Comparative proteomics of the recently and recurrently formed natural allopolyploid Tragopogon mirus (Asteraceae) and its parents

? We examined the proteomes of the recently formed natural allopolyploid Tragopogon mirus and its diploid parents (T.?dubius, T.?porrifolius), as well as a diploid F(1) hybrid and synthetic T.?mirus. ? Analyses using iTRAQ LC-MS/MS technology identified 476 proteins produced by all three species. Of these, 408 proteins showed quantitative additivity of the two parental profiles in T.?mirus (both natural and synthetic); 68 proteins were quantitatively differentially expressed. ? Comparison of F(1) hybrid, and synthetic and natural polyploid T.?mirus with the parental diploid species revealed 32 protein expression changes associated with hybridization, 22 with genome doubling and 14 that had occurred since the origin of T.?mirus c. 80?yr ago. We found six proteins with novel expression; this phenomenon appears to start in the F(1) hybrid and results from post-translational modifications. ? Our results indicate that the impact of hybridization on the proteome is more important than is polyploidization. Furthermore, two cases of homeolog-specific expression in T.?mirus suggest that silencing in T.?mirus was not associated with hybridization itself, but occurred subsequent to both hybridization and polyploidization. This study has shown the utility of proteomics in the analysis of the evolutionary consequences of polyploidy.     

Silenced rRNA genes are activated and substitute for partially eliminated active homeologs in the recently formed allotetraploid,Tragopogon mirus (Asteraceae)

To study the relationship between uniparental rDNA (encoding 18S, 5.8S and 26S ribosomal RNA) silencing (nucleolar dominance) and rRNA gene dosage, we studied a recently emerged (within the last 80 years) allotetraploid Tragopogon mirus (2n=24), formed from the diploid progenitors T. dubius (2n=12, D-genome donor) and T. porrifolius (2n=12, P-genome donor). Here, we used molecular, cytogenetic and genomic approaches to analyse rRNA gene activity in two sibling T. mirus plants (33A and 33B) with widely different rRNA gene dosages. Plant 33B had ~400 rRNA genes at the D-genome locus, which is typical for T. mirus, accounting for ~25% of total rDNA. We observed characteristic expression dominance of T. dubius-origin genes in all organs. Its sister plant 33A harboured a homozygous macrodeletion that reduced the number of T. dubius-origin genes to about 70 copies (~4% of total rDNA). It showed biparental rDNA expression in root, flower and callus, but not in leaf where D-genome rDNA dominance was maintained. There was upregulation of minor rDNA variants in some tissues. The RNA polymerase I promoters of reactivated T. porrifolius-origin rRNA genes showed reduced DNA methylation, mainly at symmetrical CG and CHG nucleotide motifs. We hypothesise that active, decondensed rDNA units are most likely to be deleted via recombination. The silenced homeologs could be used as a ‘first reserve'' to ameliorate mutational damage and contribute to evolutionary success of polyploids. Deletion and reactivation cycles may lead to bidirectional homogenisation of rRNA arrays in the long term.     

Patterns of chromosomal variation in natural populations of the neoallotetraploid Tragopogon mirus (Asteraceae)

Cytological studies have shown many newly formed allopolyploids (neoallopolyploids) exhibit chromosomal variation as a result of meiotic irregularities, but few naturally occurring neoallopolyploids have been examined. Little is known about how long chromosomal variation may persist and how it might influence the establishment and evolution of allopolyploids in nature. In this study we assess chromosomal composition in a natural neoallotetraploid, Tragopogon mirus, and compare it with T. miscellus, which is an allotetraploid of similar age (~40 generations old). We also assess whether parental gene losses in T. mirus correlate with entire or partial chromosome losses. Of 37 T. mirus individuals that were karyotyped, 23 (62%) were chromosomally additive of the parents, whereas the remaining 14 individuals (38%) had aneuploid compositions. The proportion of additive versus aneuploid individuals differed from that found previously in T. miscellus, in which aneuploidy was more common (69% Fisher''s exact test, P=0.0033). Deviations from parental chromosome additivity within T. mirus individuals also did not reach the levels observed in T. miscellus, but similar compensated changes were observed. The loss of T. dubius-derived genes in two T. mirus individuals did not correlate with any chromosomal changes, indicating a role for smaller-scale genetic alterations. Overall, these data for T. mirus provide a second example of prolonged chromosomal instability in natural neoallopolyploid populations.     

Synthetic polyploids of Tragopogon miscellus and T. mirus (Asteraceae): 60 Years after Ownbey's discovery

In plants, polyploidy has been a significant evolutionary force on both recent and ancient time scales. In 1950, Ownbey reported two newly formed Tragopogon allopolyploids in the northwestern United States. We have made the first synthetic lines of T. mirus and T. miscellus using T. dubius, T. porrifolius, and T. pratensis as parents and colchicine treatment of F(1) hybrids. We also produced allotetraploids between T. porrifolius and T. pratensis, which are not known from nature. We report on the crossability between the diploids, as well as the inflorescence morphology, pollen size, meiotic behavior, and fertility of the synthetic polyploids. Morphologically, the synthetics resemble the natural polyploids with short- and long-liguled forms of T. miscellus resulting when T. pratensis and T. dubius are reciprocally crossed. Synthetic T. mirus was also formed reciprocally, but without any obvious morphological differences resulting from the direction of the cross. Of the 27 original crosses that yielded 171 hybrid individuals, 18 of these lineages have persisted to produce 386 S(1) progeny; each of these lineages has produced S(2) seed that are viable. The successful generation of these synthetic polyploids offers the opportunity for detailed comparative studies of natural and synthetic polyploids within a nonmodel system.     

Molecular cytogenetic analysis of recently evolved Tragopogon (Asteraceae) allopolyploids reveal a karyotype that is additive of the diploid progenitors

Tragopogon mirus and T. miscellus (both 2n = 4x = 24) are recent allotetraploids derived from T. dubius × T. porrifolius and T. dubius × T. pratensis (each 2n = 2x = 12), respectively. The genome sizes of T. mirus are additive of those of its diploid parents, but at least some populations of T. miscellus have undergone genome downsizing. To survey for genomic rearrangements in the allopolyploids, four repetitive sequences were physically mapped. TPRMBO (unit size 160 base pairs [bp]) and TGP7 (532 bp) are tandemly organized satellite sequences isolated from T. pratensis and T. porrifolius, respectively. Fluorescent in situ hybridization to the diploids showed that TPRMBO is a predominantly centromeric repeat on all 12 chromosomes, while TGP7 is a subtelomeric sequence on most chromosome arms. The distribution of tandem repetitive DNA loci (TPRMBO, TGP7, 18S-5.8S-26S rDNA, and 5S rDNA) gave unique molecular karyotypes for the three diploid species, permitting the identification of the parental chromosomes in the polyploids. The location and number of these loci were inherited without apparent changes in the allotetraploids. There was no evidence for major genomic rearrangements in Tragopogon allopolyploids that have arisen multiple times in North America within the last 80 yr.     

Similar patterns of rDNA evolution in synthetic and recently formed natural populations of <Emphasis Type="Italic">Tragopogon</Emphasis>(Asteraceae) allotetraploids

Background  

Tragopogon mirus and T. miscellus are allotetraploids (2n = 24) that formed repeatedly during the past 80 years in eastern Washington and adjacent Idaho (USA) following the introduction of the diploids T. dubius, T. porrifolius, and T. pratensis (2n = 12) from Europe. In most natural populations of T. mirus and T. miscellus, there are far fewer 35S rRNA genes (rDNA) of T. dubius than there are of the other diploid parent (T. porrifolius or T. pratensis). We studied the inheritance of parental rDNA loci in allotetraploids resynthesized from diploid accessions. We investigate the dynamics and directionality of these rDNA losses, as well as the contribution of gene copy number variation in the parental diploids to rDNA variation in the derived tetraploids.     

Only seed size matters for germination in different populations of the dimorphic Tragopogon pratensis subsp. pratensis (Asteraceae)

Many studies have focused on the ecology of seed dimorphism, the production of two seed types by a single plant. Morphology and seed size are usually correlated, but how morphology affects germination percentage and seedling growth is poorly understood. Here we explicitly separate these effects for nine populations of the dimorphic species Tragopogon pratensis subsp. pratensis. Larger seeds yielded higher germination percentages, yet seed morphology had no additional direct effect on germination. Neither seed size nor seed morphology affected seedling growth. Neither germination nor seedling growth varied among populations, but seed head varied significantly. Results show that germination is mainly controlled by seed size rather than by seed morphology. This study is one of the few to distinguish explicitly between seed size and seed morphology effects on ecological characteristics and suggests that seed dimorphism may exert its ecological effects predominantly through its correlated size.     

Unreduced gametes and neopolyploids in natural populations of Achillea borealis (Asteraceae)

Polyploidy is a major mechanism of speciation and adaptation, yet little is known about the origins of polyploids in natural species. I investigated gametic nonreduction and neopolyploid formation in natural tetraploid populations of Achillea borealis (Asteraceae), an autopolyploid complex consisting of tetraploid and hexaploid cytotypes. Cytological analyses of tetraploid populations revealed the occurrence of reduced (n=2x) as well as unreduced 'big' (2n=4x) and 'jumbo' (4n=8x) pollen grains, which were clearly distinguished by size. Production of unreduced pollen was monitored in two tetraploid populations in 1997 and 1998. Mean population-level frequencies of unreduced pollen ranged from 0.030 to 0.538%, with as few as one-third and as many as one-half of sampled plants producing unreduced grains. Eight individuals were found to produce >1% unreduced pollen, with highest observed frequencies of 7.0, 13.2 and 15.8%. Experimental crosses using high unreduced pollen producers as male parents generated viable seeds. However, the frequency of neohexaploids in the progeny of experimental crosses (0.388%) was similar to that observed in progeny of randomly selected, open-pollinated control parents (0.465%). These results suggest that unreduced eggs are the most likely source of new polyploids. In spite of the inefficiency of unreduced pollen in unilateral sexual polyploidization, the overall rate of neohexaploid formation (one in 233) was several orders of magnitude greater than estimates of genic mutation rates.     

Multiple independent formations of Tragopogon tetraploids (Asteraceae): evidence from RAPD markers

Polyploidy is widely recognized as a significant force leading to the formation of new plant species. Estimates of the number of angiosperm species with polyploid origins are as high as ≈ 50%; however, in spite of this prevalence, many aspects of polyploid evolution remain poorly understood. Recent studies have suggested that recurrent origins of polyploid species are the rule rather than the exception. The present study is one of only a few designed to quantify the number of independent origins of a polyploid species. The two tetraploid species Tragopogon mirus and T. miscellus (Asteraceae) arose within the past 50 years in the Palouse region of eastern Washington and adjacent northern Idaho. Previous work using morphology, cpDNA and rDNA restriction site analyses, allozymes, cytology, and flavonoid chemistry established that T. mirus had arisen at least five times, and T. miscellus at least twice, on the Palouse. To assess the frequency of multiple origins of these species more rigorously, seven populations of T. mirus and three populations of T. miscellus that were indistinguishable based on previous markers were surveyed using random amplified polymorphic DNA (RAPD) markers; populations of the diploid progenitor species from the same sites were also analysed. Each tetraploid population had a unique RAPD marker profile, suggesting that each population surveyed originated independently of the other populations in the region. Only two of the tetraploid populations combined the RAPD marker profiles of the diploid progenitors occurring at the same site. Both polyploid species, whose ranges and numbers have greatly increased since their formation in the early part of the twentieth century, have formed repeatedly on a local geographical scale and during a short time frame. Furthermore, each tetraploid species is spreading not primarily by dispersal of propagules from a single population of origin, but through repeated, independent polyploidization events that recreate the polyploid taxa.     

Biochemical properties and level of expression of alcohol dehydrogenases in the allotetraploid plant Tragopogon miscellus and its diploid progenitors

This study demonstrates that homoeologous genes in two diploid plant species that specify different amounts of an enzyme maintain the same relative level of expression in an allotetraploid derivative. The three predominant alcohol dehydrogenase (ADH) isozymes (DD, DP, PP) in seeds of the recently evolved allotetraploid plant Tragopogon miscellus (Compositae) are dimers specified by Adh3-D and Adh3-P genes derived from its diploid progenitors T. dubius and T. pratensis. Seeds of T. pratensis contain twice as much ADH activity as those of T. dubius, while T. miscellus is intermediate. The three isozymes were similar in a number of catalytic properties; the densitometric ratio of the isozymes purified from T. miscellus was 1 DD:4DP:4PP for both ADH activity and protein; and dissociation-reassociation of the DP enzyme gave a 1:2:1 ratio of the three isozymes. Therefore, the enzymes were similar in specific activity, but twice as many P as D subunits were present in active enzymes in T. miscellus, precisely the difference in activity between the parents. In T. miscellus, the specific activity of ADH and its activity per mg tissue are intermediate to those of the diploids, because relative expression of the Adh gene in each genome is not influenced by the presence of the other genome.     

Variation in fruit set within and among natural populations of the self-incompatible herb Centaurea scabiosa (Asteraceae)

Various factors known to affect fruit set in self-incompatible plants were studied in 11 populations of Centaurea scabiosa . The importance of genetic variation was estimated using isozymes. A low overall genetic differentiation among populations suggested high levels of either current or historical gene flow. Large variation in fruit set was found among populations, among plants within populations, and among flower heads within plants. Most of this variation was explained by differences among flower heads within plants. Within the range in population size studied, there was no indication that plants growing in the smaller populations had lower fruit set than plants in larger ones. A significant positive correlation between genetic variation and population reproductive success was found. Pollinator visitation rate was very high and dominated by bumblebees. It was rendered unlikely that reproduction was limited by pollinator availability. It was even suggested that a very high visitation rate might have negative effects on fruit set in some populations due to an increased proportion of geitonogamous pollination resulting in stigma clogging with non-compatible pollen. The number of flower heads produced by individual plants did not affect fruit set in individual flower heads.     

Meiotic behavior and pollen fertility in triploid and tetraploid natural populations of Campuloclinium macrocephalum (Eupatorieae,Asteraceae)

Campuloclinium macrocephalum DC. is a perennial herb widely distributed in the New World and introduced in South Africa, where it is commonly called “pompom weed”. This species is considered one of the most important weeds of Brazil and one of the problematic invasive plants of South Africa. The meiotic system can be studied to assess the ability of a weed to spread, but only few studies on C. macrocephalum have been realized. In this study, we examined the meiotic behavior and pollen fertility of 14 natural populations of C. macrocephalum from Argentina and Uruguay. Meiotic analysis revealed 2 triploid (2n = 3x = 30), 11 tetraploid (2n = 4x = 40) and 1 mixed population (2n = 2x = 20, 2n = 4x = 40). Both, triploid and tetraploid specimens showed a widely variable meiotic behavior with irregular chromosome pairing showing univalents, bivalents, trivalents (in triploids) and tetravalents (in tetraploids) at diacinesis of first meiotic division. Different abnormalities were observed, such as: laggard chromosomes, chromatin bridges, and out of plate chromosomes at metaphase I. During meiosis I (prophase), some cells showed the phenomenon of cytomixis or chromatin transfer between pollen mother cells. The meiotic indexes suggest that only four populations were normally fertile (over 90 % of fertile pollen), indicating meiotically stable plants. The remaining populations share variable pollen fertility, with triploids ranging from 46.64 to 54.83 % and tetraploids varying from 3.54 to 45.30 %. We suggest that polyploidy seems to be recurrent in C. macrocephalum, promoting partial sterility of pollen grains, generating large numbers of individuals by apomixis promoting invasion of crop fields. This study presents the meiotic behavior of this weed, these could be useful for future studies of biological control in areas with no natural enemies.     

Fitness Traits and Dispersal Ability in the Herb Tragopogon pratensis (Asteraceae): Decoupling the Role of Inbreeding Depression and Maternal Effects

Abstract: Inbreeding depression can decrease several fitness traits and maternal effects can strongly influence the amount of inbreeding depression. Understanding the effects of inbreeding depression on plant fitness is especially important in the context of habitat fragmentation, where plant populations become smaller and more isolated, exhibiting increasing levels of inbreeding depression. We examined the joint influence of inbreeding depression and maternal effects on life cycle traits and dispersal ability in the herb Tragopogon pratensis that grows in fragmented populations in Europe. We conducted experimental crosses to obtain selfed and outcrossed progeny in two contrasted environments. In particular, we produced a first generation of seeds and plants that were self-pollinated again to produce a second generation of seeds. Individual seeds were weighed and their pappuses measured to estimate the dispersal potential. Pollination treatment only had a significant effect on seed mass and dispersal ability. Coefficients of inbreeding depression did not differ between selfed and outcrossed plants. Seed mass had a significant effect on germination date. Environment had a significant effect on mass of the second generation of seeds and the interaction between pollination treatment and family was significant for six traits, indicating the existence of strong maternal effects in T. pratensis. Results suggest population differentiation. Overall, T. pratensis populations exhibited a good performance under selfing, in terms of life cycle traits and dispersal ability, which would allow the species to cope with problems associated with fragmentation.     

Evolution of apomixis loci in Pilosella and Hieracium (Asteraceae) inferred from the conservation of apomixis-linked markers in natural and experimental populations

The Hieracium and Pilosella (Lactuceae, Asteraceae) genera of closely related hawkweeds contain species with two different modes of gametophytic apomixis (asexual seed formation). Both genera contain polyploid species, and in wild populations, sexual and apomictic species co-exist. Apomixis is known to co-exist with sexuality in apomictic Pilosella individuals, however, apomictic Hieracium have been regarded as obligate apomicts. Here, a developmental analysis of apomixis within 16 Hieracium species revealed meiosis and megaspore tetrad formation in 1 to 7% of ovules, for the first time indicating residual sexuality in this genus. Molecular markers linked to the two independent, dominant loci LOSS OF APOMEIOSIS (LOA) and LOSS OF PARTHENOGENESIS (LOP) controlling apomixis in Pilosella piloselloides subsp. praealta were screened across 20 phenotyped Hieracium individuals from natural populations, and 65 phenotyped Pilosella individuals from natural and experimental cross populations, to examine their conservation, inheritance and association with reproductive modes. All of the tested LOA and LOP-linked markers were absent in the 20 Hieracium samples irrespective of their reproductive mode. Within Pilosella, LOA and LOP-linked markers were essentially absent within the sexual plants, although they were not conserved in all apomictic individuals. Both loci appeared to be inherited independently, and evidence for additional genetic factors influencing quantitative expression of LOA and LOP was obtained. Collectively, these data suggest independent evolution of apomixis in Hieracium and Pilosella and are discussed with respect to current knowledge of the evolution of apomixis.     

Allozyme variation in sexual and apomictic Taraxacum and Pilosella (Asteraceae) populations

Allozyme spectra of peroxidase, esterase, superoxid dismutase, tyrosinase, alcohol dehydrogenase, lactate dehydrogenase, and acid phosphatase were examined in populations of sexual (Taraxacum serotinum and Pilosella echioides) and apomictic (T. officinalis and P. officinarum) plant species. The heterozygosity in these populations (0.455-0.620) proved to be considerably higher than the average level characteristic of plant populations (0.058-0.185). The populations examined did not differ in the mean phenotype number mu, i.e., they exhibited the same diversity (3.213-3.380). The proportion of rare phenotypes h also did not differ between the sexual and apomictic species of the same genus, whereas this parameter in the Pilosella populations (0.150-0.174) was significantly higher than in the Taraxacum ones (0.093-0.114). The populations were characterized by numerous isozyme spectra (more than 11 per populations) and displayed multiple allelism (the mean allele frequency was 3.63-4.38 per locus). They exhibited a high percentage of rare (occurring at a frequency lower than 5%) spectra (35-80%). This indicates that agamic complexes, to which these populations belong, may have a more complicated genetic structure of both apomictic and sexual populations than the species that do not belong to agamic complexes.