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CELL BIOLOGY & MOLECULAR GENETICS

Tracing the Phylogeny of the Hexaploid Oat Avena sativa with Satellite DNAs

Dep. of Plant Sciences & Crop Development Centre, Univ. of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada

graham.scoles{at}usask.ca

	ABSTRACT

TOP ABSTRACT INTRODUCTION Materials and methods Results Discussion REFERENCES

 
The genus Avena contains 30 different species from diploid through tetraploid to hexaploid with different genome compositions. Research regarding the origin of the different genomes in the polyploid species has been inconclusive. The objectives of this research were to investigate the phylogenetic relationships of the Avena species by means of polymorphisms in satellite, minisatellite, and microsatellite DNA. A satellite DNA sequence, ASS49, was isolated from a microsatellite-enriched library of the hexaploid oat Avena sativa L. Southern hybridization showed that ASS49 was a species-specific rather than a genome-specific satellite. ASS49 was able to distinguish species that may be the diploid and tetraploid progenitors of hexaploid oat. The phylogenetic relationship of Avena species was further investigated using 40 microsatellite and four minisatellite primers. These results appeared to support the findings with ASS49. It appears that the Ac-genome diploid species (A. canariensis Baum Raj. et Samp.) is the progenitor and A-genome donor of the hexaploid oat rather than the generally believed As-genome species (A. strigosa Schreber). Instead, A. strigosa appears to be a member of a separate lineage of diploid and tetraploid species including the tetraploid species A. abyssinica Hochst.

Abbreviations: bp, base pair • NTSYS, numerical taxonomy and multivariate analysis system • PCR, polymerase chain reaction • RAPD, random amplified polymorphic DNA • RFLP, restriction fragment length polymorphism

	INTRODUCTION

TOP ABSTRACT INTRODUCTION Materials and methods Results Discussion REFERENCES

 
THE GENUS Avena belongs to the Gramineae family. It contains 30 different species which form a distinct polyploid series ranging from diploid through tetraploid to hexaploid with a basic chromosome number of seven (Baum and Fedak, 1985; Leggett and Thomas, 1995; Rajhathy and Thomas, 1974; Thomas, 1992). On the basis of karyotype analysis and observations of meiotic chromosome pairing of inter- and intra-specific hybrids, four Avena genomes (A, B, C, and D) have been identified and the genome combinations AA, CC, AABB, AACC, and AACCDD are found in nature (Rajhathy and Thomas, 1974). Structural rearrangements of the chromosomes and a mechanism that restricts the pairing of chromosomes to homologues mask the true identity of the genome donor(s) of the polyploids (Leggett, 1992). No diploid species has been clearly identified as being the progenitor of any polyploid Avena species (Leggett and Thomas, 1995).

The cultivated oat A. sativa is a natural allohexaploid that contains three genomes (A, C, and D). It has been suggested that its evolution involved two distinct steps. The first step involved the establishment of the tetraploid (AACC) by the hybridization of two diploid species (AA and CC) followed by doubling of the chromosome number. This was followed by hybridization of this tetraploid with a third diploid species to form a hexaploid by the doubling of the chromosomes of the resulting triploid hybrid (Rajhathy, 1991; Thomas, 1992). The tetraploid species A. murphyi Ladizinsky and A. maroccana Gdgr. (formerly described as A. magna Murphy et Terrell) were formerly favored as the donors of the AC-genomes to the hexaploid species. This conclusion has been based on chromosome pairing in hybrids between hexaploid and tetraploid oat (Ladizinsky and Zohary, 1971; Ladizinsky and Fainstein, 1977) and isoenzyme analysis (Sanchez de la Hoz and Fominaya, 1989). More recently, A. insularis Ladizinsky has been shown to have even greater pairing affinity with the hexaploid and has been suggested as the most likely tetraploid ancestor of the hexaploids (Ladizinsky, 1998).

There is now good evidence from molecular studies that the A and D genomes are very closely related (Leggett and Markhand, 1995; Linares et al., 1996, 1998). It is possible that a D genome species never existed and that the D genome is in fact a derived A genome (Leggett, 1996). No B genome species have been identified and one AABB species (A. barbata Brot.) appears to be a near autoploid arising from the AsAs genome (Leggett and Thomas, 1995). However, it is still not clear which of the diploid species contributed to the polyploid species. All hybrids between A genome diploids and the hexaploids have been produced (Leggett and Thomas, 1995); however, none of these hybrid combinations exhibited the level of chromosome homology that would suggest one of them to be the donor of the A genome. Initial comparison of the karyotypes of A. sativa and diploid A. strigosa showed that the A. strigosa genome (As) matched very closely the putative A genome of the hexaploid species (Rajhathy and Thomas, 1974). However, subsequent karyotypic comparisons using C-banding revealed extensive dissimilarity between the As genome and the euchromatic A- and D-genome chromosomes in A. sativa (Jellen et al., 1993; Jellen and Gill, 1996). Genomic in situ hybridization also suggested that both A and D genomes of A. sativa were highly homologous to A. strigosa (Chen and Armstrong, 1994; Jellen et al., 1994; Linares et al., 1996). However, chromosome pairing between A. strigosa and the AC-genome tetraploids was insufficient to support the presence of the As genome in the tetraploid species (Ladizinsky and Zohary, 1968). In a recent study, a satellite DNA sequence isolated from A. strigosa failed to hybridize with the AC-genome tetraploids (Linares et al., 1998).

On the basis of karyotype, the three diploid C genome species were separated into two genome types (Cv and Cp) (Leggett and Thomas, 1995). Both of them have been proposed as the putative donors of the C genome of the hexaploids (Chen and Armstrong, 1994; Jellen et al., 1994; Rajhathy and Thomas, 1974).

Recently, repeated DNA sequences have been isolated from Avena species and genome-specific satellite DNAs have been identified. Southern and in situ hybridization using these DNA sequences could clearly distinguish the three genomes of A. sativa (Chen and Armstrong, 1994; Fabijanski et al., 1990; Fominaya et al., 1995; Gupta et al., 1992; Jellen et al., 1994; Linares et al., 1996, 1998; Solano et al., 1992). However, these studies shed very little light on the phylogeny of Avena species at the DNA level.

In the present study, a satellite DNA sequence was isolated from A. sativa and this sequence appears to identify the diploid and tetraploid progenitors of A. sativa. We have further investigated the genetic similarity of different Avena species using minisatellite and microsatellite polymorphisms. These results confirmed those obtained with the satellite DNA sequence.

	Materials and methods

TOP ABSTRACT INTRODUCTION Materials and methods Results Discussion REFERENCES

 
Materials
Thirteen Avena species were used in the present study. Their genome type and source are listed in Table 1 . Avena wiestii Steud. was not included in the microsatellite study and A. byzantina K. Koch was not included in Southern hybridizations with the satellite DNA sequence. DNA of each species was extracted using the CTAB (cetyltrimethylammonium bromide) method of Saghai-Maroof et al. (1984).

Southern Blotting
Genomic DNA (5 µg each) from 12 Avena species was digested with the restriction enzymes EcoRI, BamHI, EcoRV, and XbaI. Gel electrophoresis, DNA transfer to membranes, blotting, labeling, and filter hybridization followed a standard method (Sambrook et al., 1989). The probe, obtained by cutting the satellite clone with EcoRI, was randomly labeled with ³²P-dCTP and hybridized with the filter overnight at 65°C. The filter was washed with 2x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate), 0.1% (w/v) SDS (sodium dodecyl sulfate) at room temperature for 20 min, followed by washing at 1x SSC, 0.1% (w/v) SDS for 20 min at 65°C, then a final wash at 0.5x SSC, 0.1% (w/v) SDS for 20 min at 65°C. The film was developed after exposure for either 12 or 48 h.

Directed Amplification of Minisatellite DNA
It has been reported that directed amplification of DNA from minisatellite regions using minisatellite core sequences as primers can differentiate plant species (Somers et al., 1996; Zhou et al., 1997). Directed amplification of minisatellite-region DNA followed the method of Heath et al. (1993). A number of minisatellite core sequences were used as single primers to amplify genomic DNA. The minisatellite core sequences used were 33.6 (GGAGGTGGGCA—Jeffreys et al., 1985), rice HVR (CCTCCTCCCTCCT—Winberg et al., 1993), and two human minisatellites (ATGCACACACACAGG and TACGTGTGTGTGTCC—Murray et al., 1988). A 25-µL polymerase chain reaction (PCR) reaction contained 1x buffer (Gibco), 2.5 mM MgCl₂, 200 µM of each dNTP, 20 pmol of primer of minisatellite core sequence, 1unit of Taq polymerase and 100 ng template DNA. The reaction was denatured at 95°C for 5 min, followed by 35 cycles of 94°C for 1 min, 55°C for 1 min and 72°C for 2 min, with a final extension at 72°C for 10 min. PCR products were separated on 2%(w/v) agarose gels in 1x TBE (tris-borate/EDTA buffer) and visualized by ethidium bromide staining under UV.

Amplification of Microsatellites from the Avena Genome
Forty microsatellite primers were used: AM1, AM2, AM3, AM4, AM5, AM6, AM11, AM14, AM15, AM17, AM19, AM21, AM22, AM23, AM24, AM25, AM26, AM27, AM28, AM30, AM31, AM35, AM38, AM40, AM41, AM42, HVM3, HVM4, HVM11, HVM20, HVM22, HVM34, HVM44, HVM51, HVM54, HVM60, HVM65, HVM68, HVBAREI, and HVWAX. The AM-microsatellites were isolated from A. sativa (Li et al., 2000) and the HV-microsatellites from H. vulgare L. (Liu et al., 1996). The PCR reaction contained 50 ng template DNA, 1x buffer (Gibco), 1.5 mM MgCl₂, 200 µM each of dNTP, 10 pmol of each primer, and 1 unit of Taq polymerase. One of three different "Touchdown" PCR programs was used depending on the melting temperature of the primers (Li et al., 2000). PCR products were separated on a sequencing gel containing 6% (w/v) polyacrylamide, 7 M urea, and 1x TBE at 85 W constant power for 3 h (BioRad sequencing system, BioRad, Richmond, CA). The gel was fixed, stained, and dried by means of a DNA silver staining kit (Promega Corp., Madison, WI).

Data Analysis
DNA sequences were analyzed by DNAMAN (Lynnon BioSoft, Quebec, Canada) and DNASTAR (Lasergene, DNASTAR, Inc., Madison, WI). Sequences were aligned with DNA sequences in EMBL by default parameter settings of Basic Alignment Search Tool (Altschul et al., 1990). NTSYSpc (Version 2.0) was used to calculate the genetic similarity (Jaccard's coefficient) and for cluster analysis (Unweighted Paired Group Method Using Arithmetic Averages).

	Results

TOP ABSTRACT INTRODUCTION Materials and methods Results Discussion REFERENCES

 
Sequence Analysis of ASS49
The cloned fragment was 594 bp long with 59% (A+T) and 41% (G+C). Preliminary sequence analysis showed that this clone contained 12 tandem repeats with an average monomer length of 49 bp (46 to 51 bp). The monomer sequences exhibited an average of 85.7% nucleotide sequence similarity and three 5-bp deletions were found. Each monomer contained single restriction sites for BamHI and NdeI (data not shown). Each repeat had a conserved 5' end and a variable 3' end. No directed repeat was found in the monomer, but each had an 8-bp inverted-repeat that could form a hairpin. As this clone was isolated from A. sativa, it has been designated as ASS49. The nucleotide sequence has been deposited in the DDBJ/EMBL/GenBank nucleotide sequence databases under the accession Number AB039840.

Further sequence analysis showed that four consecutive 49-bp monomers formed a larger repeat unit, thus the entire clone was composed of three 195-bp repeats. The sequence similarity of each repeat was as high as 94.3% and only single base pair substitutions or deletions were evident (Fig. 1) .

View larger version (36K): [in this window] [in a new window]   Fig. 1 Alignment of the three 195-bp repeats in the satellite sequence ASS49. Each repeat contains four monomers with an average of 49 bp. An 8-bp inverse repeat is overlined in the monomer

View larger version (98K): [in this window] [in a new window]   Fig. 2 Southern blot analysis of the DNAs of diploid, tetraploid, and hexaploid oats determined with the satellite sequence ASS49 as a probe. Species in lanes 1, A. longiglumis; 2, A. wiestii; 3, A. canariensis; 4, A. strigosa; 5, A. clauda; 6, A. abyssinica; 7, A. barbata; 8, A. maroccana; 9, A. murphyi; 10, A. sterilis; 11, A. fatua; 12, A. sativa. (a) Ethidium bromide stained 1% (w/v) agarose gel after separation of DNA samples cut with XbaI showing similar amounts of plant DNA in each lane. (b) Autoradiogram after a 12-h exposure

View larger version (113K): [in this window] [in a new window]   Fig. 3 Directed amplification of minisatellite DNA region from 13 Avena species performed by means of a minisatellite core sequence of rice HVR as a primer. Species in lanes 1, A. longiglumis; 2, A. wiestii; 3, A. canariensis; 4, A. strigosa; 5, A. clauda; 6, A. abyssinica; 7, A. barbata; 8, A. maroccana; 9, A. murphyi; 10, A. sterilis; 11, A. fatua; 12, A. byzantina; 13, A. sativa. Lane M is a molecular ladder

View larger version (25K): [in this window] [in a new window]   Fig. 4 Prinicipal coordinate analysis of the Avena species based on the polymorphisms in minisatellites (a) and microsatellites (b)

View larger version (16K): [in this window] [in a new window]   Fig. 5 Consensus phylogenetic tree of 12 Avena species based on the polymorphisms in minisatellites and microsatellites

	Discussion

TOP ABSTRACT INTRODUCTION Materials and methods Results Discussion REFERENCES

Several satellite sequences have been isolated from different Avena species (Fabijanski et al., 1990; Fominaya et al., 1995; Gupta et al., 1992; Katsiots et al., 1996; Linares et al., 1996; Solano et al., 1992). However, these sequences were all genome specific and failed to show differences between species carrying the same genome. It seems that these satellite DNA sequences have been conserved during evolution as they are found in all diploid and polyploid species carrying the A or C genome. Consequently these sequences have not been informative in the search for the ancestor(s) of the cultivated Avena species. Genomic in situ hybridization has also provided little information about the evolution of Avena (Chen and Armstrong, 1994; Jellen et al., 1994). Recently, a satellite sequence (pAs120a) isolated from A. strigosa was able to distinguish different A-genome diploid species (Linares et al., 1998). However, this sequence failed to hybridize with the AC-genome tetraploids. Thus it again shed little light on evolution of the Avena species.

On the basis of the Southern hybridization pattern, the 594-bp cloned fragment ASS49 appears to represent a satellite DNA that is present in multiple copies in the genome of A. sativa and a number of other Avena species. ASS49 contained three virtually identical copies of a 195-bp repeat, each of which in turn consist of four 49-bp sub-repeats. A search of the EMBL sequence data bank showed that part of ASS49 shared high (92%) homology with a C-genome specific sequence pAM1 (313 bp) (Fominaya et al., 1995; Solano et al., 1992) isolated from the tetraploid species A. murphyi. This sequence contained six 51-bp tandem repeats and 131 bp of non-repeated sequence. Both ASS49 and pAM1 hybridized strongly and evenly to DNA of the hexaploids, AC-genome tetraploids and C-genome diploids (Solano et al., 1992; Fig. 2). However, ASS49 also hybridized to DNA of two A-genome diploids and one AB-genome tetraploid (Fig. 2). There are two possible explanations for this difference. Firstly, the 131-bp non-repeat sequence in pAM1 (Fominaya et al., 1995) may determine its C-genome specificity. This was the case for the genome-specific satellite sequence pAs120 (Linares et al., 1998). A sub-cloned 389-bp tandem repeat (pAs120a) did not show the genome-specificity of the complete clone with the non-repeated sequence. The second reason may be due to the different length of the probe and different hybridization conditions. In situ hybridization showed that pAM1 also hybridized with three chromosomes of the A-genome in the AC-genome tetraploid and hexaploid (Fominaya et al., 1995). These hybridization sites could represent A-C genome translocations or the A- and C-genomes may share partial homology. Unlike these satellites that appeared to be specific to certain oat genomes (Fominaya et al., 1995; Gupta et al., 1992; Linares et al., 1998; Solano et al., 1992), ASS49 could distinguish among A-genome diploids and AB-genome tetraploids. It was a unique, species-specific satellite present in Avena species with different genome compositions.

The Diploid Avena Species
In the present study, the satellite sequence ASS49 isolated from hexaploid A. sativa failed to hybridize with the DNA of the A-genome diploids A. strigosa and A. longiglumis. On the other hand, this sequence showed strong hybridization to the DNA of the A-genome diploids A. canariensis and A. wiestii (Fig. 2). In other research, a satellite sequence isolated from A. strigosa (pAs120a) strongly hybridized to DNA of A. strigosa and A. longiglumis (Linares et al., 1998) differentiating them from other A-genome diploids. Directed amplification of minisatellite-region DNA also produced a banding pattern that distinguished DNA of A. strigosa and A. longiglumis from other diploid Avena species (Fig. 3) and microsatellite data provided similar results. On the basis of minisatellite and microsatellite polymorphism, A. strigosa and A. longiglumis shared much lower genetic similarity with the tetraploid and hexaploid species compared to the other A-genome diploids A. canariensis and A. wiestii (Tables 2, 3, and 4) . Thus, the molecular evidence suggests that within the A-genome diploid species, A. strigosa and A. longiglumis are differentiated from A. canariensis and A. wiestii and the latter are closer to the AACC tetraploid and AACCDD hexaploid species and are most likely to represent the A-genome donor of these species.

The Ac-genome diploid species (A. canariensis) appears to be the most likely progenitor and A-genome donor of the AC genome tetraploid and the ACD hexaploid oats rather than the generally believed As-genome species (A. strigosa—Chen and Armstrong, 1994; Jellen et al., 1994; Linares et al., 1998). Instead, A. strigosa appears to be the progenitor of the tetraploid species A. abyssinica.

The C-genome diploids have been subdivided into two groups, CpCp and CvCv. Either could be the C-genome donor of the tetraploids and hexaploids (Rajhathy and Thomas, 1974). As only one C-genome diploid was used in the present study, we were unable to tell which C-genome diploid was more closely related to the tetraploids and the hexaploids. Nevertheless, it is clear that the C-genome diploid shared higher genetic similarity with the AC-genome tetraploids and the hexaploids rather than the A-genome diploids (Table 4) and also was close to A. barbata.

There is now good evidence from molecular techniques that the A and D genomes are very closely related (Leggett and Markhand, 1995; Linares et al., 1996, 1998). It has been suggested that a D-genome species never existed (Leggett, 1996) and that the D genome is in fact a derived A genome. If this is true, there should exist one A-genome diploid species that would share higher genetic similarity with the hexaploid species but lower genetic similarity with the AC-genome tetraploid species. No such A-genome diploid was found in the present study. Nevertheless, the minisatellite and microsatellite primers could be used to search for this A-genome diploid.

The Tetraploid Avena Species
The three AB-genome tetraploids, A. barbata, A. abyssinica, and A. vaviloviana Mordv., have similar karyotype and are interfertile. They belong to the same biological species and collectively known as the A. barbata group (Rajhathy and Morrison, 1959). From all the evidence available, it is clear that the A. barbata group arose from the A-genome diploids and are of near autoploid origin (Ladizinsky, 1973; Leggett, 1992). The present study generally supported this conclusion. However, the results of the present study suggest that they originated from different A-genome diploids. Ladizinsky (1973) suggested that A. barbata arose from either A. wiestii or A. hirtula (Table 2 and Fig 4a). However, it is not clear why A. barbata shared high genetic similarity with the C-genome diploids (Tables 2 and 3). Avena abyssinica appears to be evolutionarily close to the A-genome diploids A. strigosa and A. longiglumis (Fig. 4a and 4b).

On the basis of karyotypic, isoenzyme, and interspecific hybridization analysis, it is generally believed that A. maroccana and A. murphyi provided the tetraploid base for the formation of the hexaploid species (Leggett, 1992; Leggett and Thomas, 1995). The present study supported this assumption. Statistical analysis of both minisatellite and microsatellite polymorphisms showed that A. murphyi shared a significantly higher genetic similarity with the hexaploid species (Table 4) than A. maroccana. Thus, the former would appear to be the direct ancestor of the hexaploid species. However, a new tetraploid species A. insularis was described recently (Ladizinsky, 1998). It showed even greater chromosomal pairing affinity with the hexaploids. More research is necessary in the future to investigate the relationships between the AC-genome tetraploids.

The Hexaploid Avena Species
All the hexaploid Avena species have the same karyotype (AACCDD) and are interfertile (Rajhathy, 1963). These species should belong to a single biological species (Ladizinsky and Zohary, 1971). The current study of both minisatellite and microsatellite polymorphisms supports these conclusions. The hexaploid species shared high genetic similarity with each other (Tables 2 and 3) and were closely clustered together (Fig. 5).

It is clear that the cultivated oat species A. sativa and A. byzantina evolved from a wild hexaploid species. However, we still do not know whether A. sterilis or A. fatua L. is the immediate progenitor of cultivated oats. A. sterilis is more widely distributed and highly variable. On the other hand, A. fatua is short of variation for the traits of cultivated oats (e.g., disease resistance, cold tolerance etc.). Therefore, A. sterilis has been suggested to be the progenitor of cultivated oat (Coffman, 1946). The main morphological difference between A. fatua and A. sterilis is that the floret is the unit of dispersal in the former and the spikelet in the latter, a feature that distinguishes them as species (Leggett and Thomas, 1995). Irradiating seeds of A. sterilis resulted in mutants with A. fatua characteristics (Griffiths and Johnston, 1956). This was interpreted to suggest that A. fatua may have originated from A. sterilis. The A. fatua-like behavior of the nullisomic of chromosome IV of the Sun II monosomic series also supported cultivated oat being directly descended from A. fatua (Hacker and Riley, 1965). The present study showed that A. fatua shared higher genetic similarity with the cultivated oat species than A. sterilis based on the microsatellite polymorphisms (Table 3) but vice-versa for minisatellite polymorphisms (Table 2) and clustered with the two domesticated species overall (Fig. 5). Thus the present study does not help to identify the wild hexaploid progenitor. Zhou et al. (1999), recently suggested that the two cultivated hexaploid oat species A. byzantina and A. sativa arose independently from A. sterilis.

In summary, the molecular analysis carried out in the present study appears to suggest that the previous subdivision of A-genome species may need review. Our data suggest two distinct lineages within this group, one of which appears to be closely related to C-genome diploids and AABB and AACC tetraploids and the AACCDD hexaploids. The second lineage appears to be related to what are currently assumed to be other AABB tetraploids. A possible evolutionary tree for Avena species based on these findings is shown in Fig. 6 .

View larger version (22K): [in this window] [in a new window]   Fig. 6 A proposed evolutionary pathway of Avena species

	ACKNOWLEDGMENTS

Received for publication October 14, 1999.

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