Reprogramming of Gene Expression in the Genetically Stable Bread Allohexaploid Wheat

Polyploid and Hybrid Genomics

Volumn , Issue , 2013, Pages 195-211

  Arnaud, Dominique ^a   Chelaifa, Houda ^a   Jahier, Joseph ^b   Chalhoub, Boulos ^a  

^a INSTITUTE OF PLANT SCIENCES PARIS SACLAY IPS2   (France)

^b AGROCAMPUS OUEST   (France)

Author keywords

Gene expression; Regards; Regulation; Wheat

Indexed keywords

EID: 84886340414     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9781118552872.ch12     Document Type: Chapter

References (75)

1. Adams, K.L., Cronn, R., Percifield, R., et al. (2003) Genes duplicated by polyploidy showunequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc Natl Acad Sci USA 100, 4649-4654.
2. Akhunova, A., Matniyazov, R., Liang, H., et al. (2010) Homoeolog-specific transcriptional bias in allopolyploid wheat. BMC Genomics 11, 505.
3. Blake, N.K., Lehfeldt, B.R., Lavin, M., et al. (1999) Phylogenetic reconstruction based on low copy DNA sequence data in an allopolyploid: the B genome of wheat. Genome 42, 351-360.
4. Bottley, A., & Koebner, R.M.D. (2008) Variation for homoeologous gene silencing in hexaploid wheat. Plant J 56, 297-302.
5. Bottley, A., Xia, G.M., & Koebner, R.M.D. (2006) Homoeologous gene silencing in hexaploid wheat. Plant J 47, 897-906.
6. Chagué, V., Just, J., Mestiri, I., et al. (2010) Genome-wide gene expression changes in genetically stable synthetic and natural wheat allohexaploids. New Phytol 187, 1181-1194.
7. Chelaifa, H., Chagué, V., Chalabi, S., et al. (2013) Prevalence of gene expression additivity in genetically stable wheat allohexaploids. New Phytol 197, 730-736.
8. Charles, M., Belcram, H., Just, J., et al. (2008) Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat. Genetics 180, 1071-1086.
9. Chaudhary, B., Flagel, L., Stupar, R.M., et al. (2009) Reciprocal silencing, transcriptional bias and functional divergence of homeologs in polyploid cotton (Gossypium). Genetics 182, 503-517.
10. Chen, M., Ha, M., Lackey, E., et al. (2008) RNAi of met1 reduces DNA methylation and induces genome-specific changes in gene expression and centromeric small RNA accumulation in Arabidopsis allopolyploids. Genetics 178, 1845-1858.
11. Chen, X. (2010a) Small RNAs-secrets and surprises of the genome. Plant J 61, 941-958.
12. Chen, Z.J. (2007) Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu Rev Plant Biol 58, 377-406.
13. Chen, Z.J. (2010b) Molecular mechanisms of polyploidy and hybrid vigor. Trends Plant Sci 15, 57-71.
14. Comai, L. (2005) The advantages and disadvantages of being polyploid. Nat Rev Genet 6, 836-846.
15. Doyle, J.J., Flagel, L.E., Paterson, A.H., et al. (2008) Evolutionary genetics of genome merger and doubling in plants. Annu Rev Genet 42, 443-461.
16. Dvorak, J., & Zhang, H.B. (1990) Variation in repeated nucleotide sequences sheds light on the phylogeny of the wheat B and G genomes. Proc Natl Acad Sci USA 87, 9640-9644.
17. Feldman, M., & Levy, A.A. (2009) Genome evolution in allopolyploid wheat-a revolutionary reprogramming followed by gradual changes. J Genet Genomics 36, 511-518.
18. Feldman, M., Liu, B., Segal, G., et al. (1997) Rapid elimination of low-copy DNA sequences in polyploid wheat: a possible mechanism for differentiation of homoeologous chromosomes. Genetics 147, 1381-1387.
19. Gaeta, R.T., Yoo, S.-Y., Pires, J.C., et al. (2009) Analysis of gene expression in resynthesized Brassica napus allopolyploids using Arabidopsis 70mer oligo microarrays. PLoS ONE 4, e4760.
20. Ha, M., Lu, J., Tian, L., et al. (2009) Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids. Proc Natl Acad Sci USA 106, 17835-17840.
21. Han, F., Fedak, G., Guo,W., et al. (2005) Rapid and repeatable elimination of a parental genome-specific DNA repeat (pGc1R-1a) in newly synthesized wheat allopolyploids. Genetics 170, 1239-1245.
22. He, P., Friebe, B.R., Gill, B.S., et al. (2003) Allopolyploidy alters gene expression in the highly stable hexaploid wheat. Plant Mol Biol 52, 401-414.
23. Hegarty, M.J., Jones, J.M., Wilson, I.D., et al. (2005) Development of anonymous cDNA microarrays to study changes to the Senecio floral transcriptome during hybrid speciation. Mol Ecol 14, 2493-2510.
24. Hovav, R., Udall, J.A., Chaudhary, B., et al. (2008) Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant. Proc Natl Acad Sci USA 105, 6191-6195.
25. Huang, S., Sirikhachornkit, A., Su, X., et al. (2002) Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat. Proc Natl Acad Sci USA 99, 8133-8138.
26. Jackson, S., & Chen, Z.J. (2010) Genomic and expression plasticity of polyploidy. Curr Opin Plant Biol 13, 153-159.
27. Jones, R.N., & Hegarty, M. (2009) Order out of chaos in the hybrid plant nucleus. Cytogenet Genome Res 126, 376-389.
28. Kashkush, K., Feldman, M., & Levy, A.A. (2002) Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics 160, 1651-1659.
29. Kashkush, K., Feldman, M., & Levy, A.A. (2003) Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat Genet 33, 102-106.
30. Kasschau, K.D., Fahlgren, N., Chapman, E.J., et al. (2007) Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol 5, e57.
31. Kenan-Eichler, M., Leshkowitz, D., Tal, L., et al. (2011) Wheat hybridization and polyploidization results in deregulation of small RNAs. Genetics 188, 263-272.
32. Kerber, E.R. (1964) Wheat: reconstitution of the tetraploid component (AABB) of hexaploids. Science 143, 253-255.
33. Kihara, H. (1944) Discovery of the DD analyser, one of the ancestors of Triticum vulgare. Agric Hortic 19, 889-890.
34. Kraitshtein, Z., Yaakov, B., Khasdan, V., et al. (2011) Genetic and epigenetic dynamics of a retrotransposon after allopolyploidization of wheat. Genetics 186, 801-812.
35. Leitch, A.R., & Leitch, I.J. (2008) Genomic plasticity and the diversity of polyploid plants. Science 320, 481-483.
36. Lippman, Z., Gendrel, A.-V., Black, M., et al. (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430, 471-476.
37. Lippman, Z., & Martienssen, R. (2004) The role of RNA interference in heterochromatic silencing. Nature 431, 364-370.
38. Lukens, L.N., Pires, J.C., Leon, E., et al. (2006) Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids. Plant Physiol 140, 336-348.
39. Lynch, M., & Conery, J.S. (2000) The evolutionary fate and consequences of duplicate genes. Science 290, 1151-1155.
40. Lynch, M., & Force, A. (2000) The probability of duplicate gene preservation by subfunctionalization. Genetics 154, 459-473.
41. Madlung, A., Masuelli, R.W., Watson, B., et al. (2002) Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol 129, 733-746.
42. Madlung, A., Tyagi, A.P., Watson, B., et al. (2005) Genomic changes in synthetic Arabidopsis polyploids. Plant J 41, 221-230.
43. Mallory, A.C., & Vaucheret, H. (2006) Functions of microRNAs and related small RNAs in plants. Nat Genet 38, S31-S36.
44. Martienssen, R.A. (2010) Heterochromatin, small RNA and post-fertilization dysgenesis in allopolyploid and interploid hybrids of Arabidopsis. New Phytol 186, 46-53.
45. Matsuoka, Y. (2011) Evolution of polyploid Triticum wheats under cultivation: the role of domestication, natural hybridization and allopolyploid speciation in their diversification. Plant Cell Physiol 52, 750-764.
46. Matsuoka, Y., & Nasuda, S. (2004) Durum wheat as a candidate for the unknown female progenitor of bread wheat: an empirical study with a highly fertile F1 hybrid with Aegilops tauschii Coss. Theor Appl Genet 109, 1710-1717.
47. McClintock, B. (1984) The significance of responses of the genome to challenge. Science 226, 792-801.
48. McFadden, E.S., & Sears, E.R. (1946) The origin of Triticum spelta and its free-threshing hexaploid relatives. J Hered 37, 81-89.
49. Mestiri, I., Chagué, V., Tanguy, A.-M., et al. (2010) Newly synthesized wheat allohexaploids display progenitor-dependent meiotic stability and aneuploidy but structural genomic additivity. New Phytol 186, 86-101.
50. Mizuno, N., Hosogi, N., Park, P., et al. (2010) Hypersensitive response-like reaction is associated with hybrid necrosis in interspecific crosses between tetraploid wheat and Aegilops tauschii Coss. PLoS ONE 5, e11326.
51. Mochida, K., Yamazaki, Y., & Ogihara, Y. (2004) Discrimination of homoeologous gene expression in hexaploid wheat by SNP analysis of contigs grouped from a large number of expressed sequence tags. Mol Genet Genomics 270, 371-377.
52. Nomura, T., Ishihara, A.,Yanagita, R.C., et al. (2005) Three genomes differentially contribute to the biosynthesis of benzoxazinones in hexaploid wheat. Proc Natl Acad Sci USA 102, 16490-16495.
53. Ozkan, H., Levy, A.A., & Feldman, M. (2001) Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group. Plant Cell 13, 1735-1747.
54. Ozkan, H., Tuna, M., & Arumuganathan, K. (2003) Nonadditive changes in genome size during allopolyploidization in the wheat (Aegilops-Triticum) group. J Hered 94, 260-264.
55. Parisod, C., Alix, K., Just, J., et al. (2010) Impact of transposable elements on the organization and function of allopolyploid genomes. New Phytol 186, 37-45.
56. Petit, M., Guidat, C., Daniel, J., et al. (2010) Mobilization of retrotransposons in synthetic allotetraploid tobacco. New Phytol 186, 135-147.
57. Pont, C., Murat, F., Confolent, C., et al. (2011) RNA-seq in grain unveils fate of neo-and paleopolyploidization events in bread wheat (Triticum aestivum L.). Genome Biol 12, R119.
58. Prince, V.E., & Pickett, F.B. (2002) Splitting pairs: the diverging fates of duplicated genes. Nat Rev Genet 3, 827-837.
59. Pumphrey, M., Bai, J., Laudencia-Chingcuanco, D., et al. (2009) Nonadditive expression of homoeologous genes is established upon polyploidization in hexaploid wheat. Genetics 181, 1147-1157.
60. Qi, B., Zhong, X., Zhu, B., et al. (2010) Generality and characteristics of genetic and epigenetic changes in newly synthesized allotetraploid wheat lines. J Genet Genomics 37, 737-748.
61. Qi, B., Huang,W., Zhu, B., et al. (2012) Global transgenerational gene expression dynamics in two newly synthesized allohexaploid wheat (Triticum aestivum) lines. BMC Biol 10, 3.
62. Rapp, R., Udall, J., & Wendel, J. (2009) Genomic expression dominance in allopolyploids. BMC Biol 7, 18.
63. Ravel, C., Martre, P., Romeuf, I., et al. (2009) Nucleotide polymorphism in the wheat transcriptional activator Spa influences its pattern of expression and has pleiotropic effects on grain protein composition, dough viscoelasticity, and grain hardness. Plant Physiol 151, 2133-2144.
64. Riley, R., & Chapman, V. (1958) Genetic control of the cytologically diploid behaviour of hexaploid wheat. Nature 182, 713-715.
65. Salmon, A., Ainouche, M.L., & Wendel, J.F. (2005) Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Mol Ecol 14, 1163-1175.
66. Shaked, H., Kashkush, K., Ozkan, H., et al. (2001) Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13, 1749-1759.
67. Shitsukawa, N., Tahira, C., Kassai, K.-I., et al. (2007) Genetic and epigenetic alteration among three homoeologous genes of a class E MADS box gene in hexaploid wheat. Plant Cell 19, 1723-1737.
68. Simons, K.J., Fellers, J.P., Trick, H.N., et al. (2006) Molecular characterization of the major wheat domestication gene Q. Genetics 172, 547-555.
69. Soltis, D.E., Albert, V.A., Leebens-Mack, J., et al. (2009) Polyploidy and angiosperm diversification. Am J Bot 96, 336-348.
70. Van de Peer, Y., Maere, S., & Meyer, A. (2009) The evolutionary significance of ancient genome duplications. Nat Rev Genet 10, 725-732.
71. Wang, J., Tian, L., Lee, H.-S., et al. (2006) Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 172, 507-517.
72. Xu, Y., Zhong, L., Wu, X., et al. (2009) Rapid alterations of gene expression and cytosine methylation in newly synthesized Brassica napus allopolyploids. Planta 229, 471-483.
73. Zhang, Z., Belcram, H., Gornicki, P., et al. (2011) Duplication and partitioning in evolution and function of homoeologous Q loci governing domestication characters in polyploid wheat. Proc Natl Acad Sci USA 108, 18737-18742.
74. Zhao, N., Xu, L., Zhu, B., et al. (2011a) Chromosomal and genome-wide molecular changes associated with initial stages of allohexaploidization in wheat can be transit and incidental. Genome 54, 692-699.
75. Zhao, N., Zhu, B., Li, M., et al. (2011b) Extensive and heritable epigenetic remodeling and genetic stability accompany allohexaploidization of wheat. Genetics 188, 499-510.