Genomic and expression plasticity of polyploidy.

Polyploidy or whole genome duplication (WGD) occurs throughout the evolutionary history of many plants and some animals, including crops such as wheat, cotton, and sugarcane. Recent studies have documented rapid and dynamic changes in genomic structure and gene expression in plant polyploids, which reflects genomic and functional plasticity of duplicate genes and genomes in plants. Common features of uniparental gene regulation and nonadditive gene expression in regulatory pathways responsive to growth, development, and stresses in many polyploids have led to the conclusion that epigenetic mechanisms including chromatin modifications and small RNAs play central roles in shaping molecular and phenotypic novelty that may be selected and domesticated in many polyploid plants and crops.

[1]  Jun Wang,et al.  Analysis of 142 genes resolves the rapid diversification of the rice genus , 2008, Genome Biology.

[2]  M. A. Koch,et al.  Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). , 2000, Molecular biology and evolution.

[3]  R. Haselkorn,et al.  Acc homoeoloci and the evolution of wheat genomes , 2008, Proceedings of the National Academy of Sciences.

[4]  Z. Chen,et al.  Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. , 2007, Annual review of plant biology.

[5]  Z. Chen,et al.  Duplicate genes increase expression diversity in closely related species and allopolyploids , 2009, Proceedings of the National Academy of Sciences.

[6]  Inger Greve Alsos,et al.  Polyploidy in arctic plants , 2004 .

[7]  B. Gill,et al.  Nonadditive Expression of Homoeologous Genes Is Established Upon Polyploidization in Hexaploid Wheat , 2009, Genetics.

[8]  L. Flagel,et al.  Coordinated and fine-scale control of homoeologous gene expression in allotetraploid cotton. , 2009, The Journal of heredity.

[9]  D. Soltis,et al.  Evolution and Expression of Homeologous Loci in Tragopogon miscellus (Asteraceae), a Recent and Reciprocally Formed Allopolyploid , 2006, Genetics.

[10]  Z. Chen,et al.  Transcriptional analysis of nucleolar dominance in polyploid plants: biased expression/silencing of progenitor rRNA genes is developmentally regulated in Brassica. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[11]  Pamela S Soltis,et al.  The role of hybridization in plant speciation. , 2009, Annual review of plant biology.

[12]  S. Huet,et al.  PrBn, a major gene controlling homeologous pairing in oilseed rape (Brassica napus) haploids. , 2003, Genetics.

[13]  Brian C. Thomas,et al.  Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. , 2006, Genome research.

[14]  C. Pikaard.  Nucleolar dominance: uniparental gene silencing on a multi-megabase scale in genetic hybrids , 2000, Plant Molecular Biology.

[15]  Guillaume Blanc,et al.  Widespread Paleopolyploidy in Model Plant Species Inferred from Age Distributions of Duplicate Genes , 2004, The Plant Cell Online.

[16]  Lee Hs,et al.  Protein-coding genes are epigenetically regulated in Arabidopsis polyploids. , 2001 .

[17]  S. Lindquist,et al.  Hsp90 as a capacitor of phenotypic variation , 2002, Nature.

[18]  Jeroen Raes,et al.  Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana , 2006, Genome Biology.

[19]  J. Doyle,et al.  Testing the polyploid past of soybean using a low-copy nuclear gene--is Glycine (Fabaceae: Papilionoideae) an auto- or allopolyploid? , 2006, Molecular phylogenetics and evolution.

[20]  R W Doerge,et al.  Genomewide Nonadditive Gene Regulation in Arabidopsis Allotetraploids , 2006, Genetics.

[21]  Lex E. Flagel,et al.  Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution , 2008, BMC Biology.

[22]  Z. Jeffrey Chen,et al.  Stochastic and Epigenetic Changes of Gene Expression in Arabidopsis Polyploids , 2004, Genetics.

[23]  T. Nishio,et al.  Phylogenetic analysis of Brassiceae based on the nucleotide sequences of the S-locus related gene, SLR1 , 2002, Theoretical and Applied Genetics.

[24]  D. Baulcombe.  RNA silencing in plants , 2004, Nature.

[25]  Marta Matvienko,et al.  Multiple paleopolyploidizations during the evolution of the Compositae reveal parallel patterns of duplicate gene retention after millions of years. , 2008, Molecular biology and evolution.

[26]  Jonathan F. Wendel,et al.  Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[27]  Xiu-Jie Wang,et al.  Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids , 2009, Proceedings of the National Academy of Sciences.

[28]  A. Tyagi,et al.  Phenotypic Instability and Rapid Gene Silencing in Newly Formed Arabidopsis Allotetraploids , 2000, Plant Cell.

[29]  Jian-Min Zhou,et al.  Allopolyploidy alters gene expression in the highly stable hexaploid wheat , 2003, Plant Molecular Biology.

[30]  Jörg D. Becker,et al.  Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen , 2009, Cell.

[31]  Z. Chen,et al.  RNAi of met1 Reduces DNA Methylation and Induces Genome-Specific Changes in Gene Expression and Centromeric Small RNA Accumulation in Arabidopsis Allopolyploids , 2008, Genetics.

[32]  S. Sze,et al.  Accumulation of genome-specific transcripts, transcription factors and phytohormonal regulators during early stages of fiber cell development in allotetraploid cotton. , 2006, The Plant journal : for cell and molecular biology.

[33]  B. Mcclintock,et al.  The significance of responses of the genome to challenge. , 1984, Science.

[34]  Z. Chen,et al.  Nonadditive Regulation of FRI and FLC Loci Mediates Flowering-Time Variation in Arabidopsis Allopolyploids , 2006, Genetics.

[35]  Itay Mayrose,et al.  The frequency of polyploid speciation in vascular plants , 2009, Proceedings of the National Academy of Sciences.

[36]  J. Wendel,et al.  Polyploid formation in cotton is not accompanied by rapid genomic changes. , 2001, Genome.

[37]  Thierry Balliau,et al.  Differential regulation of gene products in newly synthesized Brassica napus allotetraploids is not related to protein function nor subcellular localization , 2007, BMC Genomics.

[38]  I. Colas,et al.  Molecular characterization of Ph1 as a major chromosome pairing locus in polyploid wheat , 2006, Nature.

[39]  Rex T. Nelson,et al.  Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing , 2007, BMC Genomics.

[40]  J. Pires,et al.  Genomic Changes in Resynthesized Brassica napus and Their Effect on Gene Expression and Phenotype[W][OA] , 2007, The Plant Cell Online.

[41]  G. Barker,et al.  Transcriptome Shock after Interspecific Hybridization in Senecio Is Ameliorated by Genome Duplication , 2006, Current Biology.

[42]  S. Bottani,et al.  Cellular reactions to gene dosage imbalance: genomic, transcriptomic and proteomic effects. , 2008, Trends in genetics : TIG.

[43]  S. Harmer,et al.  The circadian system in higher plants. , 2009, Annual review of plant biology.

[44]  B. Gaut,et al.  DNA sequence evidence for the segmental allotetraploid origin of maize. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[45]  Z. Chen,et al.  Altered circadian rhythms regulate growth vigor in hybrids and allopolyploids , 2008, Nature.

[46]  T. Mizuno,et al.  Comparative overviews of clock-associated genes of Arabidopsis thaliana and Oryza sativa. , 2007, Plant & cell physiology.

[47]  M. Lynch,et al.  The evolutionary fate and consequences of duplicate genes. , 2000, Science.

[48]  Luca Comai,et al.  The advantages and disadvantages of being polyploid , 2005, Nature Reviews Genetics.

[49]  Krystyna A. Kelly,et al.  Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis , 2009, Nature.

[50]  Michael W Young,et al.  Interplay of circadian clocks and metabolic rhythms. , 2006, Annual review of genetics.

[51]  P. Ozias‐Akins,et al.  Mendelian genetics of apomixis in plants. , 2007, Annual review of genetics.

[52]  Lex E. Flagel,et al.  Reciprocal Silencing, Transcriptional Bias and Functional Divergence of Homeologs in Polyploid Cotton (Gossypium) , 2009, Genetics.