Journal of Heredity 2003:94(3)
© 2003 The American Genetic Association 94:260-264
Brief Communication |
Nonadditive Changes in Genome Size During Allopolyploidization in the Wheat (Aegilops-Triticum) Group
From the Department of Field Crops, Faculty of Agriculture, University of Cukurova, 01330 Adana, Turkey (Ozkan); Department of Field Crops, Faculty of Agriculture, University of Trakya, 59030 Tekirda
, Turkey (Tuna); and the Center for Biotechnology, University of Nebraska, Lincoln, NE 68588 (Arumuganathan). K. Arumuganathan is now at Virginia Mason Research Center, Benaroya Research Institute, 1201 Ninth Avenue, Seattle, WA 98101.
Address correspondence to Dr. Ozkan at the address above, or e-mail: hozkan{at}mail.cu.edu.tr.
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Abstract |
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Interspecific or intergeneric hybridization, followed by chromosome doubling, can lead to the formation of new allopolyploid species. Recent studies indicate that allopolyploid formation is associated with genetic and epigenetic changes. Despite these studies, it is not yet clear whether the C value of an allopolyploid is the sum of its diploid parents. To address this question, six newly synthesized wheat allopolyploids and their parental plants were investigated. It was found that allopolyploids have a genome size significantly smaller than the expected value. The reduction of the nuclear genome size in the synthetic allotetraploids and allohexaploids was 2 pg DNA at 2C. It was also found that changes in the genome size already existed in the first generation amphiploids, indicating that the change was a rapid event. There was no difference in the reduction of nuclear genome size between the allotetraploid and the allohexaploid. These data clearly show that genome differentiation in allopolyploids was not related to the ploidy level. The data obtained clearly suggested that the nonadditive change in genome size that occurred during allopolyploidization may represent a preprogrammed adaptive response to genomic stress caused by hybridization and allopolyploidy, which serves to stabilize polyploid genomes.
Wide variation in eukaryotic genome size is a pervasive feature of evolution. Large differences in haploid DNA content (C value) are found within protozoa (5,800-fold range), arthropods (250-fold), fish (350-fold), algae (5,000-fold), and angiosperms (1,000-fold; Cavalier-Smith 1985). Many factors can affect the genome size, including polyploidy, fixation of accessory chromosomes, large duplications and expansions of satellite DNA, or transposable elements (SanMiguel et al. 1998). Polyploidy has played an important role in the evolution of higher plants. Between 50% and 70% of all angiosperm species are of polyploid origin (Wendel 2000). During the last two decades molecular data have provided new insights into the effects that changes in ploidy have on evolution, leading to significant progress in understanding the mechanisms and evolutionary aspects of polyploidy.
Among the cereals, the Aegilops and Triticum genera comprise many polyploids, including their diploid progenitors. The genome relationship between the naturally occuring Aegilops-Triticum allopolyploids and their diploid progenitors has been well established (Feldman et al. 1995). Newly formed allopolyploids of Aegilops and Triticum, therefore, are an excellent system for studying genome evolution. For instance, bread wheat (Triticum aestivum) is hexaploid (2n = 6x = 42) with three (A, B, and D) genomes, each containing seven pairs of homoeologous chromosomes. It is a classical example of allopolyploidization, originating from the hybridization of three different diploid progenitors from Aegilops and Triticum (Kihara 1944; McFadden and Sears 1944). Studies of synthetic allopolyploids such as Brassica and wheat have shown that polyploidization can lead to rapid and extensive genome changes (Feldman et al. 1997; Liu et al. 1998a, b; Song et al. 1995). In particular, studies of newly synthesized allopolyploid wheats have shown that allopolyploid formation is accompanied by extensive genome changes at the molecular level, including rapid and nonrandom elimination of specific low-copy DNA sequences, as well as other types of genomic modifications (Ozkan et al. 2001; Shaked et al. 2001).
Despite these studies, it is not yet clear whether the C value of an allopolyploid is the sum of that of its diploid parents. In the wheat (Aegilops-Triticum) group, previous studies (Furuta et al. 1974; Furuta et al. 1986; Pegington and Rees 1970) have shown that the genome size of tetraploid and hexaploid wheat were additive when they were compared to parental species. However, Boyko et al. (1984) reported that DNA content decreased during the course of triticale (X Tritisecale Wittmack) formation, as compared to the expected value for the combined wheat and rye (Secale cereale) genomes. They found a 9% decrease in genome size for octoploid triticale and as much as a 28%–30% decrease for hexaploid triticale. In the above studies, except for the work on triticale, synthetic amphiploids were compared with parental accessions rather than the exact parental plant. Therefore, it was impossible to determine the exact genome size deviation from additivity, because of intra-accession genome size polymorphism (Bennett and Leitch 1991; Furuta 1975; Nishikawa and Sawai 1969). To address this question, in this study we used six newly synthesized allopolyploids of wheat. These allopolyploids have a genome size significantly smaller than predicted with an additive model.
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Materials and Methods |
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Six newly synthesized amphiploids and their parental plants were used in this study (Table 1). The crosses were performed between species of the same ploidy level, as well as between species of different ploidy level. At the three to four tiller stages, hybrids were treated with 0.2% (w/v) colchicine (Sigma) for 5 hr at room temperature and then washed in tap water for 1 hr. After treatment plants were grown in the greenhouse until maturity, and all spikes were bagged. The designation of the different allopolyploid generations is S (selfed). Accordingly, polyploidy tissues on F1 plants are S0, the seed produced on S0 tissues (i.e., after meiosis) and plants developed from them are S1, and so on. Single plants used as parents were bagged and selfed so that the synthetic allopolyploids could be traced to specific parental lines. The parental plants and the synthetic allopolyploids are maintained in our collection (University of Çukurova, Adana, Turkey). The amphiploid T. turgidum ssp. carthlicum–Ae. tauschii is hexaploid, with a genomic constitution similar to hexaploid bread wheat (T. aestivum), whereas the amphiploid T. urartu–Ae. tauschii is tetraploid, with a genomic constitution that does not exist in nature.
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For the study, five seeds of each parental line and each amphidiploid were planted into individual containers in a greenhouse. The chromosome numbers of the newly synthesized amphiploids were counted, and aneuploid plants were discarded before analysis. Genome size was determined by measuring nuclear DNA content with flow cytometry at the University of Nebraska Flow Cytometry Core Reseach Facilities [FACScan flow cytometer (Becton Dickinson Immunocytometry system, San Jose, CA)]. Both barley (2n =2x =14) and wheat (2n = 6x = 42) were used as standards because of the large variation in DNA content of plants analyzed. The methods are described in Tuna et al. (2001). Briefly, the procedure consists of preparing suspensions of intact nuclei by chopping plant tissues and lysing protoplasts in a MgSO4 buffer mixed with DNA standards and then staining the nuclei with propidium iodide (PI) in a solution containing DNAase-free RNAase. Fluorescence intensities of the stained nuclei were measured by flow cytometry. Values for nuclear DNA contents were estimated by comparing fluorescence intensities of the nuclei of the test population with those of an appropriate internal DNA standard that was included with the tissue being tested. For each measurement, propidium iodide fluorescence area signals (FL2-A) from 1,000 nuclei were collected with use of CellQuest software (Becton Dickinson Immunocytometry system, San Jose, CA). A live gate was set using the FL2-2 and FSC parameters, allowing the fluorescence measurements from the nuclei to generate a histogram of FL2-A. The mean positions of the G0/G1 (nuclei) peaks for the samples and the internal standards were determined with use of CellQuest software to analyze the data. The mean DNA content per plant was based on the 1,000 scanned nuclei. The formula used for converting florescence values to DNA content was Nuclear DNA content = (mean position of unknown peak)/(mean position of known) x DNA content of known standard.
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Results |
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The chromosome number, the 2C nuclear DNA amounts expressed in picogram (pg), and the ploidy levels of both the newly synthesized amphiploids and their parents are given in Table 2. Table 2 also contains the expected DNA values for these newly synthesized amphiploids, estimated as a sum of the 2C DNA values of their parents. The data show that there has been a loss of DNA from the newly synthesized allopolyploids by the first generation of the amphiploid (S1), and this loss was fixed in the second amphiploid generation (S2). Genome size in the synthetic allohexaploids and allotetraploids that exist in nature were less than the expected value (Table 2). In order to determine whether DNA loss was specific for the newly synthesized allopolyploids that had a genomic constitution analogous to that of natural allopolyploids or not, we also analyzed an artificial allotetraploid and allohexaploid containing the A and D genomes (T. urartu–Ae. tauschii), and BBAA and S genomes (T. turgidum ssp. durum–Ae. sharonensis), genomic constitutions that do not exist in nature. In these allopolyploids DNA loss was also observed (Table 2). In addition, it was found that whole allopolyploids, whether they had a genomic constitution analogous to that of natural allopolyploids or not, had the same amount of DNA reduction (Table 2).
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Discussion |
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Although many higher plants, including many important crops (wheat, cotton, Brassica, etc.) underwent speciation through allopolyploidy, little is known about the nature of genome size changes during this event. The relationship between polyploidy and genome size has been discussed by several authors. For instance, Furuka et al. (1974) reported that two natural and six synthesized hexaploid wheats had similar DNA contents that were approximately equal to the sum of those of their parents. This was in agreement with the results of Rees (1963), Rees and Walters (1965), Nishikawa and Furuta (1969), and Pegington and Rees (1970) in the wheat (Aegilops-Triticum) group. The DNA content of the amphiploids in Brassica (Verma and Rees 1974), Arachis (Sing et al. 1996), Glycine (Hammatt et al. 1991), and Allium (Ohri et al. 1998) corresponded to the sum value estimated for parental species. However, this is not always the case with other plant species. For instance, Narayan (1998) found DNA content less than the sum of the putative parents in Brassica allopolyploids. He reported that the genome sizes of present-day allopolyploids of Brassica were, on average, 6.81% less than the expected value. He also compared Nicotiana allopolyploids to their putative progenitors and observed an average of 13% or 1.84 pg reduction of genome size in N. arentsii. In addition, increases in genome size have been observed (on average 2%) in N. rustica and N. tabacum (Narayan 1998). Grant (1969) postulated that a reduction in DNA content was associated with the adaptation necessary for establishment of the highest ploidy levels (12x) in Betula. Boyko et al. (1984) reported that DNA content decreased in the course of triticale breeding as compared to the expected value for the combined wheat and rye genomes. They found that this decrease was about 9% for octoploid triticale and reached 28%–30% for hexaploid triticale. Raina et al. (1994) studied the changes in DNA content in C0 (first generation) and subsequent generations of induced autopolyploids of Tephrosia and Phlox. Although DNA content increased in C0 of Tephrosia oxygona L. and T. purpure L., it decreased by 16.7 % of the expected doubled value in the C0 generation of Phlox drummondii, and in C2 an overall reduction of 25% was noticed. They reported that this loss of DNA was achieved by equal reduction in all of the chromosomes in the complement. Vogel et al. (1999) used flow cytometry to determine the base DNA content of the genomes of the perennial Triticeae and concluded that gain or loss of nuclear DNA content occurred during the evolution of perennial Triticeae and was probably a part of the speciation process. Tuna et al. (2001) used nuclear DNA content information determined by flow cytometery in the ploidy determination of bromegrass germplasm accessions. Their results indicated a slight tendency toward diminution of DNA content with increased ploidy.
A shortcoming of many of these studies reported was the absence of data for the parental plants that directly gave rise to the amphiploid. We therefore used newly synthesized amphiploids with exact parental lines. The chromosome number of newly synthesized amphiploids was counted and aneuploid plants were discarded before analysis. Moreover, parental plants were checked for homozygosity as described by Ozkan et al. (2001). Three to four individual plants randomly chosen from the S1, S2, and S3 generations of the synthetic amphiploids (Table 1), and their parental plants were analyzed. We found that the DNA content was less than the sum of the parental plants in the wheat (Aegilops-Triticum) group allopolyploids. It was also found that changes in the genome size already existed in first generation amphiploids, indicating that the change in the genome size occurs rapidly. It was found that during allopolyploidization two pg DNA at 2C was approximately eliminated in the synthetic allotetraploids and allohexaploids (Table 2). We were unable to determine whether this elimination was due to hybridity or allopolyploidization. Therefore, further work is required in order to clarify this point. There was no difference in the reduction of nuclear genome size between the allotetraploid and the allohexaploid. These data clearly show that genome differentiation in allopolyploids was not related to the ploidy level. However, using flow cytometry, we were not able to determine if all of the parental genomes were affected equally. In previous works Ozkan et al. (2001) and Shaked et al. (2001) have shown that a limited set of loci could undergo rapid elimination in newly synthesized allopolyploids from the wheat (Aegilops-Triticum) group. Ozkan et al. (2001) focused the rate and time of elimination of two kinds of low-copy DNA sequences (namely, chromosome-specific sequence and genome-specific sequences) in F1 hybrids and newly formed allopolyploids of Aegilops and Triticum. They reported that allopolyploidy-induced sequence elimination occurred in a sizable fraction of the genome and in sequences that were apparently noncoding. In addition, Shaked et al. (2001) used a different strategy to study genomic changes. Rather than monitoring a small number of known sequences in many hybrids and allopolyploids combinations, they studied F1 hybrids between diploid species from the wheat (Aegilops-Triticum) group and their derived allotetraploids. They did this by screening a large number of loci, using Amplified Fragment Length Polymorphism (AFLP) technology. Specifically, they analyzed two newly synthesized amphiploids, Ae. sharonensis–Ae. umbellulata (used in this study) and T. urartu–Ae. longissima. They found that sequence elimination was one of the major and immediate responses of the wheat genome to wide hybridization or allopolyploidy and that it affects a large fraction of both of the genomes. Interestingly, they reported that the parental genomes were not affected equally. Indeed, they provided a quantitative assessment that the process of allopolyploidization could affect up to 14% of a genome sequences in allopolyploids. They also determined that the timing of elimination was dependent on the genomic combination; most elimination occurred in the F1 hybrids of Ae. sharonensis–Ae. umbellulata, whereas in T. urartu–Ae. longissima, most elimination occurred after chromosome doubling.
The finding that 2 pg DNA could be eliminated in a single generation shows that allopolyploidy leads not only to the establishment of new species in one step, but also to rapid evolution of the individual genomes in the allopolyploid background. Such rapid evolution could explain the elusive nature of the B genome of wheat (Talbet et al. 1995). Interestingly, Kerber (1964) mentioned that the extracted tetraploid (A and B genomes) from hexaploid bread wheat (A, B, and D genomes) did not closely resemble the present-day varieties of emmer wheat, as it was dwarfish, was partially sterile, and lacked vigor. He therefore considered that genetic changes took place within the A and B genomes of tetraploid wheat after polyploidization. Kerber's conclusion can be supported by our results. These results also suggest that genomes do not have a one-way ticket to obesity (Bennetzen and Kellogg 1997).
Flow cytometry provides a fast and accurate way to look at changes in genome size during evolution and differentiation. Our work extends previous studies on wide hybrids in cereals (Ozkan et al. 2001; Shaked et al. 2001), studies which looked at single loci: here we quantified this response on a genome-wide basis, using flow cytometry. Our data concur with previous work that showed rapid sequence elimination (Ozkan et al. 2001; Shaked et al. 2001). Although allopolyploidy leads to an increase in genome size, this increase is less than expected through additivity (Table 1). Although the mechanism underlying the widespread excision of genomic sequences is unknown, several molecular mechanisms were mentioned by Shaked et al. (2001).
According to the example offered by the wheat model, genome size reduction may be a mechanism promoting successful polyploid speciation events. This kind of genetic modification with associated quantitative changes in the amount of DNA would be one of the ways by which polyploids acquire stability at both a cytological and genetic level. The present results suggest that the 2-pg DNA reduction during the allopolyploidization is partly neutralized by the remarkably inherent capacity in the wheat (Aegilops-Triticum) genomes to bring about rapid adaptative change in nuclear DNA. This change leads to other beneficial changes, such as the regulation of meiosis to ensure good seed set. According to Stebbins (1980), the quantitative change in chromosome number and nuclear DNA is only one of a series of complex processes that must take place for polyploidy to be successful in nature. For instance, significant reduction in genome size in triticale, one of the most promising human-made amphiploids (Stebbins 1956) resulted in improved agronomic performance (Bennett, 1985).
In conclusion, allopolyploidization in the wheat group induced a 2-pg DNA loss. This loss, which augments the differentiation of two genomes in the allopolyploid background, may provide the physical basis for the diploid-like meiotic behavior of the raw allopolyploids. The resultant strict bivalent pairing may prevent intergenomic recombination, and therefore may allow higher fertility and permanent heterosis between homoeoalleles. This effect fosters the successful establishment of the newly formed allopolyploid species in nature (Ozkan et al. 2001). The data obtained clearly suggest that the nonadditive change in genome size during allopolyploidization may be a one-step process with no further reduction of genome size during subsequent generations, and that this process may be one way of establishing a stable polyploid species in nature.
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Acknowledgments |
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The authors are grateful to M. Feldman, A. A. Levy (Weizmann Institute of Science), S. Abbo (Hebrew University), and J. Larkindale for their valuable comments and English editing of the manuscript. We also thank J. Flores for her diligent work in tissue preparation and DNA content determination for this study.
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Footnotes |
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Corresponding Editor: J. Perry Gustafson
Received March 28, 2002
Accepted February 6, 2003
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