Allopolyploidy-induced rapid genomic changes in newly generated synthetic hexaploid wheat

References

• Ramsey J, Schemske D. Pathways, mechanisms, and rates of polyploid formation in flowering plants. Annu Rev Ecol Evol Syst. 1998;29:467–501.
   Web of Science ®Google Scholar
• Huang S, Sirikhachornkit A, Su X, et al. 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. 2002;99:8133–8138.
   PubMed Web of Science ®Google Scholar
• Kimber G, Feldman M. Wild wheats: an introduction. Columbia (MO): College of Agriculture; 1987. p. 1–142. (Special Report; no. 353).
   Google Scholar
• Van Slageren MW. Wild wheats: a monograph of Aegilops L. and Amblyopyrum (Jaub. & Spach) Eig (Poaceae). Vol. 94–97, Wageningen Agricultural University Papers. Wageningen (Netherlands): ICARDA/Agricultural University; 1994.
   Google Scholar
• Snape JW, Butterworth K, Whitechurch E, et al. Waiting for fine times: genetics of flowering time in wheat. Euphytica. 2001;119:185–190.
   Web of Science ®Google Scholar
• Dubcovsky J, Dvorak J. Genome plasticity a key factor in the success of polyploidy wheat under domestication. Science. 2007;316:1862–1866.
   PubMed Web of Science ®Google Scholar
• Levy AA, Feldman M. Genetic and epigenetic reprogramming of the wheat genome upon allopolyploidization. Biol J Linn Soc. 2004;82:607–613.
   Web of Science ®Google Scholar
• Feldman M, Levy AA. Allopolyploidy – a shaping force in the evolution of wheat genomes. Cytogenet Genome Res. 2005;109:250–258.
   PubMed Web of Science ®Google Scholar
• Feldman M, Levy AA. Genome evolution in allopolyploid wheat – a revolutionary reprogramming followed by gradual changes. J Genet Genomics. 2009;36:511–518.
   PubMed Web of Science ®Google Scholar
• Feldman M, Levy AA. Genome evolution due to allopolyploidization in wheat. Genetics. 2012;192:763–774.
   PubMed Web of Science ®Google Scholar
• Ma J, Stiller J, Wei YM, et al. Extensive pericentric rearrangements in the bread wheat (Triticum aestivum L.) genotype “Chinese Spring” revealed from chromosome shotgun sequence data. Genome Biol Evol. 2014;6(11):3039–3048.
   PubMed Web of Science ®Google Scholar
• Griffiths S, Sharp R, Foote TN, et al. Molecular characterization of Ph1 as a major chromosome pairing locus in polyploid wheat. Nature. 2006;439:749–752.
   PubMed Web of Science ®Google Scholar
• Yousafzai FK, Al-Kaff N, Moore G. Structural and functional relationship between the Ph1 locus protein 5B2 in wheat and CDK2 in mammals. Funct Integr Genomic. 2010;10:157–166.
   PubMed Web of Science ®Google Scholar
• Yu M, Chen GY, Zhang LQ, et al. QTL mapping for important agronomic traits in synthetic hexaploid wheat derived from Aegiliops tauschii ssp. Tauschii. J Integr Agric. 2014;13(9):1835–1844
   Web of Science ®Google Scholar
• Yu M, Chen GY, Pu ZE, et al. Quantitative trait locus mapping for growth duration and its timing components in wheat. Mol Breeding. 2015;35(44):1–11.
   Google Scholar
• Zhang LQ, Liu DC, Yan ZH, et al. Rapid changes of microsatellite flanking sequence in the allopolyploidization of new synthesized hexaploid wheat. Sci China Ser C. 2004;47:553–561.
   PubMedGoogle Scholar
• Yu M, Mao SL, Chen GY, et al. QTLs for uppermost internode and spike length: whether they affect wheat height at an individual QTL level in two RIL populations? Euphytica. 2014;200(1):95–108.
   Web of Science ®Google Scholar
• Akbari M, Wenzl P, Caig V, et al. Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theor Appl Genet. 2006;113:1409–1420.
   PubMed Web of Science ®Google Scholar
• Yu M, Chen Gy. Conditional QTL mapping for waterlogging tolerance in two RILs populations of wheat. SpringerPlus [Internet]. 2013 [cited 2016 Jul 21];2:1–7. Available from: https://springerplus.springeropen.com/articles/10.1186/2193-1801-2-245
   Google Scholar
• Shaked H, Kashkush K, Ozkan H, et al. Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell. 2001;13:1749–1759.
   PubMed Web of Science ®Google Scholar
• Bento M, Gustafson JP, Viegas W, et al. Size matters in Triticeae polyploids: larger genomes have higher remodeling. Genome. 2011;54:175–183.
   PubMed Web of Science ®Google Scholar
• Kashkush K, Feldman M, Levy AA. Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics. 2002;160:1651–1659.
   PubMed Web of Science ®Google Scholar
• Eilam T, Anikster Y, Millet E, et al. Nuclear DNA amount and genome downsizing in natural and synthetic allopolyploids of the genera Aegilops and Triticum. Genome. 2008;51:616–627.
   PubMed Web of Science ®Google Scholar
• Eilam T, Anikster Y, Millet E, et al. Genome size in diploids, allopolyploids, and autopolyploids of mediterranean triticeae. Genome. 2010;52(3):275–285.
   Web of Science ®Google Scholar
• Pestsova E, Ganal MW, Röder MS. Isolation and mapping of microsatellite markers specific for the D genome of bread wheat. Genome. 2000;43:689–697.
   PubMed Web of Science ®Google Scholar
• Senerchia N, Wicker T, Felber F, et al. Evolutionary dynamics of retrotransposons assessed by high throughput sequencing in wild relatives of wheat. Genome Biol Evol. 2013;5:1010–1020.
   PubMed Web of Science ®Google Scholar
• Senerchia N, Felber F, Parisod C. Contrasting evolutionary trajectories of multiple retrotransposons following independent allopolyploidy in wild wheats. New Phytol. 2014;202(3):975–985.
   PubMed Web of Science ®Google Scholar
• Charles M, Belcram H, Just J, et al. Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat. Genetics. 2008;180:1071–1086.
   PubMed Web of Science ®Google Scholar
• Fedoroff NV. Transposable elements, epigenetics, and genome evolution. Science. 2012;338:758–767.
   PubMed Web of Science ®Google Scholar
• Feldman M, Levy AA. Origin and evolution of wheat and related triticeae species. In: Molnár-Láng M, Ceoloni C, Doležel J, editors. Alien introgression in wheat. Cytogenetics, molecular biology, and genomics. New York (NY): Springer; 2015. p. 21–76.
   Google Scholar
• Ozkan H, Levy AA, Feldman M. Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops–Triticum) group. Plant Cell. 2001;13(8):1735–1747.
   PubMed Web of Science ®Google Scholar
• Salina EA, Numerova OM, Ozkan H, et al. Alterations in subtelomeric tandem repeats during early stages of allopolyploidy in wheat. Genome. 2004;47:860–867.
   PubMed Web of Science ®Google Scholar
• Pu ZE, Yu M, He QY, et al. Quantitative trait loci associated with micronutrient concentrations in two recombinant inbred wheat lines. J Integr Agric. 2014;13(11):2322–2329.
   Web of Science ®Google Scholar