Phenotypic and epigenetic changes occurred during the autopolyploidization of &lt;i&gt;Aegilops tauschii&lt;/i&gt;

Zeng, Zhidong; Zhang, T.; Li, G. R.; Liu, C.; Yang, Zujun

doi:10.1556/crc.2012.0014

Cited by 3 publications

(3 citation statements)

References 34 publications

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“…In this study, we used synthetic isogenic autotetraploid watermelon and its diploid counterpart to elucidate the immediate effect of genome doubling on the phenotype and transcriptional regulation in watermelon. Results exemplified the advantages of polyploids at the phenotypic level, as has been repeatedly observed in several crop species (Stupar et al , 2007; Yan et al , 2019; Zeng et al , 2012; Zhang et al , 2015).…”

Section: Discussionsupporting

confidence: 77%

Altered chromatin conformation and transcriptional regulation in watermelon following genome doubling

et al. 2021

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Polyploidy has played a crucial role in plant evolution, development and function. Synthetic autopolyploid represents an ideal system to investigate the effects of polyploidization on transcriptional regulation. In this study, we deciphered the impact of genome duplication at phenotypic and molecular levels in watermelon. Overall, 88% of the genes in tetraploid watermelon followed a >1:1 dosage effect, and accordingly, differentially expressed genes were largely upregulated. In addition, a great number of hypomethylated regions (1688) were identified in an isogenic tetraploid watermelon. These differentially methylated regions were localized in promoters and intergenic regions and near transcriptional start sites of the identified upregulated genes, which enhances the importance of methylation in gene regulation. These changes were reflected in sophisticated higher-order chromatin structures. The genome doubling caused switching of 108 A and 626 B compartments that harbored genes associated with growth, development and stress responses.

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Section: Discussionsupporting

confidence: 77%

Altered chromatin conformation and transcriptional regulation in watermelon following genome doubling

et al. 2021

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“…Genetic modifications can include gene loss, genome down-sizing, variable mutation rates of the duplicated genes (homeologs), chromosomal rearrangements and regulatory incompatibilities resulting from post-transcriptional modifications in the merged genomes [ 16 – 24 ]. Epigenetic modifications involve heritable changes in gene expression without changes in the nucleotide sequence [ 25 – 27 ] and can include histone modification, DNA methylation, chromatin remodeling, or microRNA or prion activity [ 28 – 30 ]. DNA methylation, the addition of a methyl group at position 5 of the pyrimidine ring of cytosine, is a common mechanism associated with gene silencing in polyploids [ 31 – 33 ].…”

Section: Introductionmentioning

confidence: 99%

Gene silencing via DNA methylation in naturally occurring Tragopogon miscellus (Asteraceae) allopolyploids

et al. 2014

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BackgroundHybridization coupled with whole-genome duplication (allopolyploidy) leads to a variety of genetic and epigenetic modifications in the resultant merged genomes. In particular, gene loss and gene silencing are commonly observed post-polyploidization. Here, we investigated DNA methylation as a potential mechanism for gene silencing in Tragopogon miscellus (Asteraceae), a recent and recurrently formed allopolyploid. This species, which also exhibits extensive gene loss, was formed from the diploids T. dubius and T. pratensis.ResultsComparative bisulfite sequencing revealed CG methylation of parental homeologs for three loci (S2, S18 and TDF-44) that were previously identified as silenced in T. miscellus individuals relative to the diploid progenitors. One other locus (S3) examined did not show methylation, indicating that other transcriptional and post-transcriptional mechanisms are likely responsible for silencing that homeologous locus.ConclusionsThese results indicate that Tragopogon miscellus allopolyploids employ diverse mechanisms, including DNA methylation, to respond to the potential shock of genome merger and doubling.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-701) contains supplementary material, which is available to authorized users.

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“…In contrast, DNA methylation changes as direct responses to autopolyploidization have rarely been reported (39)(40)(41).…”

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Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression

Zhang

Liu

Xia

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

147

149

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Polyploidy, or whole-genome duplication (WGD), serves as a key innovation in plant evolution and is an important genomic feature for all eukaryotes. Neopolyploids have to overcome difficulties in meiosis, genomic alterations, changes of gene expression, and epigenomic reorganization. However, the underlying mechanisms for these processes are poorly understood. One of the most interesting aspects is that genome doubling events increase the dosage of all genes. Unlike allopolyploids entangled by both hybridization and polyploidization, autopolyploids, especially artificial lines, in relatively uniform genetic background offer a model system to understand mechanisms of genome-dosage effects. To investigate DNA methylation effects in response to WGD rather than hybridization, we produced autotetraploid rice with its diploid donor, Oryza sativa ssp. indica cv. Aijiaonante, both of which were independently self-pollinated over 48 generations, and generated and compared their comprehensive transcriptomes, base pair-resolution methylomes, and siRNAomes. DNA methylation variation of transposable elements (TEs) was observed as widespread in autotetraploid rice, in which hypermethylation of class II DNA transposons was predominantly noted in CHG and CHH contexts. This was accompanied by changes of 24-nt siRNA abundance, indicating the role of the RNA-directed DNA methylation pathway. Our results showed that the increased methylation state of class II TEs may suppress the expression of neighboring genes in autotetraploid rice that has obtained double alleles, leading to no significant differences in transcriptome alterations for most genes from its diploid donor. Collectively, our findings suggest that chromosome doubling induces methylation variation in TEs that affect gene expression and may become a "genome shock" response factor to help neoautopolyploids adapt to genome-dosage effects.methylome | autotetraploid rice | gene expression | genome-dosage effect | transposable elements P olyploidy or whole-genome duplication (WGD), when two or more complete sets of chromosomes co-occur in a nucleus (1), has played a pervasive role in plant evolution (2-4). Notably, all angiosperms have experienced at least one WGD event during their evolutionary history (5, 6). In general, two major categories of polyploidy exist in plants. Autopolyploidy species carry multiple similar chromosome sets, and allopolyploidy species integrate divergent chromosome sets (2, 3). Allopolyploidy is thought to have played a significant role in plant diversification and remains an important speciation process (5, 7). However, increasing evidence indicates that the real appearance of autotetraploid plants in nature might be significantly underestimated (8, 9), despite potential weaknesses, such as meiotic instability and reduced fertility (10).WGD produced by polyploidization creates a vastly increased genetic reservoir and combinatorial complexity upon which selection might act over an extended period, ultimately prompting polyploids to be successful in...

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Phenotypic and epigenetic changes occurred during the autopolyploidization of <i>Aegilops tauschii</i>

Cited by 3 publications

References 34 publications

Altered chromatin conformation and transcriptional regulation in watermelon following genome doubling

Altered chromatin conformation and transcriptional regulation in watermelon following genome doubling

Gene silencing via DNA methylation in naturally occurring Tragopogon miscellus (Asteraceae) allopolyploids

Autotetraploid rice methylome analysis reveals methylation variation of transposable elements and their effects on gene expression

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