Origins – somatic chromosome doubling vs. 2n gametes

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References for Polyploidy (incomplete – but a start)

Origins – somatic chromosome doubling vs. 2n gametes

*Harlan, J. R. and J. M. J. deWet. 1975. On Ö. Winge and a prayer: the origins of polyploidy. The Botanical Review 41: 361-390.

Bretagnolle, F. and J. D. Thompson. 1995. Tansley review no. 78 - gametes with the somatic chromosome number: mechanisms of their formation and role in the evolution of autopolyploid plants. New Phytologist 129: 1-22.

Carputo, D., L. Frusciante and S. J. Peloquin. 2003. The role of 2n gametes and endosperm balance number in the origin and evolution of polyploids in the tuber-bearing solanums. Genetics 163: 287-294.

Mendiburu, A. O. and S. J. Peloquin. 1976. Sexual polyploidization and depolyploidization: some terminology and definitions. Theoretical and Applied Genetics 48: 137-143.

Watanabe, K. and S. J. Peloquin. 1991. Genetic significance of mode of polyploidization: somatic doubling or 2n gametes? Genome 34: 28-34.

De Haan, A., N. O. Maceira, R. Lumaret and J. Delay. 1992. Production of 2n Gametes in Diploid Subspecies of Dactylis glomerata L 2. Occurrence and Frequency of 2n Eggs. Annals of Botany 69: 345-350.

Classical cytogenetics

Jackson, R. C. and J. Casey. 1980. Cytogenetics of polyploids. In W. H. Lewis (ed) Polyploidy - Biological Relevance. Plenum Press, New York, pp. 17-44.

Jackson, R. C. and J. Casey. 1982. Cytogenetic analyses of autopolyploids: models and methods for triploids to octoploids. American Journal of Botany 69: 487-501.

Expectations for phylogeny and complications

*Wendel, J. F. 2000. Genome evolution in polyploids. Plant Molecular Biology 42: 225-249.

Rieseberg, L. H. 2001. Polyploid evolution: Keeping the peace at genomic reunions. Current Biology 11: R925-R928.

Cronn, R. and J. F. Wendel. 2004. Cryptic trysts, genomic mergers, and plant speciation. New Phytologist 161: 133-142.

Ferguson, D. and T. Sang. 2001. Speciation through homoploid hybridization between allotetraploids in peonies (Paeonia). Proceedings of the National Academy of Sciences of the United States of America 98: 3915-3919.

Mason-Gamer, R. J. 2004. Reticulate evolution, introgression, and intertribal gene capture in an allohexaploid grass. Systematic Biology 53: 25-37.

Combining data from chloroplast and nuclear genomes

Wendel, J. F. 1989. New World tetraploid cottons contain Old World cytoplasm. Proceedings of the National Academy of Sciences of the United States of America 86: 4132-4136.

Soltis, D. E. and P. S. Soltis. 1989. Allopolyploid speciation in Tragopogon: insights from chloroplast DNA. American Journal of Botany 76: 1119-1124.

Soltis, D. E. and P. S. Soltis. 1990. Chloroplast DNA and nuclear rDNA variation: insights into autopolyploid and allopolyploid evolution. In S. Kawano (ed) Biological Approaches and Evolutionary Trends in Plants. Academic Press, San Diego, pp. 97-117.

Doyle, J. J., J. L. Doyle and A. H. D. Brown. 1990. Analysis of a polyploid complex in Glycine with chloroplast and nuclear DNA. Australian Systematic Botany 3: 125-136.

Doyle, J. J., J. L. Doyle and A. H. D. Brown. 1990. Chloroplast DNA Polymorphism and Phylogeny in the B-Genome of Glycine Subgenus Glycine (Leguminosae). American Journal of Botany 77: 772-782.

Potter, D., J. J. Luby and R. E. Harrison. 2000. Phylogenetic relationships among species of Fragaria (Rosaceae) inferred from non-coding nuclear and chloroplast DNA sequences. Systematic Botany 25: 337-348.

Multiple origins

Soltis, D. E. and P. S. Soltis. 1993. Molecular data and the dynamic nature of polyploidy. Critical Reviews in Plant Sciences 12: 243-273.

Soltis, D. E. and P. S. Soltis. 1999. Polyploidy: recurrent formation and genome evolution. Trends in Ecology and Evolution 14: 348-352.

Segraves, K. A., J. N. Thompson, P. S. Soltis and D. E. Soltis. 1999. Multiple origins of polyploidy and the geographic structure of Heuchera grossulariifolia. Molecular Ecology 8: 253-262.

Doyle, J. J., J. L. Doyle, A. H. D. Brown and J. P. Grace. 1990. Multiple Origins of Polyploids in the Glycine tabacina Complex Inferred From Chloroplast DNA Polymorphism. Proceedings of the National Academy of Sciences of the United States of America 87: 714-717.

Rauscher, J. T., J. J. Doyle and A. H. D. Brown. 2004. Multiple origins and nrDNA internal transcribed spacer homeologue evolution in the Glycine tomentella (Leguminosae) allopolyploid complex. Genetics 166: 987-998.

Doyle, J. J., J. L. Doyle, A. H. D. Brown and R. G. Palmer. 2002. Genomes, multiple origins, and lineage recombination in the Glycine tomentella (Leguminosae) polyploid complex: Histone H3- D gene sequences. Evolution 56: 1388-1402.

Vogel, J. C., J. A. Barrett, F. J. Rumsey and M. Gibbey. 1999. Identifying multiple origins in polyploid homosporous pteridophytes. In P. M. Hollingsworth, R. M. Bateman and R. J. Gornall (eds), Molecular Systematics and Plant Evolution, pp. 101-107. Taylor and Francis, London.

Pires, J.C., K.Y. Lim, A. Kovarik, R. Maytasek, A. Boyd, A. Leitch, I. Leitch, M. Bennett, P.S. Soltis, and D.E. Soltis, 2004. Molecular analysis of recently evolved Tragopogon (Asteraceae) allopolyploids reveal a karyotype that is additive of the diploid progenitors. American Jouranl of Botany 91: 1022-1035.

Soltis, D.E., P.S. Soltis, J.C. Pires, A. Kovarik, J. Tate, and E. Madrodiev. 2004. Recent and recurrent polyploidy in Tragopogon (Asteraceae): cytogenetic, genomic, and genetic comparisons. Biol. J. Linn. Soc. 82:485-501.

Paleopolyploids & neopolyploids

Soltis, P. S. 2005. Ancient and recent polyploidy in angiosperms. New Phytologist 166: 5-8.

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 of the United States of America 101: 9903-9908.

Gaut, B. S., M. Le Thierry d'Ennequin, A. S. Peek and M. C. Sawkins. 2000. Maize as a Model for the Evolution of Plant Nuclear Genomes. Proceedings of the National Academy of Sciences of the United States of America 97: 7008-7015.

Evolution of duplicated loci

Small, R. L. and J. F. Wendel. 2002. Differential Evolutionary Dynamics of Duplicated Paralogous Adh Loci in Allotetraploid Cotton (Gossypium). Mol Biol Evol 19: 597-607.

Brubaker, C. L., A. Paterson and J. F. Wendel. 1996. Evolution of homoeologous chromosomes in polyploids: Evidence from comparative mapping of allopolyploid and diploid Gossypium. American Journal of Botany 83: 93.

Cronn, R. C., R. L. Small and J. F. Wendel. 1999. Duplicated genes evolve independently after polyploid formation in cotton. Proceedings of the National Academy of Sciences of the United States of America 96: 14406-14411.

Osborn, T. C., D. V. Butrulle, A. G. Sharpe, K. J. Pickering, I. A. P. Parkin, J. S. Parker and D. J. Lydiate. 2003. Detection and effects of a homeologous reciprocal transposition in Brassica napus. Genetics 165: 1569-1577.

Chromosome pairing in polyploids

Sanchez-Moran, E., E. Benavente and J. Orellana. 2001. Analysis of karyotypic stability of homoeologous-pairing (ph) mutants in allopolyploid wheats. Chromosoma 110: 371-377.

Benavente, E. and J. Orellana. 1991. Chromosome Differentiation and Pairing Behavior of Polyploids - an Assessment On Preferential Metaphase-I Associations in Colchicine-Induced Autotetraploid Hybrids Within the Genus Secale. Genetics 128: 433-442.

Cao, D. C., T. C. Osborn and R. W. Doerge. 2004. Correct estimation of preferential chromosome pairing in autotetraploids. Genome Research 14: 459-462.

Feldman, M. 1993. Cytogenetic activity and mode of action of the pairing homoeologous (Ph1) gene of wheat. Crop Science 33: 894-897.

Vega, J. M., S. Abbo, M. Feldman and A. A. Levy. 1994. Chromosome Painting in Plants - in-Situ Hybridization With a DNA Probe From a Specific Microdissected Chromosome Arm of Common Wheat. Proceedings of the National Academy of Sciences of the United States of America 91: 12041-12045.

Vega, J. M. and M. Feldman. 1998. Effect of the pairing gene Ph1 and premeiotic colchicine treatment on intra- and interchromosome pairing of isochromosomes in common wheat. Genetics 150: 1199-1208.

Rapid changes following polyploid formation

Liu, B. and J. F. Wendel. 2003. Epigenetic phenomena and the evolution of plant allopolyploids. Molecular Phylogenetics and Evolution 29: 365-379.

Pikaard, C. S. 2001. Genomic change and gene silencing in polyploids. Trends in Genetics 17: 675-677.

Eckardt, N. A. 2001. A Sense of Self: The Role of DNA Sequence Elimination in Allopolyploidization. Plant Cell 13: 1699-1704.

Pires, J. C., J. W. Zhao, M. E. Schranz, E. J. Leon, P. A. Quijada, L. N. Lukens and T. C. Osborn. 2004. Flowering time divergence and genomic rearrangements in resynthesized Brassica polyploids (Brassicaceae). Biological Journal of the Linnean Society 82: 675-688.

Shaked, H., K. Kashkush, H. Ozkan, M. Feldman and A. A. Levy. 2001. Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13: 1749-59.

Kashkush, K., M. Feldman and A. A. Levy. 2002. Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics 160: 1651-1659.

Liu, B., C. L. Brubaker, G. Mergeai, R. C. Cronn and J. F. Wendel. 2001. Polyploid formation in cotton is not accompanied by rapid genomic changes. Genome 44: 321-330.

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: 535-42.

Liu, B., J. M. Vega, G. Segal, S. Abbo, H. Rodova and M. Feldman. 1998. Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. I. Changes in low-copy noncoding DNA sequences. Genome 41: 272-277.

Song, K., P. Lu, K. 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 of the United States of America 92: 7719-7723.

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.

Ozkan, H., M. Tuna and K. Arumuganathan. 2003. Nonadditive Changes in Genome Size During Allopolyploidization in the Wheat (Aegilops-Triticum) Group. J Hered 94: 260-264.

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: 311-20.

Wang, X. Y., X. L. Shi, B. L. Hao, S. Ge and J. C. Luo. 2005. Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytologist 165: 937-946.

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 of the United States of America 100: 4649-4654.

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.

Concerted evolution across homeologous ribosomal loci

Wendel, J. F., A. Schnabel and T. Seelanan. 1995. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proceedings of the National Academy of Sciences of the United States of America 92: 280-4.

PCR recombination caveats

Cronn, R., M. Cedroni, T. Haselkorn, C. Grover and J. F. Wendel. 2002. PCR-mediated recombination in amplification products derived from polyploid cotton. Theoretical and Applied Genetics 104: 482-489.

Polyploidy and domesticates

Paterson, A. H. 2005. Polyploidy, evolutionary opportunity, and crop adaptation. Genetica 123: 191-196.

Hilu, K. W. 1993. Polyploidy and the Evolution of Domesticated Plants. American Journal of Botany 80: 1494-1499.

Wendel, J. F. and R. C. Cronn. 2003. Polyploidy and the evolutionary history of cotton. Advances in Agronomy, Vol 78, pp. 139-186.

Adams, K. L. and J. F. Wendel. 2004. Exploring the genomic mysteries of polyploidy in cotton. Biological Journal of the Linnean Society 82: 573-581.

Osborn, T. C. 2004. The contribution of polyploidy to variation in Brassica species. Physiologia Plantarum 121: 531-536.

Ingram, A. L. and J. J. Doyle. 2003. The origin and evolution of Eragrostis tef (Poaceae) and related polyploids: evidence from nuclear waxy and plastid rps16. American Journal of Botany 90: 116-122.

Emshwiller, E. and J. J. Doyle. 2002. Origins of domestication and polyploidy in oca (Oxalis tuberosa: Oxalidaceae). 2. Chloroplast-expressed glutamine synthetase data. American Journal of Botany 89: 1042-1056.

Atkinson, R. G., G. Cipriani, D. J. Whittaker and R. C. Gardner. 1997. The allopolyploid origin of kiwifruit, Actinidia deliciosa (Actinidiaceae). Plant Systematics and Evolution 205: 111-124.

Galili, S., Y. Avivi, E. Millet and M. Feldman. 2000. RFLP-based analysis of three RbcS subfamilies in diploid and polyploid species of wheat. Molecular and General Genetics 263: 674-680.

Gene expression

Song, K. and C. Osborn Thomas. 1994. A method for examining expression of homologous genes in plant polyploids. Plant Molecular Biology 26: 1065-1071.

Adams, K. L. and J. F. Wendel. 2005. Novel patterns of gene expression in polyploid plants. Trends in Genetics 21: 539-543.

Mapping QTLs in polyploids

Ming, R., Y. W. Wang, X. Draye, P. H. Moore, J. E. Irvine and A. H. Paterson. 2002. Molecular dissection of complex traits in autopolyploids: mapping QTLs affecting sugar yield and related traits in sugarcane. Theoretical and Applied Genetics 105: 332-345.

Transposons in polyploids

Hanson, R. E., M. N. Islam-Faridi, C. F. Crane, M. S. Zwick, D. G. Czeschin, J. F. Wendel, T. D. McKnight, H. J. Price and D. M. Stelly. 2000. Ty1-copia-retrotransposon behavior in a polyploid cotton. Chromosome Research 8: 73-76.

Vanderwiel, P. L., D. F. Voytas and J. F. Wendel. 1993. Copia-Like Retrotransposable Element Evolution in Diploid and Polyploid Cotton (Gossypium L). Journal of Molecular Evolution 36: 429-447.

Response to selection

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 of the United States of America 95: 4419-4424.

Cytotype exclusion

Husband, B. C. 2000. Constraints on polyploid evolution: A test of the minority cytotype exclusion principle. Proceedings of the Royal Society Biological Sciences Series B 267: 217-223.

Zeven, A. C. 1980. Polyploidy and plant domestication: the origin and survival of polyploids in cytotype mixtures. In W. H. Lewis (ed) Polyploidy - Biological Relevance, pp. 385-407. Plenum Press, New York.

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