Doubling down on genomes: Polyploidy and crop plants

American Journal of Botany

Volumn 101, Issue 10, 2014, Pages 1711-1725

  Renny Byfield, Simon ^a   Wendel, Jonathan F ^a  

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

Crop improvement; Domestication; Epigenetics; Gene duplication; Genomic shock; Next Generation sequencing; Polyploidy; Whole Genome duplication

Indexed keywords

ANGIOSPERM; CROP IMPROVEMENT; CROP PLANT; GENOME; PHENOTYPE; POLYPLOIDY;

AGRICULTURE; ANGIOSPERM; CROP; EVOLUTION; GENETICS; PLANT GENOME; POLYPLOIDY;

AGRICULTURE; ANGIOSPERMS; BIOLOGICAL EVOLUTION; CROPS, AGRICULTURAL; GENOME, PLANT; POLYPLOIDY;

EID: 84907342844     PISSN: 00029122     EISSN: None     Source Type: Journal    
DOI: 10.3732/ajb.1400119     Document Type: Article

References (196)

1. ABROUK, M., F. MURAT, C. PONT, J. MESSING, S. JACKSON, T. FARAUT, E. TANNIER, et al. 2010. Palaeogenomics of plants: Synteny-based modelling of extinct ancestors. Trends in Plant Science 15: 479-487.
2. ADAMS, K. L., R. CRONN, R. PERCIFIELD, and J. F. WENDEL. 2003. Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proceedings of the National Academy of Sciences, USA 100: 4649-4654.
3. ADAMS, K. L., R. PERCIFIELD, and J. F. WENDEL. 2004. Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics 168: 2217-2226.
4. ADAMS, K. L., and J. F. WENDEL. 2005. Polyploidy and genome evolution in plants. Current Opinion in Plant Biology 8: 135-141.
5. ALBERT, V. A., W. B. BARBAZUK, C. W. DEPAMPHILIS, J. P. DER, J. Leebens-Mack, H. MA, J. D. PALMER, et al. 2013. The Amborella genome and the evolution of flowering plants. Science 342: 1467.
6. THE ARABIDOPSIS GENOME INITIATIVE. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796–815.
7. AUGER, B., C. BARON, M.-O. LUCAS, S. VAUTRIN, H. BERGES, B. CHALHOUB, A. FAUTREL, et al. 2009. Brassica orthologs from BANYULS belong to a small multigene family, which is involved in procyanidin accumulation in the seed. Planta 230: 1167-1183.
8. AURY, J.-M., O. JAILLON, L. DURET, B. NOEL, C. JUBIN, B. M. PORCEL, B. SEGURENS, et al. 2006. Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 444: 171-178.
9. BALDWIN, B. G., B. L. WESSA, and J. L. PANERO. 2002. Nuclear rDNA evidence for major lineages of helenioid Heliantheae (Compositae). Systematic Botany 27: 161-198.
10. BANCROFT, I., C. MORGAN, F. FRASER, J. HIGGINS, R. WELLS, L. CLISSOLD, D. BAKER, et al. 2011. Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing. Nature Biotechnology 29: 762-766.
11. BARDIL, A., J. D. DE ALMEIDA, M. C. COMBES, P. LASHERMES, and B. BERTRAND. 2011. Genomic expression dominance in the natural allopolyploid Coffea arabica is massively affected by growth temperature. New Phytologist 192: 760-774.
12. BARKER, M. S., N. C. KANE, M. MATVIENKO, A. KOZIK, W. MICHELMORE, S. J. KNAPP, and L. H. RIESEBERG. 2008. Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. Molecular Biology and Evolution 25: 2445-2455.
13. BAUMEL, A., M. AINOUCHE, R. KALENDAR, and A. H. SCHULMAN. 2002. Retrotransposons and genomic stability in populations of the young allopolyploid species Spartina anglica CE Hubbard (Poaceae). Molecular Biology and Evolution 19: 1218-1227.
14. BENDER, J. 2002. Plant epigenetics. Current Biology 12: R412-R414.
15. BERGER, E., D. YORUKOGLU, J. PENG, and B. BERGER. 2014. HapTree: A novel Bayesian framework for single individual polyplotyping using NGS data. In R. Sharan [ed.], Research in computational molecular biology, Lecture notes in computer science, vol. 8394, 18-19. Springer International Publishing, Cham, Switzerland. doi:10.1007/978-3-319-05269-4_2
16. BIRCHLER, J. A., U. BHADRA, M. P. BHADRA, and D. L. AUGER. 2001. Dosage-dependent gene regulation in multicellular eukaryotes: Implications for dosage compensation, aneuploid syndromes, and quantitative traits. Developmental Biology 234: 275-288.
17. BIRCHLER, J., and R. VEITIA. 2012. Gene balance hypothesis: Connecting issues of dosage sensitivity across biological disciplines. Proceedings of the National Academy of Sciences, USA 109: 14746-14753.
18. BIRCHLER, J. A., and R. A. VEITIA. 2007. The gene balance hypothesis: From classical genetics to modern genomics. Plant Cell 19: 395-402.
19. BIRCHLER, J. A., and R. A. VEITIA. 2010. The gene balance hypothesis: Implications for gene regulation, quantitative traits and evolution. New Phytologist 186: 54-62.
20. BLACKMAN, B. K., D. A. RASMUSSEN, J. L. STRASBURG, A. R. RADUSKI, J. M. BURKE, S. J. KNAPP, S. D. MICHAELS, et al. 2011. Contributions of flowering time genes to sunflower domestication and improvement. Genetics 187: 271-287.
21. BLACKMAN, B. K., J. L. STRASBURG, A. R. RADUSKI, S. D. MICHAELS, and L. H. RIESEBERG. 2010. The role of recently derived FT paralogs in sunflower domestication. Current Biology 20: 629-635.
22. BLANC, G., A. BARAKAT, R. GUYOT, R. COOKE, and I. DELSENY. 2000. Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell 12: 1093-1101.
23. BLANC, G., K. HOKAMP, and K. H. WOLFE. 2003. A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Research 13: 137-144.
24. BLANC, G., and K. H. WOLFE. 2004. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16: 1667-1678.
25. BLUM, A. 2013. Heterosis, stress, and the environment: A possible road map towards the general improvement of crop yield. Journal of Experimental Botany 64: 4829-4837.
26. BOTTLEY, A., and R. M. D. KOEBNER. 2008. Variation for homoeologous gene silencing in hexaploid wheat. The Plant Journal 56: 297-302.
27. BOWERS, J. E., B. A. CHAPMAN, J. K. RONG, and A. H. PATERSON. 2003. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422: 433-438.
28. BRUCE, A. B. 1910. The Mendelian theory of heredity and the augmentation of vigor. Science 32: 627-628.
29. BUGGS, R. J., S. CHAMALA, W. WU, L. GAO, G. D. MAY, P. S. SCHNABLE, D. E. SOLTIS, et al. 2010a. Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by nextgeneration sequencing and Sequenom iPLEX MassARRAY genotyping. Molecular Ecology 19: 132-146.
30. BUGGS, R. J., N. M. ELLIOTT, L. J. ZHANG, J. KOH, L. F. VICCINI, D. E. SOLTIS, and P. S. SOLTIS. 2010b. Tissue-specific silencing of homoeologs in natural populations of the recent allopolyploid Tragopogon mirus. New Phytologist 186: 175-183.
31. BUGGS, R. J., L. ZHANG, N. MILES, J. TATE, L. GAO, W. WEI, P. SCHNABLE, et al. 2010c. Transcriptomic shock generates evolutionary novelty in a newly formed, natural allopolyploid plant. Current Biology 21: 551–556.
32. CAVANAGH, C. R., S. CHAO, S. WANG, B. E. HUANG, S. STEPHEN, S. KIANI, K. FORREST, et al. 2013. Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proceedings of the National Academy of Sciences, USA 110: 8057-8062.
33. CENCI, A., M.-C. COMBES, and P. LASHERMES. 2010. Comparative sequence analyses indicate that Coffea (asterids) and Vitis (rosids) derive from the same paleo-hexaploid ancestral genome. Molecular Genetics and Genomics 283: 493-501.
34. CHANG, P. L., B. P. DILKES, M. MCMAHON, L. COMAI, and S. V. NUZHDIN. 2010. Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners. Genome Biology 11: R125.
35. CHANTRET, N., J. SALSE, F. SABOT, S. RAHMAN, A. BELLEC, B. LAUBIN, I. DUBOIS, et al. 2005. Molecular basis of evolutionary events that shaped the Hardness locus in diploid and polyploid wheat species (Triticum and Aegilops). Plant Cell 17: 1033-1045.
36. CHAPMAN, B. A., J. E. BOWERS, F. A. FELTUS, and A. H. PATERSON. 2006. Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication. Proceedings of the National Academy of Sciences, USA 103: 2730-2735.
37. CHELAIFA, H., A. MONNIER, and M. AINOUCHE. 2010. Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina × townsendii and Spartina anglica (Poaceae). New Phytologist 186: 161-174.
38. CHEN, L. Z., and J. F. CHEN. 2008. Changes of cytosine methylation induced by wide hybridization and allopolyploidy in Cucumis. Genome 51: 789-799.
39. CHEN, Z. J. 2007. Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids, Annual Review of Plant Biology 58: 377-406.
40. CHEN, Z. J. 2010. Molecular mechanisms of polyploidy and hybrid vigor. Trends in Plant Science 15: 57-71.
41. CHENG, F., S. LIU, J. WU, L. FANG, S. SUN, B. LIU, P. LI, et al. 2011. BRAD, the genetics and genomics database for Brassica plants. BMC Plant Biology 11: 136.
42. CHENG, S.-H., J.-Y. ZHUANG, Y.-Y. FAN, J.-H. DU, and L.-Y. CAO. 2007. Progress in research and development on hybrid rice: A super-domesticate in china. Annals of Botany 100: 959-966.
43. CHESTER, M., J. P. GALLAGHER, V. V. SYMONDS, A. V. CRUZ DA SILVA, E. V. MAVRODIEV, A. R. LEITCH, P. S. SOLTIS, and D. E. SOLTIS. 2012. Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae). Proceedings of the National Academy of Sciences, USA 109: 1176-1181.
44. CHIA, J.-M., C. SONG, P. J. BRADBURY, D. COSTICH, N. DE LEON, J. DOEBLEY, R. J. ELSHIRE, et al. 2012. Maize HapMap2 identifies extant variation from a genome in flux. Nature Genetics 44: 803-807.
45. COCKRAM, J., J. WHITE, D. L. ZULUAGA, D. SMITH, J. COMADRAN, M. MACAULAY, Z. LUO, et al. 2010. Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome. Proceedings of the National Academy of Sciences, USA 107: 21611-21616.
46. COMAI, L. 2005. The advantages and disadvantages of being polyploid. Nature Reviews Genetics 6: 836-846.
47. CORTIJO, S., R. WARDENAAR, M. Colomé-Tatché, A. GILLY, M. ETCHEVERRY, K. LABADIE, E. CAILLIEUX, et al. 2014. Mapping the epigenetic basis of complex traits. Science doi:10.1126/science.1248127.
48. CROW, J. F. 1998. 90 years ago: The beginning of hybrid maize. Genetics 148: 923-928.
49. D’HONT, A., F. DENOEUD, J.-M. AURY, F.-C. BAURENS, F. CARREEL, O. GARSMEUR, B. NOEL, et al. 2012. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488: 213.
50. DEAL, R. B., and S. HENIKOFF. 2011. Histone variants and modifications in plant gene regulation. Current Opinion in Plant Biology 14: 116-122.
51. DES MARAIS, D. L., and M. D. RAUSHER. 2008. Escape from adaptive conflict after duplication in an anthocyanin pathway gene. Nature 454: 762-765.
52. DUBCOVSKY, J., and J. DVORAK. 2007. Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 316: 1862-1866.
53. DUVICK, D. N. 2001. Biotechnology in the 1930s: The development of hybrid maize. Nature Reviews. Genetics 2: 69-74.
54. EAST, E. M. 1936. Heterosis. Genetics 21: 375-397.
55. EILAM, T., Y. ANIKSTER, E. MILLET, J. MANISTERSKI, and M. FELDMAN. 2008. Nuclear DNA amount and genome downsizing in natural and synthetic allopolyploids of the genera Aegilops and Triticum. Genome 51: 616-627.
56. EILAM, T., Y. ANIKSTER, E. MILLET, J. MANISTERSKI, and M. FELDMAN. 2010. Genome size in diploids, allopolyploids, and autopolyploids of Mediterranean Triticeae. Le Journal de Botanique 2010: 341-380.
57. FAINO, L., and B. P. H. J. THOMMA. 2014. Get your high-quality low-cost genome sequence. Trends in Plant Science 19: 288-291.
58. FELDMAN, M., and A. A. LEVY. 2009. Genome evolution in allopolyploid wheat—A revolutionary reprogramming followed by gradual changes. Journal of Genetics and Genomics 36: 511-518.
59. FELDMAN, M., and A. A. LEVY. 2012. Genome evolution due to allopolyploidization in wheat. Genetics 192: 763-774.
60. FELDMAN, M., B. LIU, G. SEGAL, S. ABBO, A. A. LEVY, and J. M. VEGA. 1997. Rapid elimination of low-copy DNA sequences in polyploidy wheat: A possible mechanism for differentiation of homoeologous chromosomes. Genetics 147: 1381-1387.
61. FLAGEL, L., J. UDALL, D. NETTLETON, and J. WENDEL. 2008. Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution. BMC Biology 6: 16.
62. FLAGEL, L. E., J. F. WENDEL, and J. A. UDALL. 2012. Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton. BMC Genomics 13: 302.
63. FORCE, A., M. LYNCH, F. B. PICKETT, A. AMORES, Y. L. YAN, and J. POSTLETHWAIT. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.
64. FREELING, M., and B. C. THOMAS. 2006. Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Research 16: 805-814.
65. FREELING, M., M. R. WOODHOUSE, S. SUBRAMANIAM, G. TURCO, D. LISCH, and J. C. SCHNABLE. 2012. Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants. Current Opinion in Plant Biology 15: 131-139.
66. GAETA, R. T., J. C. PIRES, F. Iniguez-Luy, E. LEON, and T. C. OSBORN. 2007. Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Plant Cell 19: 3403-3417.
67. GARSMEUR, O., J. C. SCHNABLE, A. ALMEIDA, C. JOURDA, A. D’hont, and M. FREELING. 2014. Two evolutionarily distinct classes of paleopolyploidy. Molecular Biology and Evolution 31: 448-454.
68. GOODSPEED, T. H. 1933. Chromosome number and morphology in Nicotiana VI. Chromosome numbers of forty species. Proceedings of the National Academy of Sciences, USA 19: 649-653.
69. GROVER, C. E., J. P. GALLAGHER, E. P. SZADKOWSKI, M. J. YOO, L. E. FLAGEL, and J. F. WENDEL. 2012. Homoeolog expression bias and expression level dominance in allopolyploids. New Phytologist 196: 966-971.
70. GROVER, C. E., H. KIM, R. A. WING, A. H. PATERSON, and J. F. WENDEL. 2007. Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium). Plant Journal 50: 995-1006.
71. HAMILTON, J. P., C. N. HANSEY, B. R. WHITTY, K. STOFFEL, A. N. MASSA, A. VAN DEYNZE, W. S. DE JONG, et al. 2011. Single nucleotide polymorphism discovery in elite North American potato germplasm. BMC Genomics 12: 302.
72. HAMMER, K. 1984. The domestication syndrome. Die Kulturpflanze 32: 11-34.
73. HAN, F. P., G. FEDAK, W. L. GUO, and B. LIU. 2005. Rapid and repeatable elimination of a parental genome-specific DNA repeat (pGcIR-1a) in newly synthesized wheat allopolyploids. Genetics 170: 1239-1245.
74. HANSEY, C. N., B. VAILLANCOURT, R. S. SEKHON, N. DE LEON, S. M. KAEPPLER, and C. R. BUELL. 2012. Maize (Zea mays L.) Genome diversity as revealed by RNA-sequencing. PLoS ONE 7: e33071.
75. HARPER, A. L., M. TRICK, J. HIGGINS, F. FRASER, L. CLISSOLD, R. WELLS, C. HATTORI, et al. 2012. Associative transcriptomics of traits in the polyploid crop species Brassica napus. Nature Biotechnology 30: 798–802.
76. HE, P., B. R. FRIEBE, B. S. GILL, and J. M. ZHOU. 2003. Allopolyploidy alters gene expression in the highly stable hexaploid wheat. Plant Molecular Biology 52: 401-414.
77. HE, Z., W. ZHAI, H. WEN, T. TANG, Y. WANG, X. LU, A. J. GREENBERG, et al. 2011. Two evolutionary histories in the genome of rice: The roles of domestication genes. PLOS Genetics 7: e1002100.
78. HEGARTY, M. J., G. L. BARKER, I. D. WILSON, R. J. ABBOTT, K. J. EDWARDS, and S. J. HISCOCK. 2006. Transcriptome shock after interspecific hybridization in Senecio is ameliorated by genome duplication. Current Biology 16: 1652-1659.
79. HILU, K. W. 1993. Polyploidy and the evolution of domesticated plants. American Journal of Botany 80: 1494-1499.
80. HOFBERGER, J. A., E. LYONS, P. P. EDGER, J. C. PIRES, and M. E. SCHRANZ. 2013. Whole genome and tandem duplicate retention facilitated glucosinolate pathway diversification in the mustard family. Genome Biology and Evolution 5: 2155-2173.
81. HOVAV, R., J. A. UDALL, B. CHAUDHARY, R. RAPP, L. FLAGEL, and J. F. WENDELL. 2008. Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant. Proceedings of the National Academy of Sciences, USA 105: 6191-6195.
82. HU, Z., Z. HAN, N. SONG, L. CHAI, Y. YAO, H. PENG, Z. NI, and Q. SUN. 2013. Epigenetic modification contributes to the expression divergence of three TaEXPA1 homoeologs in hexaploid wheat (Triticum aestivum). New Phytologist 197: 1344-1352.
83. HUANG, S., L. DENG, M. GUAN, J. LI, K. LU, H. WANG, D. FU, et al. 2013. Identification of genome-wide single nucleotide polymorphisms in allopolyploid crop Brassica napus. BMC Genomics 14: 717.
84. HUGHES, A. L. 1994. The evolution of functionally novel proteins after gene duplication. Proceedings of the Royal Society of London, B, Biological Sciences 256: 119-124.
85. HUSTED, L. 1936. Cytological studies on the peanut, Arachis. II. Chromosome number, morphology and behavior, and their application to the problem of the origin of the cultivated forms. Cytologia 7: 396-423.
86. JAILLON, O., J.-M. AURY, B. NOEL, A. POLICRITI, C. CLEPET, A. CASAGRANDE, N. CHOISNE, et al. 2007. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449: 463-467.
87. JIANG, C. X., R. J. WRIGHT, K. M. El-Zik, and A. H. PATERSON. 1998. Polyploid formation created unique avenues for response to selection in Gossypium (cotton). Proceedings of the National Academy of Sciences, USA 95: 4419-4424.
88. JIAO, Y., N. J. WICKETT, S. AYYAMPALAYAM, A. S. CHANDERBALI, L. LANDHERR, P. E. RALPH, L. P. TOMSHO, et al. 2011. Ancestral polyploidy in seed plants and angiosperms. Nature 473: 97-100.
89. JIAO, Y., H. ZHAO, L. REN, W. SONG, B. ZENG, J. GUO, B. WANG, et al. 2012. Genome-wide genetic changes during modern breeding of maize. Nature Genetics 44: 812-815.
90. KASHKUSH, K., M. FELDMAN, and A. A. LEVY. 2002. Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics 160: 1651-1659.
91. KELLY, L. J., A. R. LEITCH, M. F. FAY, S. Renny-Byfield, J. PELLICER, J. MACAS, and I. J. LEITCH. 2012. Why size really matters when sequencing plant genomes. Plant Ecology & Diversity 5: 415-425.
92. KHERA, P., H. D. UPADHYAYA, M. K. PANDEY, M. ROORKIWAL, M. SRISWATHI, P. JANILA, Y. GUO, et al. 2013. Single nucleotide polymorphismbased genetic diversity in the reference set of peanut (Arachis spp.) by developing and applying cost-effective competitive allele specific polymerase chain reaction genotyping assays. Plant Genome 6.
93. KOH, J., P. S. SOLTIS, and D. E. SOLTIS. 2010. Homeolog loss and expression changes in natural populations of the recently and repeatedly formed allotetraploid Tragopogon mirus (Asteraceae). BMC Genomics 11: 97.
94. KOVARIK, A., M. DADEJOVA, Y. K. LIM, M. W. CHASE, J. J. CLARKSON, S. KNAPP, and A. R. LEITCH. 2008. Evolution of rDNA in Nicotiana allopolyploids: A potential link between rDNA homogenization and epigenetics. Annals of Botany 101: 815-823.
95. KOVARIK, A., R. MATYASEK, K. Y. LIM, K. SKALICKA, B. KOUKALOVA, S. KNAPP, M. CHASE, and A. R. LEITCH. 2004. Concerted evolution of 18-5.8-26S rDNA repeats in Nicotiana allotetraploids. Biological Journal of the Linnean Society 82: 615-625.
96. KSIAZCZYK, T., A. KOVARIK, F. EBER, V. HUTEAU, L. KHAITOVA, Z. TESARIKOVA, O. CORITON, and A.-M. CHEVRE. 2011. Immediate unidirectional epigenetic reprogramming of NORs occurs independently of rDNA rearrangements in synthetic and natural forms of a polyploid species Brassica napus. Chromosoma 120: 557-571.
97. LAGERCRANTZ, U. 1998. Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements. Genetics 150: 1217-1228.
98. LAM, H.-M., X. XU, X. LIU, W. CHEN, G. YANG, F.-L. WONG, M.-W. LI, et al. 2010. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nature Genetics 42: 1053-1059.
99. LANGHAM, R. J., J. WALSH, M. DUNN, C. KO, S. A. GOFF, and M. FREELING. 2004. Genomic duplication, fractionation and the origin of regulatory novelty. Genetics 166: 935-945.
100. LASHERMES, P., M. C. COMBES, J. ROBERT, P. TROUSLOT, A. D'hont, F. ANTHONY, and A. CHARRIER. 1999. Molecular characterisation and origin of the Coffea arabica L. genome. Molecular & General Genetics 261: 259–266.
101. LATZEL, V., E. ALLAN, A. B. SILVEIRA, V. COLOT, M. FISCHER, and O. BOSSDORF. 2013. Epigenetic diversity increases the productivity and stability of plant populations. Nature Communications 4: article 2875.
102. LEE, H. S., and Z. J. CHEN. 2001. Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. Proceedings of the National Academy of Sciences, USA 98: 6753-6758.
103. LEITCH, A. R., and I. J. LEITCH. 2008. Perspective—Genomic plasticity and the diversity of polyploid plants. Science 320: 481-483.
104. LEITCH, I. J., and M. D. BENNETT. 2004. Genome downsizing in polyploidy plants. Biological Journal of the Linnean Society 82: 651-663.
105. LEITCH, I. J., M. W. CHASE, and M. D. BENNETT. 1998. Phylogenetic analysis of DNA C-values provides evidence for a small ancestral genome size in flowering plants. Annals of Botany 82: 85-94.
106. LEITCH, I. J., L. HANSON, K. Y. LIM, A. KOVARIK, M. W. CHASE, J. J. CLARKSON, and A. R. LEITCH. 2008. The ups and downs of genome size evolution in polyploid species of Nicotiana (Solanaceae). Annals of Botany 101: 805-814.
107. LESCOT, M., P. PIFFANELLI, A. Y. CIAMPI, M. RUIZ, G. BLANC, J. Leebens-Mack, F. R. DA SILVA, et al. 2008. Insights into the Musa genome: Syntenic relationships to rice and between Musa species. BMC Genomics 9: 58.
108. LIM, K. Y., A. KOVARIK, R. MATYASEK, M. W. CHASE, J. J. CLARKSON, M. A. GRANDBASTIEN, and A. R. LEITCH. 2007. Sequence of events leading to near-complete genome turnover in allopolyploid Nicotiana within five million years. New Phytologist 175: 756-763.
109. LIM, K. Y., K. Souckova-Skalicka, V. SARASAN, J. J. CLARKSON, M. W. CHASE, A. KOVARIK, and A. R. LEITCH. 2006. A genetic appraisal of a new synthetic Nicotiana tabacum (Solanaceae) and the Kostoff synthetic tobacco. American Journal of Botany 93: 875-883.
110. LIU, B., J. M. VEGA, and M. FELDMAN. 1998. Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. II. Changes in low-copy coding DNA sequences. Genome 41: 535-542.
111. LUKENS, L. N., J. C. PIRES, E. LEON, R. VOGELZANG, L. OSLACH, and T. OSBORN. 2006. Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids. Plant Physiology 140: 336-348.
112. LYNCH, M., and J. S. CONERY. 2000. The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
113. LYNCH, M., and A. FORCE. 2000. The probability of duplicate gene preservation by subfunctionalization. Genetics 154: 459-473.
114. MADLUNG, A., A. P. TYAGI, B. WATSON, H. M. JIANG, T. KAGOCHI, R. W. DOERGE, R. MARTIENSSEN, and L. COMAI. 2005. Genomic changes in synthetic Arabidopsis polyploids. Plant Journal 41: 221-230.
115. MADLUNG, A., and J. F. WENDEL. 2013. Genetic and epigenetic aspects of polyploid evolution in plants. Cytogenetic and Genome Research 140: 270-285.
116. MAHER, B. 2008. Personal genomes: The case of the missing heritability. Nature 456: 18-21.
117. MATYASEK, R., S. Renny-Byfield, J. FULNECEK, J. MACAS, M.-A. GRANDBASTIEN, R. NICHOLS, A. LEITCH, and A. KOVARIK. 2012. Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids. BMC Genomics 13: 722.
118. MATZINGER, D. F., and E. A. WERNSMAN. 1967. Genetic diversity and heterosis in Nicotiana. Zuchter 37: 188-191.
119. MCCLINTOCK, B. 1984. The significance of responses of the genome to challenge. Science 226: 792-801.
120. MEYER, R. S., A. E. DUVAL, and H. R. JENSEN. 2012. Patterns and processes in crop domestication: An historical review and quantitative analysis of 203 global food crops. New Phytologist 196: 29-48.
121. MOCHIDA, K., Y. YAMAZAKI, and Y. OGIHARA. 2003. Discrimination of homoeologous gene expression in hexaploid wheat by SNP analysis of contigs grouped from a large number of expressed sequence tags. Molecular Genetics and Genomics 270: 371-377.
122. NAKASUGI, K., R. CROWHURST, J. BALLY, and P. WATERHOUSE. 2014. Combining transcriptome assemblies from multiple de novo assemblers in the allo-tetraploid plant Nicotiana benthamiana. PLoS ONE 9: e91776.
123. NI, Z., E.-D. KIM, M. HA, E. LACKEY, J. LIU, Y. ZHANG, Q. SUN, and Z. J. CHEN. 2009. Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 457: 327-331.
124. OHNO, S. 1970. Evolution by gene duplication. Spiringer-Verlag, New York, New York, USA.
125. OLSEN, K. M., and J. F. WENDEL. 2013. A bountiful harvest: Genomic insights into crop domestication phenotypes. Annual Review of Plant Biology 64: 47-70.
126. OZKAN, H., A. A. LEVY, and M. FELDMAN. 2001. Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group. Plant Cell 13: 1735-1747.
127. PAGE, J. T., A. R. GINGLE, and J. A. UDALL. 2013a. PolyCat: A resource for genome categorization of sequencing reads from allopolyploid organisms. G3—Genes Genomes Genetics 3: 517-525.
128. PAGE, J. T., M. D. HUYNH, Z. S. LIECHTY, K. GRUPP, D. STELLY, A. M. HULSE, H. ASHRAFI, et al. 2013b. Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing. G3—Genes Genomes Genetics 3: 1809-1818.
129. PARISOD, C., A. SALMON, T. ZERJAL, M. TENAILLON, M.-A. GRANDBASTIEN, and M. AINOUCHE. 2009. Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina. New Phytologist 184: 1003-1015.
130. PATERSON, A. H. 2005. Polyploidy, evolutionary opportunity, and crop adaptation. Genetica 123: 191-196.
131. PATERSON, A. H., J. E. BOWERS, and B. A. CHAPMAN. 2004. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proceedings of the National Academy of Sciences, USA 101: 9903-9908.
132. PATERSON, A. H., J. F. WENDEL, H. GUNDLACH, H. GUO, J. JENKINS, D. JIN, D. LLEWELLYN, et al. 2012. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492: 423-427.
133. PFEIL, B. E., J. A. SCHLUETER, R. C. SHOEMAKER, and J. J. DOYLE. 2005. Placing paleopolyploidy in relation to taxon divergence: A phylogenetic analysis in legumes using 39 gene families. Systematic Biology 54: 441-454.
134. PRINCE, V. E., and F. B. PICKETT. 2002. Splitting pairs: The diverging fates of duplicated genes. Nature Reviews Genetics 3: 827-837.
135. QI, B., W. HUANG, B. ZHU, X. ZHONG, J. GUO, N. ZHAO, C. XU, et al. 2012. Global transgenerational gene expression dynamics in two newly synthesized allohexaploid wheat (Triticum aestivum) lines. BMC Biology 10: 3.
136. RAMBANI, A., J. T. PAGE, and J. A. UDALL. 2014. Polyploidy and the petal transcriptome of Gossypium. BMC Plant Biology 14: 3.
137. RAPP, R. A., C. H. HAIGLER, L. FLAGEL, R. H. HOVAV, J. A. UDALL, and J. F. WENDEL. 2010. Gene expression in developing fibres of Upland cotton (Gossypium hirsutum L.) was massively altered by domestication. BMC Biology 8: 139.
138. RAPP, R. A., J. A. UDALL, and J. F. WENDEL. 2009. Genomic expression dominance in allopolyploids. BMC Biology 7: 18.
139. Renny-Byfield, S., M. CHESTER, A. KOVA ÍK, S. C. LE COMBER, M.-A. GRANDBASTIEN, M. DELOGER, R. A. NICHOLS, et al. 2011. Next generation sequencing reveals genome downsizing in allotetraploid Nicotiana tabacum, predominantly through the elimination of paternally derived repetitive DNAs. Molecular Biology and Evolution 28: 2843-2854.
140. Renny-Byfield, S., A. KOVARIK, M. CHESTER, R. A. NICHOLS, J. MACAS, P. NOVAK, and A. R. LEITCH. 2012. Independent, rapid and targeted loss of a highly repetitive DNA sequence derived from the paternal genome donor in natural and synthetic Nicotiana tabacum. PLoS ONE 7: e36963.
141. Renny-Byfield, S., A. KOVARIK, L. J. KELLY, J. MACAS, P. NOVAK, M. W. CHASE, R. A. NICHOLS, et al. 2013. Diploidization and genome size change in allopolyploids is associated with differential dynamics of lowand high-copy sequences. Plant Journal 74: 829-839.
142. RENSING, S. A., J. ICK, J. A. FAWCETT, D. LANG, A. ZIMMER, Y. V. DE PEER, and R. RESKI. 2007. An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens. BMC Evolutionary Biology 7: 130.
143. RONG, J., F. A. FELTUS, V. N. WAGHMARE, G. J. PIERCE, P. W. CHEE, X. DRAYE, Y. SARANGA, et al. 2007. Meta-analysis of polyploid cotton QTL shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development. Genetics 176: 2577-2588.
144. SALMON, A., M. L. AINOUCHE, and J. F. WENDEL. 2005. Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Molecular Ecology 14: 1163-1175.
145. SALMON, A., J. A. UDALL, J. A. JEDDELOH, and J. WENDEL. 2012. Targeted capture of homoeologous coding and noncoding sequence in polyploid cotton. G3—Genes Genomes Genetics 2: 921-930.
146. SATO, S., S. TABATA, H. HIRAKAWA, E. ASAMIZU, K. SHIRASAWA, S. ISOBE, T. KANEKO, et al. 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635-641.
147. SCHLUETER, J. A., P. DIXON, C. GRANGER, D. GRANT, L. CLARK, J. J. DOYLE, and R. C. SHOEMAKER. 2004. Mining EST databases to resolve evolutionary events in major crop species. Genome 47: 868-876.
148. SCHMUTZ, J., S. B. CANNON, J. SCHLUETER, J. MA, T. MITROS, W. NELSON, D. L. HYTEN, et al. 2010. Genome sequence of the palaeopolyploid soybean. Nature 463: 178-183.
149. SCHNABLE, J. C., N. M. SPRINGER, and M. FREELING. 2011. Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proceedings of the National Academy of Sciences, USA 108: 4069-4074.
150. SHEN, G., W. ZHAN, H. CHEN, and Y. XING. 2014. Dominance and epistasis are the main contributors to heterosis for plant height in rice. Plant Science 215-216: 11-18.
151. SHIRASU, K., A. H. SCHULMAN, T. LAHAYE, and P. Schulze-Lefert. 2000. A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Research 10: 908-915.
152. SIERRO, N., J. N. D. BATTEY, S. OUADI, L. BOVET, S. GOEPFERT, N. BAKAHER, M. C. PEITSCH, and N. V. IVANOV. 2013. Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis. Genome Biology 14: R60.
153. SKALICKA, K., K. Y. LIM, R. MATYASEK, B. KOUKALOVA, A. R. LEITCH, and A. KOVARIK. 2003. Rapid evolution of parental rDNA in a synthetic tobacco allotetraploid line. American Journal of Botany 90: 988-996.
154. SOLTIS, D. E., V. A. ALBERT, J. Leebens-Mack, C. D. BELL, A. H. PATERSON, C. F. ZHENG, D. SANKOFF, et al. 2009. Polyploidy and angiosperm diversification. American Journal of Botany 96: 336-348.
155. SONG, K. M., P. LU, K. L. TANG, and T. C. OSBORN. 1995. Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proceedings of the National Academy of Sciences, USA 92: 7719-7723.
156. SPRINGER, N. M. 2013. Epigenetics and crop improvement. Trends in Genetics 29: 241-247.
157. STEBBINS, G. L. 1950. Variation and evolution in plants. Columbia, New York, New York, USA.
158. STEBBINS, G. L. 1971. Chromosome evolution in higher plants. AddisonWesley Press, London, UK.
159. STEPHENS, S. G. 1951a. “Homologous” genetic loci in Gossypium. Cold Spring Harbor Symposia on Quantitative Biology 16: 131-141.
160. STEPHENS, S. G. 1951b. Possible significance of duplication in evolution. Advances in Genetics 4: 247-265.
161. Swanson-Wagner, R., R. BRISKINE, R. SCHAEFER, M. B. HUFFORD, J. Ross-Ibarra, C. L. MYERS, P. TIFFIN, and N. M. SPRINGER. 2012. Reshaping of the maize transcriptome by domestication. Proceedings of the National Academy of Sciences, USA 109: 11878-11883.
162. SZADKOWSKI, E., F. EBER, V. HUTEAU, M. LODE, C. HUNEAU, H. BELCRAM, O. CORITON, et al. 2010. The first meiosis of resynthesized Brassica napus, a genome blender. New Phytologist 186: 102-112.
163. TANG, H., J. E. BOWERS, X. WANG, and A. H. PATERSON. 2010. Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proceedings of the National Academy of Sciences, USA 107: 472-477.
164. TANG, H., M. R. WOODHOUSE, F. CHENG, J. C. SCHNABLE, B. S. PEDERSEN, G. CONANT, X. WANG, et al. 2012. Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy. Genetics 190: 1563-1574.
165. THOMAS, B. C., B. PEDERSEN, and M. FREELING. 2006. Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Research 16: 934-946.
166. TIAN, F., P. J. BRADBURY, P. J. BROWN, H. HUNG, Q. SUN, S. Flint-Garcia, T. R. ROCHEFORD, et al. 2011. Genome-wide association study of leaf architecture in the maize nested association mapping population. Nature Genetics 43: 159-162.
167. TRICK, M., N. M. ADAMSKI, S. G. MUGFORD, C.-C. JIANG, M. FEBRER, and C. UAUY. 2012. Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat. BMC Plant Biology 12: 14.
168. TRICK, M., Y. LONG, J. MENG, and I. BANCROFT. 2009. Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. Plant Biotechnology Journal 7: 334-346.
169. UDDIN, M. N., F. W. ELLISON, L. OBRIEN, and B. D. H. LATTER. 1992. Heterosis in F1 hybrids derived from crosses of adapted Australian wheats. Australian Journal of Agricultural Research 43: 907-919.
170. VAN HEERWAARDEN, J., M. B. HUFFORD, and J. Ross-Ibarra. 2012. Historical genomics of North American maize. Proceedings of the National Academy of Sciences, USA 109: 12420-12425.
171. VELASCO, R., A. ZHARKIKH, J. AFFOURTIT, A. DHINGRA, A. CESTARO, A. KALYANARAMAN, P. FONTANA, et al. 2010. The genome of the domesticated apple (Malus × domestica Borkh.). Nature Genetics 42: 833-839.
172. VITTE, C., and O. PANAUD. 2003. Formation of solo-LTRs through unequal homologous recombination counterbalances amplifications of LTR retrotransposons in rice Oryza sativa L. Molecular Biology and Evolution 20: 528-540.
173. VOLKOV, R. A., N. V. BORISJUK, I. I. PANCHUK, D. SCHWEIZER, and V. HEMLEBEN. 1999. Elimination and rearrangement of parental rDNA in the allotetraploid Nicotiana tabacum. Molecular Biology and Evolution 16: 311-320.
174. WANG, J. L., L. TIAN, A. MADLUNG, H. S. LEE, M. CHEN, J. J. LEE, B. WATSON, et al. 2004. Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics 167: 1961-1973.
175. WANG, X., H. WANG, J. WANG, R. SUN, J. WU, S. LIU, Y. BAI, et al. 2011. The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics 43: 1035-1039.
176. WANG, Y., X. WANG, and A. H. PATERSON. 2012. Genome and gene duplications and gene expression divergence: A view from plants. Year in Evolutionary Biology 1256: 1-14.
177. WEI, F., E. COE, W. NELSON, A. K. BHARTI, F. ENGLER, E. BUTLER, H. KIM, et al. 2007. Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLOS Genetics 3: e123.
178. WENDEL, J., and J. DOYLE. 2005. Polyploidy and evolution in plants. CABI publishing, Wallingford, UK.
179. WENDEL, J. F., and R. C. CRONN. 2003. Polyploidy and the evolutionary history of cotton. In D. L. Sparks [ed.], Advances in agronomy, vol. 78, 139-186.
180. WENDEL, J. F., A. SCHNABEL, and T. SEELANAN. 1995. Bidirectioanl interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proceedings of the National Academy of Sciences, USA 92: 280-284.
181. WOLFE, K. H. 2001. Yesterday's polyploids and the mystery of diploidization. Nature Reviews. Genetics 2: 333-341.
182. WOODHOUSE, M. R., J. C. SCHNABLE, B. S. PEDERSEN, E. LYONS, D. LISCH, S. SUBRAMANIAM, and M. FREELING. 2010. Following Tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homeologs. PLoS Biology 8: e1000409.
183. XIONG, Z., R. T. GAETA, and J. C. PIRES. 2011. Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus. Proceedings of the National Academy of Sciences, USA 108: 7908-7913.
184. XU, X., X. LIU, S. GE, J. D. JENSEN, F. HU, X. LI, Y. DONG, et al. 2012. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnology 30: 105-U157.
185. XU, X., S. PAN, S. CHENG, B. ZHANG, D. MU, P. NI, G. ZHANG, et al. 2011. Genome sequence and analysis of the tuber crop potato. Nature 475: 189-195.
186. XU, Y., L. ZHONG, X. WU, X. FANG, and J. WANG. 2009. Rapid alterations of gene expression and cytosine methylation in newly synthesized Brassica napus allopolyploids. Planta 229: 471-483.
187. YANG, S. S., F. CHEUNG, J. J. LEE, M. HA, N. E. WEI, S.-H. SZE, D. M. STELLY, et al. 2006. Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton. Plant Journal 47: 761-775.
188. YOO, M. J., E. SZADKOWSKI, and J. F. WENDEL. 2013. Homoeolog expression bias and expression level dominance in allopolyploid cotton. Heredity 110: 171-180.
189. YOO, M.-J., and J. F. WENDEL. 2014. Comparative Evolutionary and Developmental Dynamics of the Cotton (Gossypium hirsutum) Fiber Transcriptome. PLOS Genetics 10: e1004073.
190. YU, S. B., J. X. LI, Y. F. TAN, Y. J. GAO, X. H. LI, Q. F. ZHANG, and M. A. S. MAROOF. 1997. Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid. Proceedings of the National Academy of Sciences, USA 94: 9226-9231.
191. ZEVEN, A. C., and P. M. ZHUKOVSKY. 1975. Dictionary of cultivated plants and their centres of diversity, Excluding ornamentals, forest trees and lower plants. Centre for Agricultural Publishing and Documentation, Wageningen. Netherlands
192. ZHANG, H., Y. BIAN, X. GOU, Y. DONG, S. RUSTGI, B. ZHANG, C. XU, et al. 2013a. Intrinsic karyotype stability and gene copy number variations may have laid the foundation for tetraploid wheat formation. Proceedings of the National Academy of Sciences, USA 110: 19466–19471.
193. ZHANG, H., Y. BIAN, X. GOU, B. ZHU, C. XU, B. QI, N. LI, et al. 2013b. Persistent whole-chromosome aneuploidy is generally associated with nascent allohexaploid wheat. Proceedings of the National Academy of Sciences, USA 110: 3447-3452.
194. ZHANG, Y.-Y., M. FISCHER, V. COLOT, and O. BOSSDORF. 2013c. Epigenetic variation creates potential for evolution of plant phenotypic plasticity. New Phytologist 197: 314-322.
195. ZHANG, Z., H. BELCRAM, P. GORNICKI, M. CHARLES, J. JUST, C. HUNEAU, G. MAGDELENAT, et al. 2011. Duplication and partitioning in evolution and function of homoeologous Q loci governing domestication characters in polyploid wheat. Proceedings of the National Academy of Sciences, USA 108: 18737-18742.
196. ZHAO, K., C.-W. TUNG, G. C. EIZENGA, M. H. WRIGHT, M. L. ALI, A. H. PRICE, G. J. NORTON, et al. 2011. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nature Communications 2: 467.