A strategy for characterization of persistent heteroduplex DNA in higher plants

Plant Journal

Volumn 80, Issue 2, 2014, Pages 282-291

  Dong, Chun Bo ^a   Mao, Jian Feng ^a   Suo, Yu Jing ^a   Shi, Le ^a   Wang, Jun ^a   Zhang, Ping Dong ^a   Kang, Xiang Yang ^a  

^a BEIJING FORESTRY UNIVERSITY   (China)

Author keywords

Heteroduplex DNA; Populus 3 beijingensis; Populus pseudo simonii 3 Populus nigra 'Zheyin3 '; Post meiotic segregation; Triploid

Indexed keywords

CHROMOSOMES; DNA; DNA SEQUENCES; NUCLEIC ACIDS;

HETERODUPLEX; HIGH-THROUGHPUT SEQUENCING; HOMOLOGOUS RECOMBINATION; POPULUS; POPULUS NIGRA; PROTEIN-CODING TRANSCRIPTS; SIMPLE SEQUENCE-REPEAT MARKERS; TRIPLOID;

PLANTS (BOTANY);

HETERODUPLEX; PLANT DNA;

GENETICS; HOMOLOGOUS RECOMBINATION; PLANT;

DNA, PLANT; HOMOLOGOUS RECOMBINATION; NUCLEIC ACID HETERODUPLEXES; PLANTS;

EID: 84908088839     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/tpj.12631     Document Type: Article

References (56)

1. Aleza, P., Juarez, J., Ollitrault, P. and Navarro, L. (2009) Production of tetraploid plants of non apomictic citrus genotypes. Plant Cell Rep. 28, 1837-1846.
2. Allers, T. and Lichten, M. (2001) Differential timing and control of noncrossover and crossover recombination during meiosis. Cell, 106, 47-57.
3. Anderson, L.K., Stack, S.M., Fox, M.H. and Zhang, C.S. (1985) The relationship between genome size and synaptonemal complex length in higher plants. Exp. Cell Res. 156, 367-378.
4. Anderson, L.K., Lai, A., Stack, S.M., Rizzon, C. and Gaut, B.S. (2006) Uneven distribution of expressed sequence tag loci on maize pachytene chromosomes. Genome Res. 16, 115-122.
5. Backstrom, N., Forstmeier, W., Schielzeth, H. et al. (2010) The recombination landscape of the zebra finch Taeniopygia guttata genome. Genome Res. 20, 485-495.
6. Basheva, E.A., Bidau, C.J. and Borodin, P.M. (2008) General pattern of meiotic recombination in male dogs estimated by MLH1 and RAD51 immunolocalization. Chromosome Res. 16, 709-719.
7. Beye, M., Gattermeier, I., Hasselmann, M. et al. (2006) Exceptionally high levels of recombination across the honey bee genome. Genome Res. 16, 1339-1344.
8. Bishop, D.K. and Zickler, D. (2004) Early decision; meiotic crossover interference prior to stable strand exchange and synapsis. Cell, 117, 9-15.
9. Copenhaver, G.P., Nickel, K., Kuromori, T. et al. (1999) Genetic definition and sequence analysis of Arabidopsis centromeres. Science, 286, 2468-2474.
10. Dhamayanthi, K.P.M. and Gotmare, V. (2010) Induction of polyploidy in two diploid wild cotton (G. armourianum and G. aridum) species by colchicine treatment. Electronic J. Plant Breed. 1, 966-972.
11. Drouaud, J., Camilleri, C., Bourguignon, P.Y. et al. (2006) Variation in crossing- over rates across chromosome 4 of Arabidopsis thaliana reveals the presence of meiotic recombination "hot spots". Genome Res. 16, 106-114.
12. Evans, E. and Alani, E. (2000) Roles for mismatch repair factors in regulating genetic recombination. Mol. Cell. Biol. 20, 7839-7844.
13. Galbraith, D.W., Harkins, K.R., Maddox, J.M., Ayres, N.M., Sharma, D.P. and Firoozabady, E. (1983) Rapid flow cytometric analysis of the cell cycle in intact plant tissues. Science, 220, 1049-1051.
14. Gilbertson, L.A. and Stahl, F.W. (1996) A test of the double-strand break repair model for meiotic recombination in Saccharomyces cerevisiae. Genetics, 144, 27-41.
15. Giraut, L., Falque, M., Drouaud, J., Pereira, L., Martin, O.C. and Mezard, C. (2011) Genome-wide crossover distribution in Arabidopsis thaliana meiosis reveals sex-specific patterns along chromosomes. PLoS Genet. 7, e1002354.
16. Gore, M.A., Chia, J.M., Elshire, R.J. et al. (2009) A first-generation haplotype map of maize. Science, 326, 1115-1117.
17. Hamill, S.D., Smith, M.K. and Dodd, W.A. (1992) In vitro induction of banana autotetraploids by colchicine treatment of micropropagated diploids. Aust. J. Bot. 40, 887-896.
18. Henikoff, S., Ahmad, K. and Malik, H.S. (2001) The centromere paradox: stable inheritance with rapidly evolving DNA. Science, 293, 1098-1102.
19. Hoffmann, E.R., Eriksson, E., Herbert, B.J. and Borts, R.H. (2005) MLH1 and MSH2 promote the symmetry of double-strand break repair events at the HIS4 hotspot in Saccharomyces cerevisiae. Genetics, 169, 1291-1303.
20. Holliday, R. (1964) A mechanism for gene conversion in fungi. Genet. Res. 5, 282-304.
21. Hulce, D., Li, X., Snyder-Leiby, T. and Liu, C.J. (2011) GeneMarker Genotyping software: tools to increase the statistical power of DNA fragment analysis. J. Biomol. Tech. 22, S35.
22. Jensen-Seaman, M.I., Furey, T.S., Payseur, B.A., Lu, Y., Roskin, K.M., Chen, C.F., Thomas, M.A., Haussler, D. and Jacob, H.J. (2004) Comparative recombination rates in the rat, mouse, and human genomes. Genome Res. 14, 528-538.
23. Jones, G.H. (1984) The control of chiasma distribution. Symp. Soc. Exp. Biol. 38, 293-320.
24. Kleckner, N., Storlazzi, A. and Zickler, D. (2003) Coordinate variation in meiotic pachytene SC length and total crossover/chiasma frequency under conditions of constant DNA length. Trends Genet. 19, 623-628.
25. Knoll, A., Schröpfer, S. and Puchta, H. (2014) The RTR complex as caretaker of genome stability and its unique meiotic function in plants. Front. Plant Sci. 5, 33.
26. Kurata, N. and Omura, T. (1978) Karyotype analysis in rice. I. A New method for identifying all chromosome pairs. Jpn. J. Genet. 53, 251-255.
27. Leblon, G. and Rossignol, J.L. (1973) Mechanism of gene conversion in Ascobolus immersus. 3. The interaction of heteroallelas in the conversion process. Mol. Gen. Genet. 122, 165-182.
28. Lynn, A., Koehler, K.E., Judis, L., Chan, E.R., Cherry, J.P., Schwartz, S., Seftel, A., Hunt, P.A. and Hassold, T.J. (2002) Covariation of synaptonemal complex length and mammalian meiotic exchange rates. Science, 296, 2222-2225.
29. Mancera, E., Bourgon, R., Brozzi, A., Huber, W. and Steinmetz, L.M. (2008) High-resolution mapping of meiotic crossovers and non-crossovers in yeast. Nature, 454, 479-485.
30. Mancera, E., Bourgon, R., Huber, W. and Steinmetz, L.M. (2011) Genome-wide survey of post-meiotic segregation during yeast recombination. Genome Biol. 12, R36.
31. Marais, G., Charlesworth, B. and Wright, S.I. (2004) Recombination and base composition: the case of the highly self-fertilizing plant Arabidopsis thaliana. Genome Biol. 5, R45.
32. Marsolier-Kergoat, M.C. and Yeramian, E. (2009) GC content and recombination: reassessing the causal effects for the Saccharomyces cerevisiae genome. Genetics, 183, 31-38.
33. Martini, E., Borde, V., Legendre, M., Audic, S., Regnault, B., Soubigou, G., Dujon, B. and Llorente, B. (2011) Genome-wide analysis of heteroduplex DNA in mismatch repair-deficient yeast cells reveals novel properties of meiotic recombination pathways. PLoS Genet. 7, e1002305.
34. McMahill, M.S., Sham, C.W. and Bishop, D.K. (2007) Synthesis-dependent strand annealing in meiosis. PLoS Biol. 5, e299.
35. Merker, J.D., Dominska, M. and Petes, T.D. (2003) Patterns of heteroduplex formation associated with the initiation of meiotic recombination in the yeast Saccharomyces cerevisiae. Genetics, 165, 47-63.
36. Meselson, M.S. and Radding, C.M. (1975) A general model for genetic recombination. Proc. Natl Acad. Sci. USA 72, 358-361.
37. Nachman, M.W. (2002) Variation in recombination rate across the genome: evidence and implications. Curr. Opin. Genet. Dev. 12, 657-663.
38. Notsuka, K., Tsuru, T. and Shiraishi, M. (2000) Induced polyploid grapes via in vitro chromosome doubling. J. Japan. Soc. Hort. Sci. 69, 543-551.
39. Osman, K., Higgins, J.D., Sanchez-Moran, E., Armstrong, S.J. and Franklin, F.C. (2011) Pathways to meiotic recombination in Arabidopsis thaliana. New Phytol. 190, 523-544.
40. Paques, F. and Haber, J.E. (1999) Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 63, 349-404.
41. Peterson, D.G., Stack, S.M., Healy, J.L., Donohoe, B.S. and Anderson, L.K. (1994) The relationship between synaptonemal complex length and genome size in four vertebrate classes (Osteicthyes, Reptilia, Aves, Mammalia). Chromosome Res. 2, 153-162.
42. Petes, T.D. (2001) Meiotic recombination hot spots and cold spots. Nat. Rev. Genet. 2, 360-369.
43. Sanchez-Moran, E., Santos, J.L., Jones, G.H. and Franklin, F.C. (2007) ASY1 mediates AtDMC1-dependent interhomolog recombination during meiosis in Arabidopsis. Genes Dev. 21, 2220-2233.
44. Schuelke, M. (2000) An economic method for the fluorescent labeling of PCR fragments. Nat. Biotechnol. 18, 233-234.
45. Serrentino, M.E. and Borde, V. (2012) The spatial regulation of meiotic recombination hotspots: are all DSB hotspots crossover hotspots? Exp. Cell Res. 318, 1347-1352.
46. Slavov, G.T., DiFazio, S.P., Martin, J. et al. (2012) Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. New Phytol. 196, 713-725.
47. Sun, Y., Ambrose, J.H., Haughey, B.S. et al. (2012) Deep genome-wide measurement of meiotic gene conversion using tetrad analysis in Arabidopsis thaliana. PLoS Genet. 8, e1002968.
48. Surtees, J.A., Argueso, J.L. and Alani, E. (2004) Mismatch repair proteins: key regulators of genetic recombination. Cytogenet. Genome Res. 107, 146-159.
49. Szostak, J.W., Orr-Weaver, T.L., Rothstein, R.J. and Stahl, F.W. (1983) The double-strand-break repair model for recombination. Cell, 33, 25-35.
50. Vining, K.J., Pomraning, K.R., Wilhelm, L.J., Priest, H.D., Pellegrini, M., Mockler, T.C., Freitag, M. and Strauss, S.H. (2012) Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression. BMC Genomics, 13, 27.
51. Wang, J., Kang, X.Y., Li, D.L., Chen, H.W. and Zhang, P.D. (2010) Induction of diploid eggs with colchicine during embryo sac. development in Populus. Silvae Genet. 59, 40-48.
52. Waterworth, W.M., Drury, G.E., Bray, C.M. and West, C.E. (2011) Repairing breaks in the plant genome: the importance of keeping it together. New Phytol. 192, 805-822.
53. Wijnker, E., Velikkakam James, G., Ding, J. et al. (2013) The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana. elife, 2, e01426.
54. Wright, S.I., Agrawal, N. and Bureau, T.E. (2003) Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana. Genome Res. 13, 1897-1903.
55. Yan, H., Jin, W., Nagaki, K., Tian, S., Ouyang, S., Buell, C.R., Talbert, P.B., Henikoff, S. and Jiang, J. (2005) Transcription and histone modifications in the recombination-free region spanning a rice centromere. Plant Cell, 17, 3227-3238.
56. Yeadon, P.J. and Catcheside, D.E. (1998) Long, interrupted conversion tracts initiated by cog in Neurospora crassa. Genetics, 148, 113-122.