Polyploidy is a very common phenomenon in the plant kingdom, where even diploid species are often described as paleopolyploids. The polyploid condition may bring about several advantages compared to the diploid state. Polyploids often show phenotypes that are not present in their diploid progenitors or exceed the range of the contributing species. Some of these traits may play a role in heterosis or could favor adaptation to new ecological niches. Advances in genomics and sequencing technology may create unprecedented opportunities for discovering and monitoring the molecular effects of polyploidization. Through this review, we provide an overview of technologies and strategies that may allow an in-depth analysis of polyploid genomes. After introducing some basic aspects on the origin and genetics of polyploids, we highlight the main tools available for genome and gene expression analysis and summarize major findings. In the last part of this review, the implications of next generation sequencing are briefly discussed. The accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists to understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement.
References
[1]
Masterson, J. Stomatal size in fossil plants: Evidence for polyploidy in majority of angiosperms. Science 1994, 264, 421–424.
Carputo, D.; Frusciante, L.; Peloquin, S.J. The role of 2n gametes and endosperm balance number in the origin and evolution of polyploids in the tuber-bearing Solanums. Genetics 2003, 163, 287–294.
[9]
Chen, Z.J. Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu. Rev. Plant. Biol 2007, 58, 377–406.
[10]
Bretagnolle, F.; Thompson, J.D. Tansley review no. 78. Gametes with the stomatic chromosome number: Mechanisms of their formation and role in the evolution of autopolypoid plants. New Phytol 1995, 129, 1–22.
[11]
D’Erfurth, I.; Jolivet, S.; Froger, N.; Catrice, O.; Novatchkova, M.; Simon, M.; Jenczewski, E.; Mercier, R. Mutations in ATPS1 (Arabidopsis Thaliana Parallel Spindle 1) lead to the production of diploid pollen grains. PLoS Genet 2008, 4, e1000274.
[12]
Erilova, A.; Brownfield, L.; Exner, V.; Rosa, M.; Twell, D.; Scheid, O.M.; Hennig, L.; K？hler, C. Imprinting of the polycomb group gene MEDEA serves as a ploidy sensor in Arabidopsis. PLoS Genet 2009, 5, e1000663.
[13]
Mercier, R.; Vezon, D.; Bullier, E.; Motamayor, J.C.; Sellier, A.; Lefèvre, F.; Pelletier, G.; Horlow, C. SWITCH1 (SWI1): A novel protein required for the establishment of sister chromatid cohesion and for bivalent formation at meiosis. Genes Dev 2001, 15, 1859–1871.
[14]
Agashe, B.; Prasad, C.K.; Siddiqi, I. Identification and analysis of DYAD: A gene required for meiotic chromosome organisation and female meiotic progression in Arabidopsis. Development 2002, 129, 3935–3943.
[15]
D’Erfurth, I.; Jolivet, S.; Froger, N.; Catrice, O.; Novatchkova, M.; Mercier, R. Turning meiosis into mitosis. PLoS Biol 2009, 7, e1000124.
[16]
D’Erfurth, I.; Cromer, L.; Jolivet, S.; Girard, C.; Horlow, C.; Sun, Y.; To, J.P.C.; Berchowitz, L.E.; Copenhaver, G.P.; Mercier, R. The CYCLIN-A CYCA1;2/TAM is required for the meiosis I to meiosis II transition and cooperates with OSD1 for the prophase to first meiotic division transition. PLoS Genet 2010, 6, e1000989.
[17]
Fawcett, J.A.; Maere, S.; van de Peer, Y. Plants with double genomes might have had a better chance to survive the cretaceous-tertiary extinction event. Proc. Natl. Acad. Sci. USA 2009, 106, 5737–5742.
[18]
Comai, L. The advantages and disadvantages of being polyploid. Nat. Rev. Genet 2005, 6, 836–846.
Pires, J.C.; Lim, K.Y.; Kovarík, A.; Matyásek, R.; Boyd, A.; Leitch, A.R.; Leitch, I.J.; Bennett, M.D.; Soltis, P.S.; Soltis, D.E. Molecular cytogenetic analysis of recently evolved Tragopogon (Asteraceae) allopolyploids reveal a karyotype that is additive of the diploid progenitors. Am. J. Bot 2004, 91, 1022–1035.
[22]
Szadkowski, E.; Eber, F.; Huteau, V.; Lode, M.; Huneau, C.; Belcram, H.; Coriton, O.; Manzanares-Dauleux, M.J.; Delourme, R.; King, G.J.; et al. The first meiosis of resynthesized Brassica napus, a genome blender. New Phytol 2010, 186, 102–112.
[23]
Wang, K.; Guo, W.; Yang, Z.; Hu, Y.; Zhang, W.; Zhou, B.; Stelly, D.; Chen, Z.; Zhang, T. Structure and size variations between 12A and 12D homoeologous chromosomes based on high-resolution cytogenetic map in allotetraploid cotton. Chromosoma 2010, 119, 255–266.
[24]
Chester, M.; Gallagher, J.P.; Symonds, V.V.; Cruz da Silva, A.V.; Mavrodiev, E.V.; Leitch, A.R.; Soltis, P.S.; Soltis, D.E. Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae). Proc. Natl. Acad. Sci. USA 2012, 109, 1176–1181.
[25]
Porceddu, A.; Albertini, E.; Barcaccia, G.; Falistocco, E.; Falcinelli, M. Linkage mapping in apomictic and sexual Kentucky bluegrass (Poa pratensis L.) genotypes using a two way pseudo-testcross strategy based on AFLP and SAMPl markers. Theor. Appl. Genet 2002, 104, 273–280.
[26]
Gaeta, R.T.; Pires, J.C.; Iniguez-Luy, F.; Leon, E.; Osborn, T.C. Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Plant Cell 2007, 19, 3403–3417.
[27]
Nicolas, S.D.; Leflon, M.; Monod, H.; Eber, F.; Coriton, O.; Huteau, V.; Chèvre, A.-M.; Jenczewski, E. Genetic regulation of meiotic cross-overs between related genomes in Brassica napus haploids and hybrids. Plant Cell 2009, 21, 373–385.
[28]
Cifuentes, M.; Eber, F.; Lucas, M.-O.; Lode, M.; Chèvre, A.-M.; Jenczewski, E. Repeated polyploidy drove different levels of crossover suppression between homoeologous chromosomes in Brassica napus allohaploids. Plant Cell 2010, 22, 2265–2276.
Liu, B.; Vega, J.M.; Feldman, M. Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. II. Changes in low-copy coding DNA sequences. Genome 1998, 41, 535–542.
Song, K.; Lu, P.; Tang, K.; Osborn, T.C. Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proc. Natl. Acad. Sci. USA 1995, 92, 7719–7723.
[33]
Salmon, A.; Ainouche, M.L.; Wendel, J.F. Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Mol. Ecol 2005, 14, 1163–1175.
[34]
Wu, K.K.; Burnquist, W.; Sorrells, M.E.; Tew, T.L.; Moore, P.H.; Tanksley, S.D. The detection and estimation of linkage in polyploids using single-dose restriction fragments. Theor. Appl. Genet 1992, 83, 294–300.
[35]
Hackett, C.A.; Bradshaw, J.E.; Meyer, R.C.; McNicol, J.W.; Milbourne, D.; Waugh, R. Linkage analysis in tetraploid species: A simulation study. Genet. Res 1998, 71, 143–154.
[36]
Ripol, M.I.; Churchill, G.A.; da Silva, J.A.G.; Sorrells, M. Statistical aspects of genetic mapping in autopolyploids. Gene 1999, 235, 31–41.
[37]
Wu, R.; Ma, C.-X.; Casella, G. A bivalent polyploid model for mapping quantitative trait loci in outcrossing tetraploids. Genetics 2004, 166, 581–595.
[38]
Li, J.; Das, K.; Liu, J.; Fu, G.; Li, Y.; Tobias, C.; Wu, R. Statistical models for genetic mapping in polyploids: Challenges and opportunities. Methods Mol. Biol 2012, 871, 245–261.
[39]
Ma, J.F.; Shen, R.; Zhao, Z.; Wissuwa, M.; Takeuchi, Y.; Ebitani, T.; Yano, M. Response of rice to Al stress and identification of quantitative trait loci for Al tolerance. Plant Cell Physiol 2002, 43, 652–659.
[40]
Julier, B.; Flajoulot, S.; Barre, P.; Cardinet, G.; Santoni, S.; Huguet, T.; Huyghe, C. Construction of two genetic linkage maps in cultivated tetraploid alfalfa (Medicago sativa) using microsatellite and AFLP markers. BMC Plant Biol 2003, 3, doi:10.1186/1471-2229-3-9.
[41]
Barcaccia, G.; Meneghetti, S.; Albertini, E.; Triest, L.; Lucchin, M. Linkage mapping in tetraploid willows: Segregation of molecular markers and estimation of linkage phases support an allotetraploid structure for Salix alba × Salix fragilis interspecific hybrids. Heredity 2003, 90, 169–180.
[42]
Le Cunff, L.; Garsmeur, O.; Raboin, L.M.; Pauquet, J.; Telismart, H.; Selvi, A.; Grivet, L.; Philippe, R.; Begum, D.; Deu, M.; et al. Diploid/polyploid syntenic shuttle mapping and haplotype-specific chromosome walking toward a rust resistance gene (Bru1) in highly polyploid sugarcane (2n~12x~115). Genetics 2008, 180, 649–660.
[43]
Esselink, G.D.; Nybom, H.; Vosman, B. Assignment of allelic configuration in polyploids using the MAC-PR (microsatellite DNA allele counting—peak ratios) method. Theor. Appl. Genet 2004, 109, 402–408.
[44]
Van Dijk, T.; Noordijk, Y.; Dubos, T.; Bink, M.; Meulenbroek, B.; Visser, R.; van de Weg, E. Microsatellite allele dose and configuration establishment (MADCE): An integrated approach for genetic studies in allopolyploids. BMC Plant Biol 2012, 12, doi:10.1186/1471-2229-12-25.
[45]
Oliver, R.; Jellen, E.; Ladizinsky, G.; Korol, A.; Kilian, A.; Beard, J.; Dumlupinar, Z.; Wisniewski-Morehead, N.; Svedin, E.; Coon, M.; et al. New Diversity Arrays Technology (DArT) markers for tetraploid oat (Avena magna Murphy et Terrell) provide the first complete oat linkage map and markers linked to domestication genes from hexaploid A. sativa L. Theor. Appl. Genet 2011, 123, 1159–1171.
[46]
Reyna-López, G.E.; Simpson, J.; Ruiz-Herrera, J. Differences in DNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms. Mol. Gen. Genet 1997, 253, 703–710.
[47]
Madlung, A.; Masuelli, R.W.; Watson, B.; Reynolds, S.H.; Davison, J.; Comai, L. Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol 2002, 129, 733–746.
[48]
Liu, B.; Brubaker, C.L.; Mergeai, G.; Cronn, R.C.; Wendel, J.F. Polyploid formation in cotton is not accompanied by rapid genomic changes. Genome 2001, 44, 321–330.
Jannoo, N.; Grivet, L.; Chantret, N.; Garsmeur, O.; Glaszmann, J.C.; Arruda, P.; D’Hont, A. Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome. Plant J 2007, 50, 574–585.
[51]
Paterson, A.H. Leafing through the genomes of our major crop plants: Strategies for capturing unique information. Nat. Rev. Genet 2006, 7, 174–184.
[52]
Schranz, M.E.; Song, B.-H.; Windsor, A.J.; Mitchell-Olds, T. Comparative genomics in the Brassicaceae: A family-wide perspective. Curr. Opin. Plant Biol 2007, 10, 168–175.
[53]
Margulies, E.H.; Birney, E. Approaches to comparative sequence analysis: Towards a functional view of vertebrate genomes. Nat. Rev. Genet 2008, 9, 303–313.
[54]
Chantret, N.; Salse, J.; Sabot, F.; Rahman, S.; Bellec, A.; Laubin, B.; Dubois, I.; Dossat, C.; Sourdille, P.; Joudrier, P.; et al. Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and Aegilops). Plant Cell 2005, 17, 1033–1045.
[55]
Gao, S.; Gu, Y.; Wu, J.; Coleman-Derr, D.; Huo, N.; Crossman, C.; Jia, J.; Zuo, Q.; Ren, Z.; Anderson, O.; et al. Rapid evolution and complex structural organization in genomic regions harboring multiple prolamin genes in the polyploid wheat genome. Plant Mol. Biol 2007, 65, 189–203.
[56]
Innes, R.W.; Ameline-Torregrosa, C.; Ashfield, T.; Cannon, E.; Cannon, S.B.; Chacko, B.; Chen, N.W.G.; Couloux, A.; Dalwani, A.; Denny, R.; et al. Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean. Plant Physiol 2008, 148, 1740–1759.
[57]
Town, C.D.; Cheung, F.; Maiti, R.; Crabtree, J.; Haas, B.J.; Wortman, J.R.; Hine, E.E.; Althoff, R.; Arbogast, T.S.; Tallon, L.J.; et al. Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell 2006, 18, 1348–1359.
[58]
Li, W.; Huang, L.; Gill, B.S. Recurrent deletions of puroindoline genes at the grain hardness locus in four independent lineages of polyploid wheat. Plant Physiol 2008, 146, 200–212.
[59]
De Bodt, S.; Maere, S.; van de Peer, Y. Genome duplication and the origin of angiosperms. Trends Ecol. Evol 2005, 20, 591–597.
[60]
Soltis, D.E.; Bell, C.D.; Kim, S.; Soltis, P.S. Origin and early evolution of angiosperms. Ann. N. Y. Acad. Sci 2008, 1133, 3–25.
[61]
Velasco, R.; Zharkikh, A.; Affourtit, J.; Dhingra, A.; Cestaro, A.; Kalyanaraman, A.; Fontana, P.; Bhatnagar, S.K.; Troggio, M.; Pruss, D.; et al. The genome of the domesticated apple (Malus domestica Borkh.). Nat. Genet 2010, 42, 833–839.
[62]
The Tomato Genome Consortium. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 2012, 485, 635–641.
Levasseur, A.; Pontarotti, P. The role of duplications in the evolution of genomes highlights the need for evolutionary-based approaches in comparative genomics. Biol. Direct 2011, 6, doi:10.1186/1745-6150-6-11.
[65]
Wawrzynski, A.; Ashfield, T.; Chen, N.W.G.; Mammadov, J.; Nguyen, A.; Podicheti, R.; Cannon, S.B.; Thareau, V.; Ameline-Torregrosa, C.; Cannon, E.; et al. Replication of nonautonomous retroelements in soybean appears to be both recent and common. Plant Physiol 2008, 148, 1760–1771.
[66]
Kraitshtein, Z.; Yaakov, B.; Khasdan, V.; Kashkush, K. Genetic and epigenetic dynamics of a retrotransposon after allopolyploidization of wheat. Genetics 2010, 186, 801–812.
[67]
Ainouche, M.; Fortune, P.; Salmon, A.; Parisod, C.; Grandbastien, M.A.; Fukunaga, K.; Ricou, M.; Misset, M.T. Hybridization, polyploidy and invasion: Lessons from Spartina (Poaceae). Biol. Invasions 2009, 11, 1159–1173.
[68]
Beaulieu, J.; Jean, M.; Belzile, F. The allotetraploid Arabidopsis thaliana–Arabidopsis lyrata subsp. petraea as an alternative model system for the study of polyploidy in plants. Mol. Genet. Genomics 2009, 281, 421–435.
[69]
Kaur, S.; Francki, M.G.; Forster, J.W. Identification, characterization and interpretation of single-nucleotide sequence variation in allopolyploid crop species. Plant Biotechnol. J 2012, 10, 125–138.
Bancroft, I.; Morgan, C.; Fraser, F.; Higgins, J.; Wells, R.; Clissold, L.; Baker, D.; Long, Y.; Meng, J.; Wang, X.; et al. Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing. Nat. Biotech 2011, 29, 762–766.
[73]
Paux, E.; Sourdille, P.; Salse, J.; Saintenac, C.; Choulet, F.; Leroy, P.; Korol, A.; Michalak, M.; Kianian, S.; Spielmeyer, W.; et al. A physical map of the 1-gigabase bread wheat chromosome 3B. Science 2008, 322, 101–104.
[74]
Saintenac, C.; Jiang, D.; Akhunov, E. Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome. Genome Biol 2011, 12, doi:10.1186/gb-2011-12-9-r88.
[75]
Akhunov, E.; Nicolet, C.; Dvorak, J. Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina GoldenGate assay. Theor. Appl. Genet 2009, 119, 507–517.
[76]
Allen, A.; Islamovic, E.; Kaur, J.; Gold, S.; Shah, D.; Smith, T.J. Transgenic maize plants expressing the Totivirus antifungal protein, KP4, are highly resistant to corn smut. Plant Biotechnol. J 2011, 9, 857–864.
[77]
Lai, J.; Li, R.; Xu, X.; Jin, W.; Xu, M.; Zhao, H.; Xiang, Z.; Song, W.; Ying, K.; Zhang, M.; et al. Genome-wide patterns of genetic variation among elite maize inbred lines. Nat. Genet 2010, 42, 1027–1030.
[78]
Bundock, P.C.; Eliott, F.G.; Ablett, G.; Benson, A.D.; Casu, R.E.; Aitken, K.S.; Henry, R.J. Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing. Plant Biotechnol. J 2009, 7, 347–354.
[79]
Buggs, R.J.; Chamala, S.; Wu, W.; Gao, L.; May, G.D.; Schnable, P.S.; Soltis, D.E.; Soltis, P.S.; Barbazuk, W.B. Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping. Mol. Ecol 2010, 19, S132–S146.
[80]
Gabriel, S.; Ziaugra, L.; Tabbaa, D. Current Protocols in Human Genetics; John Wiley & Sons, Inc, 2009; Volume Chapter 2.12, pp. 1–16.
[81]
Han, Y.; Kang, Y.; Torres-Jerez, I.; Cheung, F.; Town, C.; Zhao, P.; Udvardi, M.; Monteros, M. Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis. BMC Genomics 2011, 12, doi:10.1186/1471-2164-12-350.
Trick, M.; Long, Y.; Meng, J.; Bancroft, I. Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. Plant Biotechnol. J 2009, 7, 334–346.
[86]
Guo, M.; Davis, D.; Birchler, J.A. Dosage effects on gene expression in a maize ploidy series. Genetics 1996, 142, 1349–1355.
[87]
Comai, L.; Tyagi, A.P.; Winter, K.; Holmes-Davis, R.; Reynolds, S.H.; Stevens, Y.; Byers, B. Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids. Plant Cell 2000, 12, 1551–1567.
[88]
Lee, H.-S.; Chen, Z.J. Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proc. Natl. Acad. Sci. USA 2001, 98, 6753–6758.
Adams, K.L.; Cronn, R.; Percifield, R.; Wendel, J.F. Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proc. Natl. Acad. Sci. USA 2003, 100, 4649–4654.
[91]
Tate, J.A.; Ni, Z.; Scheen, A.-C.; Koh, J.; Gilbert, C.A.; Lefkowitz, D.; Chen, Z.J.; Soltis, P.S.; Soltis, D.E. Evolution and expression of homeologous loci in Tragopogon miscellus (Asteraceae), a recent and reciprocally formed allopolyploid. Genetics 2006, 173, 1599–1611.
Schena, M.; Shalon, D.; Davis, R.W.; Brown, P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270, 467–470.
[94]
Chagué, V.; Just, J.; Mestiri, I.; Balzergue, S.; Tanguy, A.-M.; Huneau, C.; Huteau, V.; Belcram, H.; Coriton, O.; Jahier, J.; et al. Genome-wide gene expression changes in genetically stable synthetic and natural wheat allohexaploids. New Phytol 2010, 187, 1181–1194.
[95]
Pumphrey, M.; Bai, J.; Laudencia-Chingcuanco, D.; Anderson, O.; Gill, B.S. Nonadditive expression of homoeologous genes is established upon polyploidization in hexaploid wheat. Genetics 2009, 181, 1147–1157.
[96]
Chaudhary, B.; Hovav, R.; Flagel, L.; Mittler, R.; Wendel, J. Parallel expression evolution of oxidative stress-related genes in fiber from wild and domesticated diploid and polyploid cotton (Gossypium). BMC Genomics 2009, 10, doi:10.1186/1471-2164-10-378.
[97]
Marmagne, A.; Brabant, P.; Thiellement, H.; Alix, K. Analysis of gene expression in resynthesized Brassica napus allotetraploids: Transcriptional changes do not explain differential protein regulation. New Phytol 2010, 186, 216–227.
[98]
Chelaifa, H.; Monnier, A.; Ainouche, M. Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina × townsendii and Spartina anglica (Poaceae). New Phytol 2010, 186, 161–174.
[99]
Buggs, R.J.A.; Doust, A.N.; Tate, J.A.; Koh, J.; Soltis, K.; Feltus, F.A.; Paterson, A.H.; Soltis, P.S.; Soltis, D.E. Gene loss and silencing in Tragopogon miscellus (Asteraceae): Comparison of natural and synthetic allotetraploids. Heredity 2009, 103, 73–81.
[100]
Doyle, J.J.; Flagel, L.E.; Paterson, A.H.; Rapp, R.A.; Soltis, D.E.; Soltis, P.S.; Wendel, J.F. Evolutionary genetics of genome merger and doubling in plants. Annu. Rev. Genet 2008, 42, 443–461.
[101]
Yu, Z.; Haberer, G.; Matthes, M.; Rattei, T.; Mayer, K.F.X.; Gierl, A.; Torres-Ruiz, R.A. Impact of natural genetic variation on the transcriptome of autotetraploid Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 2010, 107, 17809–17814.
Riddle, N.; Jiang, H.; An, L.; Doerge, R.; Birchler, J. Gene expression analysis at the intersection of ploidy and hybridity in maize. Theor. Appl. Genet 2010, 120, 341–353.
[104]
Havecker, E.R. Detection of small RNAs and microRNAs using deep sequencing technology. Methods Mol. Biol 2011, 732, 55–68.
[105]
Ha, M.; Lu, J.; Tian, L.; Ramachandran, V.; Kasschau, K.D.; Chapman, E.J.; Carrington, J.C.; Chen, X.; Wang, X.-J.; Chen, Z.J. Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids. Proc. Natl. Acad. Sci. USA 2009, 106, 17835–17840.
[106]
Ng, D.W.-K.; Zhang, C.; Miller, M.; Palmer, G.; Whiteley, M.; Tholl, D.; Chen, Z.J. Cis- and trans-regulation of miR163 and target genes confers natural variation of secondary metabolites in two Arabidopsis species and their allopolyploids. Plant Cell 2011, 23, 1729–1740.
[107]
Wang, Z.; Gerstein, M.; Snyder, M. RNA-Seq: A revolutionary tool for transcriptomics. Nat. Rev. Genet 2009, 10, 57–63.
[108]
Croate, E.C.; Doyle, J.J. Quantifying whole transcriptome size, a prerequisite for understanding transcriptome evolution across species: An example from a plant allopolyploid. Genome Biol. Evol 2010, 2, 534–546.
[109]
Ilut, D.C.; Coate, J.E.; Luciano, A.K.; Owens, T.G.; May, G.D.; Farmer, A.; Doyle, J.J. A comparative transcriptomic study of an allotetraploid and its diploid progenitors illustrates the unique advantages and challenges of RNA-seq in plant species. Am. J. Bot 2012, 99, 383–396.
[110]
Birchler, J.A.; Newton, K.J. Modulation of protein levels in chromosomal dosage series of maize: The biochemical basis of aneuploid syndromes. Genetics 1981, 99, 247–266.
[111]
Islam, N.; Tsujimoto, H.; Hirano, H. Proteome analysis of diploid, tetraploid and hexaploid wheat: Towards understanding genome interaction in protein expression. Proteomics 2003, 3, 549–557.
[112]
Albertin, W.; Balliau, T.; Brabant, P.; Chèvre, A.-M.; Eber, F.; Malosse, C.; Thiellement, H. Numerous and rapid nonstochastic modifications of gene products in newly synthesized Brassica napus allotetraploids. Genetics 2006, 173, 1101–1113.
[113]
Albertin, W.; Langella, O.; Joets, J.; Négroni, L.; Zivy, M.; Damerval, C.; Thiellement, H. Comparative proteomics of leaf, stem, and root tissues of synthetic Brassica napus. Proteomics 2009, 9, 793–799.
[114]
Song, X.; Ni, Z.; Yao, Y.; Xie, C.; Li, Z.; Wu, H.; Zhang, Y.; Sun, Q. Wheat (Triticum aestivum L.) root proteome and differentially expressed root proteins between hybrid and parents. Proteomics 2007, 7, 3538–3557.
[115]
Yao, H.; Kato, A.; Mooney, B.; Birchler, J. Phenotypic and gene expression analyses of a ploidy series of maize inbred Oh43. Plant Mol. Biol 2011, 75, 237–251.
[116]
Ng, D.W.K.; Zhang, C.; Miller, M.; Shen, Z.; Briggs, S.P.; Chen, Z.J. Proteomic divergence in Arabidopsis autopolyploids and allopolyploids and their progenitors. Heredity 2012, 108, 419–430.
[117]
Elshire, R.J.; Glaubitz, J.C.; Sun, Q.; Poland, J.A.; Kawamoto, K.; Buckler, E.S.; Mitchell, S.E. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 2011, 6, e19379.
[118]
Grover, C.E.; Salmon, A.; Wendel, J.F. Targeted sequence capture as a powerful tool for evolutionary analysis. Am. J. Bot 2012, 99, 312–319.
[119]
Cronn, R.; Knaus, B.J.; Liston, A.; Maughan, P.J.; Parks, M.; Syring, J.V.; Udall, J. Targeted enrichment strategies for next-generation plant biology. Am. J. Bot 2012, 99, 291–311.
[120]
Kvam, V.M.; Liu, P.; Si, Y. A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data. Am. J. Bot 2012, 99, 248–256.
[121]
Ercolano, M.R. University of Naples Federico II: Portici (NA), Italy. Unpublished work, 2012.
