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. 1997 Oct;147(2):815–821. doi: 10.1093/genetics/147.2.815

Analysis of Recombination Sites within the Maize Waxy Locus

R J Okagaki 1, C F Weil 1
PMCID: PMC1208201  PMID: 9335616

Abstract

Genetic fine structure analysis of the maize wx locus has determined that the ratio of genetic to physical distance within wx was one to two orders of magnitude higher than the average for the maize genome. Similar results have been found at other maize loci. In this study, we examined several mechanisms that could account for this pattern. First, crossovers in two other maize genes resolve preferentially at specific sites. By mapping exchanges between wx-B1 and wx-I relative to a polymorphic SstI site, we found no evidence for such a hotspot at wx. Second, deletion of promoter sequences from wx alleles had little effect on recombination frequencies, in contrast to results in yeast where promoter sequences are important for initiating recombination in some genes. Third, high levels of insertion polymorphism may suppress intergenic recombination. However, the presence of a 2-kb Ds element 470 bp upstream of the wx transcription start site did not further suppress recombination between Ds insertions in nearby wx sequences. Thus, none of these mechanisms is sufficient to explain the difference between intergenic and intragenic recombination rates at wx.

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Selected References

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  1. Borts R. H., Haber J. E. Meiotic recombination in yeast: alteration by multiple heterozygosities. Science. 1987 Sep 18;237(4821):1459–1465. doi: 10.1126/science.2820060. [DOI] [PubMed] [Google Scholar]
  2. Brenner D. A., Smigocki A. C., Camerini-Otero R. D. Effect of insertions, deletions, and double-strand breaks on homologous recombination in mouse L cells. Mol Cell Biol. 1985 Apr;5(4):684–691. doi: 10.1128/mcb.5.4.684. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bureau T. E., Wessler S. R. Tourist: a large family of small inverted repeat elements frequently associated with maize genes. Plant Cell. 1992 Oct;4(10):1283–1294. doi: 10.1105/tpc.4.10.1283. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cao L., Alani E., Kleckner N. A pathway for generation and processing of double-strand breaks during meiotic recombination in S. cerevisiae. Cell. 1990 Jun 15;61(6):1089–1101. doi: 10.1016/0092-8674(90)90072-m. [DOI] [PubMed] [Google Scholar]
  5. Civardi L., Xia Y., Edwards K. J., Schnable P. S., Nikolau B. J. The relationship between genetic and physical distances in the cloned a1-sh2 interval of the Zea mays L. genome. Proc Natl Acad Sci U S A. 1994 Aug 16;91(17):8268–8272. doi: 10.1073/pnas.91.17.8268. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Dooner H. K. Genetic Fine Structure of the BRONZE Locus in Maize. Genetics. 1986 Aug;113(4):1021–1036. doi: 10.1093/genetics/113.4.1021. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Eggleston W. B., Alleman M., Kermicle J. L. Molecular organization and germinal instability of R-stippled maize. Genetics. 1995 Sep;141(1):347–360. doi: 10.1093/genetics/141.1.347. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Fan Q., Xu F., Petes T. D. Meiosis-specific double-strand DNA breaks at the HIS4 recombination hot spot in the yeast Saccharomyces cerevisiae: control in cis and trans. Mol Cell Biol. 1995 Mar;15(3):1679–1688. doi: 10.1128/mcb.15.3.1679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Freeling M. Intragenic recombination in maize: pollen analysis methods and the effect of parental adh1 isoalleles. Genetics. 1976 Aug;83(4):701–717. doi: 10.1093/genetics/83.4.701. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Godwin A. R., Liskay R. M. The effects of insertions on mammalian intrachromosomal recombination. Genetics. 1994 Feb;136(2):607–617. doi: 10.1093/genetics/136.2.607. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Johns M. A., Strommer J. N., Freeling M. Exceptionally High Levels of Restriction Site Polymorphism in DNA near the Maize Adh1 Gene. Genetics. 1983 Nov;105(3):733–743. doi: 10.1093/genetics/105.3.733. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Moore C. W., Creech R. G. Genetic Fine Structure Analysis of the AMYLOSE-EXTENDER Locus in ZEA MAYS L. Genetics. 1972 Apr;70(4):611–619. doi: 10.1093/genetics/70.4.611. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Nelson O. E. The WAXY Locus in Maize. II. the Location of the Controlling Element Alleles. Genetics. 1968 Nov;60(3):507–524. doi: 10.1093/genetics/60.3.507. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Nicolas A., Treco D., Schultes N. P., Szostak J. W. An initiation site for meiotic gene conversion in the yeast Saccharomyces cerevisiae. Nature. 1989 Mar 2;338(6210):35–39. doi: 10.1038/338035a0. [DOI] [PubMed] [Google Scholar]
  15. Okagaki R. J., Neuffer M. G., Wessler S. R. A deletion common to two independently derived waxy mutations of maize. Genetics. 1991 Jun;128(2):425–431. doi: 10.1093/genetics/128.2.425. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Patterson G. I., Kubo K. M., Shroyer T., Chandler V. L. Sequences required for paramutation of the maize b gene map to a region containing the promoter and upstream sequences. Genetics. 1995 Aug;140(4):1389–1406. doi: 10.1093/genetics/140.4.1389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Ralston E. J., English J. J., Dooner H. K. Sequence of three bronze alleles of maize and correlation with the genetic fine structure. Genetics. 1988 May;119(1):185–197. doi: 10.1093/genetics/119.1.185. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Ralston E., English J., Dooner H. K. Chromosome-breaking structure in maize involving a fractured Ac element. Proc Natl Acad Sci U S A. 1989 Dec;86(23):9451–9455. doi: 10.1073/pnas.86.23.9451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Robbins T. P., Walker E. L., Kermicle J. L., Alleman M., Dellaporta S. L. Meiotic instability of the R-r complex arising from displaced intragenic exchange and intrachromosomal rearrangement. Genetics. 1991 Sep;129(1):271–283. doi: 10.1093/genetics/129.1.271. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. SanMiguel P., Tikhonov A., Jin Y. K., Motchoulskaia N., Zakharov D., Melake-Berhan A., Springer P. S., Edwards K. J., Lee M., Avramova Z. Nested retrotransposons in the intergenic regions of the maize genome. Science. 1996 Nov 1;274(5288):765–768. doi: 10.1126/science.274.5288.765. [DOI] [PubMed] [Google Scholar]
  21. Selva E. M., New L., Crouse G. F., Lahue R. S. Mismatch correction acts as a barrier to homeologous recombination in Saccharomyces cerevisiae. Genetics. 1995 Mar;139(3):1175–1188. doi: 10.1093/genetics/139.3.1175. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Shattuck-Eidens D. M., Bell R. N., Neuhausen S. L., Helentjaris T. DNA sequence variation within maize and melon: observations from polymerase chain reaction amplification and direct sequencing. Genetics. 1990 Sep;126(1):207–217. doi: 10.1093/genetics/126.1.207. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Thomas B. J., Rothstein R. Elevated recombination rates in transcriptionally active DNA. Cell. 1989 Feb 24;56(4):619–630. doi: 10.1016/0092-8674(89)90584-9. [DOI] [PubMed] [Google Scholar]
  24. Waldman A. S., Liskay R. M. Dependence of intrachromosomal recombination in mammalian cells on uninterrupted homology. Mol Cell Biol. 1988 Dec;8(12):5350–5357. doi: 10.1128/mcb.8.12.5350. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Weil C. F., Marillonnet S., Burr B., Wessler S. R. Changes in state of the Wx-m5 allele of maize are due to intragenic transposition of Ds. Genetics. 1992 Jan;130(1):175–185. doi: 10.1093/genetics/130.1.175. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Wessler S. R., Baran G., Varagona M., Dellaporta S. L. Excision of Ds produces waxy proteins with a range of enzymatic activities. EMBO J. 1986 Oct;5(10):2427–2432. doi: 10.1002/j.1460-2075.1986.tb04517.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Wessler S. R., Varagona M. J. Molecular basis of mutations at the waxy locus of maize: correlation with the fine structure genetic map. Proc Natl Acad Sci U S A. 1985 Jun;82(12):4177–4181. doi: 10.1073/pnas.82.12.4177. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Wessler S., Tarpley A., Purugganan M., Spell M., Okagaki R. Filler DNA is associated with spontaneous deletions in maize. Proc Natl Acad Sci U S A. 1990 Nov;87(22):8731–8735. doi: 10.1073/pnas.87.22.8731. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. White M. A., Detloff P., Strand M., Petes T. D. A promoter deletion reduces the rate of mitotic, but not meiotic, recombination at the HIS4 locus in yeast. Curr Genet. 1992 Feb;21(2):109–116. doi: 10.1007/BF00318468. [DOI] [PubMed] [Google Scholar]
  30. White S. E., Habera L. F., Wessler S. R. Retrotransposons in the flanking regions of normal plant genes: a role for copia-like elements in the evolution of gene structure and expression. Proc Natl Acad Sci U S A. 1994 Dec 6;91(25):11792–11796. doi: 10.1073/pnas.91.25.11792. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Xu X., Hsia A. P., Zhang L., Nikolau B. J., Schnable P. S. Meiotic recombination break points resolve at high rates at the 5' end of a maize coding sequence. Plant Cell. 1995 Dec;7(12):2151–2161. doi: 10.1105/tpc.7.12.2151. [DOI] [PMC free article] [PubMed] [Google Scholar]

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