Dooner, H.K. (2006). Organization and variability of the maize genome. Curr. Opin. Plant Biol. 9, 157–163.PubMedGoogle Scholar
  71. Messing, J., Bharti, A.K., Karlowski, W.M., Gundlach, H., Kim, H.R., Yu, Y., Wei, F., Fuks, G., Soderlund, C.A., Mayer, K.F., and Wing, R.A. (2004). Sequence composition and genome organization of maize. Proc. Natl. Acad. Sci. USA 101, 14349–14354.PubMedGoogle Scholar
  72. Mezard, C. (2006). Meiotic recombination hotspots in plants. Biochem. Soc. Trans. 34, 531–534.PubMedGoogle Scholar
  73. Nelson, O.E. (1962). The waxy locus in maize. I. Intralocus recombination frequency estimates by pollen and by conventional analysis. Genetics 47, 737–742.PubMedGoogle Scholar
  74. Nelson, O.E. (1968). The waxy locus in maize. II. The location of the controlling element alleles. Genetics 60, 507–524.PubMedGoogle Scholar
  75. Okagaki, R.J., and Weil, C.F. (1997). Analysis of recombination sites within the maize waxy locus. Genetics 147, 815–821.PubMedGoogle Scholar
  76. Okuzaki, A., and Toriyama, K. (2004). Chimeric RNA/DNA oligonucleotide-directed gene target- ing in rice. Plant Cell Rep. 22, 509–512.PubMedGoogle Scholar
  77. Osborne, B.I., Wirtz, U., and Baker, B. (1995). A system for insertional mutagenesis and chromo- somal rearrangement using the Ds transposon and Cre-lox. Plant J. 7, 687–701.PubMedGoogle Scholar
  78. Ow, D.W. (2007). GM maize from site-specific recombination technology, what next? Curr. Opin. Biotechnol. 18, 115–120.Google Scholar
  79. Paques, F., and Haber, J.E. (1999). Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microb. Mol. Biol. Rev. 63, 349–404.Google Scholar
  80. Patterson, G.I., Kubo, K.M., Shroyer, T., and Chandler, V.L. (1995). Sequences required for par-amutation of the maize b gene map to a region containing the promoter and upstream sequences. Genetics 140, 1389–1406.PubMedGoogle Scholar
  81. Petes, T.D. (2001). Meiotic recombination hot spots and cold spots. Nat Rev Genet 2, 360–369.PubMedGoogle Scholar
  82. Petes, T.D., Malone, R.E., and Symington, L.E. (1991). Recombination in yeast. In The Molecular and Cellular Biology of the Yeast Saccharomyces: Genome Dynamics, Protein Synthesis and Energetics. (Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press), pp. 407–521.Google Scholar
  83. Puchta, H. (2002). Gene replacement by homologous recombination in plants. Plant Mol. Biol. 48, 173–182.PubMedGoogle Scholar
  84. Puchta, H. (2003). Towards the ideal GMP: homologous recombination and marker gene excision. J. Plant Physiol. 160, 743–754.PubMedGoogle Scholar
  85. Puchta, H., Dujon, B., and Hohn, B. (1993). Homologous recombination in plant cells is enhanced by in vivo induction of double strand breaks into DNA by a site-specific endonuclease. Nucleic Acids Res. 21, 5034–5040.PubMedGoogle Scholar
  86. Ramakrishna, W., Emberton, J., Ogden, M., SanMiguel, P., and Bennetzen, J.L. (2002). Structural analysis of the maize rp1 complex reveals numerous sites and unexpected mechanisms of local rearrangement. Plant Cell 14, 3213–3223.PubMedGoogle Scholar
  87. Ream, T.S., Strobel, J., Roller, B., Auger, D.L., Kato, A., Halbrook, C., Peters, E.M., Theuri, J., Bauer, M.J., Addae, P., Dioh, W., Staub, J.M., Gilbertson, L.A., and Birchler, J.A. (2005). A test for ectopic exchange catalyzed by Cre recombinase in maize. Theor. Appl. Genet. 111, 378–385.PubMedGoogle Scholar
  88. Richter, T.E., Pryor, T.J., Bennetzen, J.L., and Hulbert, S.H. (1995). New rust resistance specifici- ties associated with recombination in the Rp1 complex in maize. Genetics 141, 373–381.PubMedGoogle Scholar
  89. Robbins, T.P., Walker, E.L., Kermicle, J.L., Alleman, M., and Dellaporta, S.L. (1991). Meiotic instability of the R-r complex arising from displaced intragenic exchange and intrachromo-somal rearrangement. Genetics 129, 271–283.PubMedGoogle Scholar
  90. Ruiter, R., van den Brande, I., Stals, E., Delaure, S., Cornelissen, M., and D'Halluin, K. (2003). Spontaneous mutation frequency in plants obscures the effect of chimeraplasty. Plant Mol. Biol. 53, 675–689.PubMedGoogle Scholar
  91. Sadder, T., and Weber, G. (2002). Comparison between genetic and physical maps in Zea mays L. of molecular markers linked to resistance against Diatraea spp. Theor. Appl. Genet. 104, 908–915.PubMedGoogle Scholar
  92. SanMiguel, P., and Bennetzen, J.L. (1998). Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Ann. Botany 82, 37–44.Google Scholar
  93. SanMiguel, 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.PubMedGoogle Scholar
  94. Schultes, N.P., and Szostak, J.W. (1990). Decreasing gradients of gene conversion on both sides of the initiation site for meiotic recombination at the ARG4 locus in yeast. Genetics 126, 813–822.PubMedGoogle Scholar
  95. Smith, J., Bibikova, M., Whitby, F.G., Reddy, A.R., Chandrasegaran, S., and Carroll, D. (2000). Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains. Nucleic Acids Res. 28, 3361–3369.PubMedGoogle Scholar
  96. Srivastava, V., and Ow, D.W. (2001). Single-copy primary transformants of maize obtained through the co-introduction of a recombinase-expressing construct. Plant Mol. Biol. 46, 561–566.PubMedGoogle Scholar
  97. Srivastava, V., Ariza-Nieto, M., and Wilson, A.J. (2004). Cre-mediated site-specific gene integra- tion for consistent transgene expression in rice. Plant Biotechnol. J. 2, 169–179.PubMedGoogle Scholar
  98. Stack, S.M., and Anderson, L.K. (2002). Crossing over as assessed by late recombination nodules is related to the pattern of synapsis and the distribution of early recombination nodules in maize. Chromosome Res. 10, 329–345.PubMedGoogle Scholar
  99. Stadler, L.J. (1926). The variability of crossing over in maize. Genetics 11, 1–37.PubMedGoogle Scholar
  100. Stadler, L.J., and Neuffer, M.G. (1953). Problems of gene structure. II. Separation of R-r elements (S) and (P) by unequal crossing over. Science 117, 471–472.Google Scholar
  101. Stam, M., Belele, C., Dorweiler, J.E., and Chandler, V.L. (2002a). Differential chromatin structure within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutation. Genes Dev 16, 1906–1918.Google Scholar
  102. Stam, M., Belele, C., Ramakrishna, W., Dorweiler, J.E., Bennetzen, J.L., and Chandler, V.L. (2002b). The regulatory regions required for B′ paramutation and expression are located far upstream of the maize b1 transcribed sequences. Genetics 162, 917–930.Google Scholar
  103. Sternberg, N., and Hamilton, D. (1981). Bacteriophage P1 site-specific recombination. I. Recombination between loxP sites. J. Mol Biol 150, 467–486.PubMedGoogle Scholar
  104. Stinard, P.S., Robertson, D.S., and Schnable, P.S. (1993). Genetic isolation, cloning, and analysis of a Mutator-induced, dominant antimorph of the maize amylose extender1 locus. Plant Cell 5, 1555–1566.PubMedGoogle Scholar
  105. Sturtevant, A.H. (1925). The effects of unequal crossing over at the Bar locus in Drosophila. Genetics 10, 117–147.PubMedGoogle Scholar
  106. Sudupak, M.A., Bennetzen, J.L., and Hulbert, S.H. (1993). Unequal exchange and meiotic insta- bility of disease-resistance genes in the Rp1 region of maize. Genetics 133, 119–125.PubMedGoogle Scholar
  107. Sun, Q., Collins, N.C., Ayliffe, M., Smith, S.M., Drake, J., Pryor, T., and Hulbert, S.H. (2001). Recombination between paralogues at the Rp1 rust resistance locus in maize. Genetics 158, 423–438.PubMedGoogle Scholar
  108. Thuriaux, P. (1977). Is recombination confined to structural genes on the eukaryotic genome? Nature 268, 460–462.PubMedGoogle Scholar
  109. Timmermans, M.C., Das, O.P., and Messing, J. (1996). Characterization of a meiotic crossover in maize identified by a restriction fragment length polymorphism-based method. Genetics 143, 1771–1783.PubMedGoogle Scholar
  110. Timmermans, M.C., Das, O.P., Bradeen, J.M., and Messing, J. (1997). Region-specific cis- and trans-acting factors contribute to genetic variability in meiotic recombination in maize. Genetics 146, 1101–1113.PubMedGoogle Scholar
  111. Tulsieram, L., Compton, W.A., Morris, R., Thomas-Compton, M., and Eskridge, K. (1992). Analysis of genetic recombination in maize populations using molecular markers. Theor. Appl. Genet. 84, 65–72.Google Scholar
  112. Vergunst, A.C., and Hooykaas, P.J. (1998). Cre/lox-mediated site-specific integration of Agrobacterium T-DNA in Arabidopsis thaliana by transient expression of cre. Plant Mol. Biol. 38, 393–406.PubMedGoogle Scholar
  113. Walker, E.L., Robbins, T.P., Bureau, T.E., Kermicle, J., and Dellaporta, S.L. (1995). Transposon- mediated chromosomal rearrangements and gene duplications in the formation of the maize R-r complex. EMBO journal 14, 2350–2363.PubMedGoogle Scholar
  114. Wang, C.J., Harper, L., and Cande, W.Z. (2006). High-resolution single-copy gene fluorescence in situ hybridization and its use in the construction of a cytogenetic map of maize chromosome 9. Plant Cell 18, 529–544.PubMedGoogle Scholar
  115. 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. USA 103, 17644–17649.PubMedGoogle Scholar
  116. Webb, C.A., Richter, T.E., Collins, N.C., Nicolas, M., Trick, H.N., Pryor, T., and Hulbert, S.H. (2002). Genetic and molecular characterization of the maize rp3 rust resistance locus. Genetics 162, 381–394.PubMedGoogle Scholar
  117. Wessler, S., and Varagona, R. (1985). Molecular basis of mutations at the waxy locus of maize: correlation with the fine structure genetic map. Proc. Natl. Acad. Sci. USA 82, 4177–4181.PubMedGoogle Scholar
  118. Williams, C.G., Goodman, M.M., and Stuber, C.W. (1995). Comparative recombination distances among Zea mays L. inbreds, wide crosses and interspecific hybrids. Genetics 141, 1573–1581.PubMedGoogle Scholar
  119. Woody, S.T., Austin-Phillips, S., Amasino, R.M., and Krysan, P.J. (2007). The WiscDsLox T-DNA collection: an Arabidopsis community resource generated by using an improved high- throughput T-DNA sequencing pipeline. J. Plant Res 120, 157–165.PubMedGoogle Scholar
  120. Wright, D.A., Townsend, J.A., Winfrey, R.J., Jr., Irwin, P.A., Rajagopal, J., Lonosky, P.M., Hall, B.D., Jondle, M.D., and Voytas, D.F. (2005). High-frequency homologous recombination in plants mediated by zinc-finger nucleases. Plant J. 44, 693–705.PubMedGoogle Scholar
  121. Wu, J., Kandavelou, K., and Chandrasegaran, S. (2007). Custom-designed zinc finger nucleases: What is next? Cell. Mol. Life Sci.1420–682X.Google Scholar
  122. Xiao, Y.L., and Peterson, T. (2000). Intrachromosomal homologous recombination in Arabidopsis induced by a maize transposon. Mol. Gen. Genet. 263, 22–29.PubMedGoogle Scholar
  123. Xiao, Y.L., Li, X., and Peterson, T. (2000). Ac insertion site affects the frequency of transposon- induced homologous recombination at the maize p1 locus. Genetics 156, 2007–2017.PubMedGoogle Scholar
  124. Xu, X., Hsia, A.P., Zhang, L., Nikolau, B.J., and Schnable, P.S. (1995). Meiotic recombination break points resolve at high rates at the 5′ end of a maize coding sequence. Plant Cell 7, 2151–2161.PubMedGoogle Scholar
  125. Yandeau-Nelson, M.D., Nikolau, B.J., and Schnable, P.S. (2006a). Effects of trans-acting genetic modifiers on meiotic recombination across the a1-sh2 interval of maize. Genetics 174, 101–112.Google Scholar
  126. Yandeau-Nelson, M.D., Xia, Y., Li, J., Neuffer, M.G., and Schnable, P.S. (2006b). Unequal sister chromatid and homolog recombination at a tandem duplication of the A1 locus in maize. Genetics 173, 2211–2226.Google Scholar
  127. Yandeau-Nelson, M.D., Zhou, Q., Yao, H., Xu, X., Nikolau, B.J., and Schnable, P.S. (2005). MuDR transposase increases the frequency of meiotic crossovers in the vicinity of a Mu insertion in the maize a1 gene. Genetics 169, 917–929.PubMedGoogle Scholar
  128. Yao, H., and Schnable, P.S. (2005). Cis-effects on meiotic recombination across distinct a1-sh2 intervals in a common Zea genetic background. Genetics 170, 1929–1944.PubMedGoogle Scholar
  129. Yao, H., Zhou, Q., Li, J., Smith, H., Yandeau, M., Nikolau, B.J., and Schnable, P.S. (2002). Molecular characterization of meiotic recombination across the 140-kb multigenic a1-sh2 interval of maize. Proc. Natl. Acad. Sci. USA 99, 6157–6162.PubMedGoogle Scholar
  130. Zeng, Z., and Sachs, M.M. (1994). Intragenic recombination among alleles of the Adh1 gene in maize. Maydica 39, 265–272.Google Scholar
  131. Zhang, W., Subbarao, S., Addae, P., Shen, A., Armstrong, C., Peschke, V., and Gilbertson, L. (2003). Cre/lox-mediated marker gene excision in transgenic maize (Zea mays L.) plants. Theor. Appl. Genet. 107, 1157–1168.PubMedGoogle Scholar
  132. Zhu, T., Mettenburg, K., Peterson, D.J., Tagliani, L., and Baszczynski, C.L. (2000). Engineering herbicide-resistant maize using chimeric RNA/DNA oligonucleotides. Nat Biotechnol. 18, 555–558.PubMedGoogle Scholar
  133. Zhu, T., Peterson, D.J., Tagliani, L., St Clair, G., Baszczynski, C.L., and Bowen, B. (1999). Targeted manipulation of maize genes in vivo using chimeric RNA/DNA oligonucleotides. Proc Natl Acad Sci U S A 96, 8768–8773.PubMedGoogle Scholar

Copyright information

© Springer Science + Business Media, LLC 2009

Authors and Affiliations

  1. 1.Waksman Institute and Department of Plant BiologyRutgers UniversityPiscatawayUSA
  2. 2.Department of AgronomyIowa State UniversityAmesUSA
  3. 3.Center for Plant Genomics and Department of AgronomyIowa State UniversityAmesUSA

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