Genetic Variation in Tragopogon Species: Additional Origins of the Allotetraploids T. mirus and T. miscellus (Compositae)

Soltis, Pamela S.; Plunkett, Gregory M.; Novak, Stephen J.; Soltis, Douglas E.

doi:10.2307/2446255

Cited by 68 publications

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“…Earlier allozyme studies also suggested that the three diploid progenitors were well differentiated genetically 16, 28. Likewise, comparisons of cDNA-AFLP genetic markers between the diploid species reveal that T. pratensis and T. dubius share only between 30-40% of markers [12], again suggesting considerable genomic divergence.…”

Section: Discussionmentioning

confidence: 88%

Rapid Chromosome Evolution in Recently Formed Polyploids in Tragopogon (Asteraceae)

et al. 2008

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BackgroundPolyploidy, frequently termed “whole genome duplication”, is a major force in the evolution of many eukaryotes. Indeed, most angiosperm species have undergone at least one round of polyploidy in their evolutionary history. Despite enormous progress in our understanding of many aspects of polyploidy, we essentially have no information about the role of chromosome divergence in the establishment of young polyploid populations. Here we investigate synthetic lines and natural populations of two recently and recurrently formed allotetraploids Tragopogon mirus and T. miscellus (formed within the past 80 years) to assess the role of aberrant meiosis in generating chromosomal/genomic diversity. That diversity is likely important in the formation, establishment and survival of polyploid populations and species.Methodology/Principal FindingsApplications of fluorescence in situ hybridisation (FISH) to natural populations of T. mirus and T. miscellus suggest that chromosomal rearrangements and other chromosomal changes are common in both allotetraploids. We detected extensive chromosomal polymorphism between individuals and populations, including (i) plants monosomic and trisomic for particular chromosomes (perhaps indicating compensatory trisomy), (ii) intergenomic translocations and (iii) variable sizes and expression patterns of individual ribosomal DNA (rDNA) loci. We even observed karyotypic variation among sibling plants. Significantly, translocations, chromosome loss, and meiotic irregularities, including quadrivalent formation, were observed in synthetic (S0 and S1 generations) polyploid lines. Our results not only provide a mechanism for chromosomal variation in natural populations, but also indicate that chromosomal changes occur rapidly following polyploidisation.Conclusions/SignificanceThese data shed new light on previous analyses of genome and transcriptome structures in de novo and establishing polyploid species. Crucially our results highlight the necessity of studying karyotypes in young (<150 years old) polyploid species and synthetic polyploids that resemble natural species. The data also provide insight into the mechanisms that perturb inheritance patterns of genetic markers in synthetic polyploids and populations of young natural polyploid species.

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Section: Discussionmentioning

confidence: 88%

Rapid Chromosome Evolution in Recently Formed Polyploids in Tragopogon (Asteraceae)

et al. 2008

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“…Furthermore, multivalents have also been observed in synthetic T. mirus and T. miscellus [88,106]. In addition, rare patterns observed in analysis of allozyme variation in Tragopogon are consistent with non-homologous recombination [84]. Non-homologous recombination could provide a mechanism of homeolog loss in T. mirus and T. miscellus , as in Brassica [55].…”

Section: Discussionmentioning

confidence: 99%

Homeolog loss and expression changes in natural populations of the recently and repeatedly formed allotetraploid Tragopogon mirus (Asteraceae)

Koh

Soltis

2010

BMC Genomics

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BackgroundAlthough polyploidy has long been recognized as a major force in the evolution of plants, most of what we know about the genetic consequences of polyploidy comes from the study of crops and model systems. Furthermore, although many polyploid species have formed repeatedly, patterns of genome evolution and gene expression are largely unknown for natural polyploid populations of independent origin. We therefore examined patterns of loss and expression in duplicate gene pairs (homeologs) in multiple individuals from seven natural populations of independent origin of Tragopogon mirus (Asteraceae), an allopolyploid that formed repeatedly within the last 80 years from the diploids T. dubius and T. porrifolius.ResultsUsing cDNA-AFLPs, we found differential band patterns that could be attributable to gene silencing, novel expression, and/or maternal/paternal effects between T. mirus and its diploid parents. Subsequent cleaved amplified polymorphic sequence (CAPS) analyses of genomic DNA and cDNA revealed that 20 of the 30 genes identified through cDNA-AFLP analysis showed additivity, whereas nine of the 30 exhibited the loss of one parental homeolog in at least one individual. Homeolog loss (versus loss of a restriction site) was confirmed via sequencing. The remaining gene (ADENINE-DNA GLYCOSYLASE) showed ambiguous patterns in T. mirus because of polymorphism in the diploid parent T. dubius. Most (63.6%) of the homeolog loss events were of the T. dubius parental copy. Two genes, NUCLEAR RIBOSOMAL DNA and GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, showed differential expression of the parental homeologs, with the T. dubius copy silenced in some individuals of T. mirus.ConclusionsGenomic and cDNA CAPS analyses indicated that plants representing multiple populations of this young natural allopolyploid have experienced frequent and preferential elimination of homeologous loci. Comparable analyses of synthetic F1 hybrids showed only additivity. These results suggest that loss of homeologs and changes in gene expression are not the immediate result of hybridization, but are processes that occur following polyploidization, occurring during the early (<40) generations of the young polyploid. Both T. mirus and a second recently formed allopolyploid, T. miscellus, exhibit more homeolog losses than gene silencing events. Furthermore, both allotetraploids undergo biased loss of homeologs contributed by their shared diploid parent, T. dubius. Further studies are required to assess whether the results for the 30 genes so far examined are representative of the entire genome.

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“…both homoeologues expressed), and 15% of assays showed silencing of a homoeologue that could have arisen since hybridization. However, 12% showed silencing of a homoeologue in all tissues of a plant, which is most likely to indicate loss of that homoeologue from the genome [28,29,[83][84][85]). This leaves 3% of assays that showed novel changes in the control of homoeologue expression subsequent to allopolyploidization.…”

Section: (A) Tragopogon Mirusmentioning

confidence: 99%

The legacy of diploid progenitors in allopolyploid gene expression patterns

Buggs

Wendel

Doyle

et al. 2014

Phil. Trans. R. Soc. B

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103

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Allopolyploidization (hybridization and whole-genome duplication) is a common phenomenon in plant evolution with immediate saltational effects on genome structure and gene expression. New technologies have allowed rapid progress over the past decade in our understanding of the consequences of allopolyploidy. A major question, raised by early pioneer of this field Leslie Gottlieb, concerned the extent to which gene expression differences among duplicate genes present in an allopolyploid are a legacy of expression differences that were already present in the progenitor diploid species. Addressing this question necessitates phylogenetically well-understood natural study systems, appropriate technology, availability of genomic resources and a suitable analytical framework, including a sufficiently detailed and generally accepted terminology. Here, we review these requirements and illustrate their application to a natural study system that Gottlieb worked on and recommended for this purpose: recent allopolyploids of Tragopogon (Asteraceae). We reanalyse recent data from this system within the conceptual framework of parental legacies on duplicate gene expression in allopolyploids. On a broader level, we highlight the intellectual connection between Gottlieb's phrasing of this issue and the more contemporary framework of cis- versus trans- regulation of duplicate gene expression in allopolyploid plants.

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Genetic Variation in Tragopogon Species: Additional Origins of the Allotetraploids T. mirus and T. miscellus (Compositae)

Cited by 68 publications

References 0 publications

Rapid Chromosome Evolution in Recently Formed Polyploids in Tragopogon (Asteraceae)

Rapid Chromosome Evolution in Recently Formed Polyploids in Tragopogon (Asteraceae)

Homeolog loss and expression changes in natural populations of the recently and repeatedly formed allotetraploid Tragopogon mirus (Asteraceae)

The legacy of diploid progenitors in allopolyploid gene expression patterns

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