Interspecific variation in C-banded chromosomes of diploid Aegilops species

Development of Aegilops comosa and Aegilops caudata-specific molecular markers and fluorescence in situ hybridization probes based on specific-locus amplified fragment sequencing

As tertiary gene pools of wheat, Aegilops comosa and Ae. caudata contain many excellent genes/traits and gradually become important and noteworthy wild resources for wheat improvement worldwide. However, the lack of molecular markers and cytological probes with good specificity and high sensitivity limits the development and utilization of Triticum aestivum-Ae. comosa (Ta. Aeco)/Ae. caudata (Ta. Aeca) introgression lines. Using specific-locus amplified fragment sequencing, two Ae. comosa and one Ae. caudata accessions, Chinese Spring, and three Ta. Aeco and Ta. Aeca introgression lines each were sequenced to develop new molecular markers and cytological probes. After strict sequence comparison and verification in different materials, a total of 39 molecular markers specific to three chromosomes in Ae. comosa (nine, seven, and 10 markers for 1M, 2M, and 7M, respectively) and Ae. caudata (two, six, and five markers for 3C, 4C, and 5C, respectively) and 21 fluorescence in situ hybridization (FISH) probes (one centromeric probe with signals specific to the M chromosomes, two centromeric probes with signals in all the tested genomes, and six, eight, and four FISH probes specific to the M, C, and M, C, and U chromosomes, respectively) were successfully exploited. The newly developed molecular markers and cytological probes could be used in karyotype studies, centromere evolutionary analyses of Aegilops, and had the ability to detect the fusion centromeres and small-fragment translocations in introgression lines.

Intraspecific divergence of diploid grass Aegilopscomosa is associated with structural chromosome changes

Aegilopscomosa Smith in Sibthorp et Smith, 1806 is diploid grass with MM genome constitution occurring mainly in Greece. Two morphologically distinct subspecies - Ae.c.comosa Chennaveeraiah, 1960 and Ae.c.heldreichii (Holzmann ex Boissier) Eig, 1929 are discriminated within Ae.comosa, however, genetic and karyotypic bases of their divergence are not fully understood. We used Fluorescence in situ hybridization (FISH) with repetitive DNA probes and electrophoretic analysis of gliadins to characterize the genome and karyotype of Ae.comosa to assess the level of their genetic diversity and uncover mechanisms leading to radiation of subspecies. We show that two subspecies differ in size and morphology of chromosomes 3M and 6M, which can be due to reciprocal translocation. Subspecies also differ in the amount and distribution of microsatellite and satellite DNA sequences, the number and position of minor NORs, especially on 3M and 6M, and gliadin spectra mainly in the a-zone. Frequent occurrence of hybrids can be caused by open pollination, which, along with genetic heterogeneity of accessions and, probably, the lack of geographic or genetic barrier between the subspecies, may contribute to extremely broad intraspecific variation of GAA_n and gliadin patterns in Ae.comosa, which are usually not observed in endemic plant species.

Evolution of the S-Genomes in Triticum-Aegilops Alliance: Evidences From Chromosome Analysis

Five diploid Aegilops species of the Sitopsis section: Ae. speltoides, Ae. longissima, Ae. sharonensis, Ae. searsii, and Ae. bicornis, two tetraploid species Ae. peregrina (= Ae. variabilis) and Ae. kotschyi (Aegilops section) and hexaploid Ae. vavilovii (Vertebrata section) carry the S-genomes. The B- and G-genomes of polyploid wheat are also the derivatives of the S-genome. Evolution of the S-genome species was studied using Giemsa C-banding and fluorescence in situ hybridization (FISH) with DNA probes representing 5S (pTa794) and 18S-5.8S-26S (pTa71) rDNAs as well as nine tandem repeats: pSc119.2, pAesp_SAT86, Spelt-1, Spelt-52, pAs1, pTa-535, and pTa-s53. To correlate the C-banding and FISH patterns we used the microsatellites (CTT)₁₀ and (GTT)₉, which are major components of the C-banding positive heterochromatin in wheat. According to the results obtained, diploid species split into two groups corresponding to Emarginata and Truncata sub-sections, which differ in the C-banding patterns, distribution of rDNA and other repeats. The B- and G-genomes of polyploid wheat are most closely related to the S-genome of Ae. speltoides. The genomes of allopolyploid wheat have been evolved as a result of different species-specific chromosome translocations, sequence amplification, elimination and re-patterning of repetitive DNA sequences. These events occurred independently in different wheat species and in Ae. speltoides _. The 5S rDNA locus of chromosome 1S was probably lost in ancient Ae. speltoides prior to formation of Timopheevii wheat, but after the emergence of ancient emmer. Evolution of Emarginata species was associated with an increase of C-banding and (CTT)₁₀-positive heterochromatin, amplification of Spelt-52, re-pattering of the pAesp_SAT86, and a gradual decrease in the amount of the D-genome-specific repeats pAs1, pTa-535, and pTa-s53. The emergence of Ae. peregrina and Ae. kotschyi did not lead to significant changes of the S^*-genomes. However, partial elimination of 45S rDNA repeats from 5S^* and 6S^* chromosomes and alterations of C-banding and FISH-patterns have been detected. Similarity of the S^v-genome of Ae. vavilovii with the S^s genome of diploid Ae. searsii confirmed the origin of this hexaploid. A model of the S-genome evolution is suggested.

Genetic classification of Aegilops columnaris Zhuk. (2n=4x=28, UcUcXcXc) chromosomes based on FISH analysis and substitution patterns in common wheat × Ae. columnaris introgressive lines

Aegilops columnaris is a tetraploid species originated from Ae. umbellulata (2n=2x=14, UU) and a yet unknown diploid grass species. Although Ae. columnaris possesses some agronomically valuable traits, such as heat and drought tolerance and resistance to pests, it has never been used in wheat breeding because of difficulties in producing hybrids and a lack of information on the relationships between Ae. columnaris and common wheat chromosomes. In this paper, we report the development of 57 wheat - Ae. columnaris introgressive lines covering 8 of the14 chromosomes of Aegilops. Based on substitution spectra of hybrids and the results of FISH analysis of the parental Ae. columnaris line with seven DNA probes, we have developed the genetic nomenclature of the U^c and X^c chromosomes. Genetic groups and genome affinities were established for 11 of 14 chromosomes; the classification of the remaining three chromosomes remains unsolved. Each Ae. columnaris chromosome was characterized on the basis of C-banding pattern and the distribution of seven DNA sequences. Introgression processes were shown to depend on the parental wheat genotype and the level of divergence of homoeologous chromosomes. We found that lines carrying chromosome 5X^c are resistant to leaf rust; therefore, this chromosome could possess novel resistance genes that have never been utilized in wheat breeding.

Aegilops tauschii Accessions with Geographically Diverse Origin Show Differences in Chromosome Organization and Polymorphism of Molecular Markers Linked to Leaf Rust and Powdery Mildew Resistance Genes

Aegilops tauschii (2n = 2x = 14) is a diploid wild species which is reported as a donor of the D-genome of cultivated bread wheat. The main goal of this study was to examine the differences and similarities in chromosomes organization among accessions of Ae. tauschii with geographically diversed origin, which is believed as a potential source of genes, especially determining resistance to fungal diseases (i.e., leaf rust and powdery mildew) for breeding of cereals. We established and compared the fluorescence in situ hybridization patterns of 21 accessions of Ae. tauschii using various repetitive sequences mainly from the BAC library of wheat cultivar Chinese Spring. Results obtained for Ae. tauschii chromosomes revealed many similarities between analyzed accessions, however, some hybridization patterns were specific for accessions, which become from cognate regions of the World. The most noticeable differences were observed for accessions from China which were characterized by presence of distinct signals of pTa-535 in the interstitial region of chromosome 3D, less intensity of pTa-86 signals in chromosome 2D, as well as lack of additional signals of pTa-86 in chromosomes 1D, 5D, or 6D. Ae. tauschii of Chinese origin appeared homogeneous and separate from landraces that originated in western Asia. Ae. tauschii chromosomes showed similar hybridization patterns to wheat D-genome chromosomes, but some differences were also observed among both species. What is more, we identified reciprocal translocation between short arm of chromosome 1D and long arm of chromosome 7D in accession with Iranian origin. High polymorphism between analyzed accessions and extensive allelic variation were revealed using molecular markers associated with resistance genes. Majority of the markers localized in chromosomes 1D and 2D showed the diversity of banding patterns between accessions. Obtained results imply, that there is a moderate or high level of polymorphism in the genome of Ae. tauschii determined by a geographical origin, which we proved by cytogenetic and molecular markers analysis. Therefore, selected accessions might constitute an accessible source of variation for improvement of Triticeae species like wheat and triticale.

The dynamics of histone H3 modifications is species-specific in plant meiosis

Different histone modifications often modify DNA-histone interactions affecting both local and global structure of chromatin, thereby providing a vast potential for functional responses. Most studies have focused on the role of several modifications in gene transcription regulation, being scarce on other aspects of eukaryotic chromosome structure during cell division, mainly in meiosis. To solve this issue we have performed a cytological analysis to determine the chromosomal distribution of several histone H3 modifications throughout all phases of both mitosis and meiosis in different plant species. We have chosen Aegilops sp. and Secale cereale (monocots) and Arabidopsis thaliana (dicots) because they differ in their phylogenetic affiliation as well as in content and distribution of constitutive heterochromatin. In the species analyzed, the patterns of H3 acetylation and methylation were held constant through mitosis, including modifications associated with "open chromatin". Likewise, the immunolabeling patterns of H3 methylation remained invariable throughout meiosis in all cases. On the contrary, there was a total loss of acetylated H3 immunosignals on condensed chromosomes in both meiotic divisions, but only in monocot species. Regarding the phosphorylation of histone H3 at Ser10, present on condensed chromosomes, although we did not observe any difference in the dynamics, we found slight differences between the chromosomal distribution of this modification between Arabidopsis and cereals (Aegilops sp. and rye). Thus far, in plants chromosome condensation throughout cell division appears to be associated with a particular combination of H3 modifications. Moreover, the distribution and dynamics of these modifications seem to be species-specific and even differ between mitosis and meiosis in the same species.

Isolation and characterization of S genome specific sequences from Aegilops sect. sitopsis species

Three S genome specific sequences were isolated from Aegilops sect. sitopsis species using different experimental approaches. Two clones, UTV86 and UTV39, were isolated from a partial genomic library obtained from DNA of Aegilops sharonensis, whereas a third clone, UTV5, was isolated from Aegilops speltoides. The three clones were characterized by sequencing, analysis of methylation, and sequence organization and abundance in some Aegilops and Triticum species. The clones UTV39 and UTV5 belong to the same family of tandem repeated sequences and showed high homology with a sequence already present in nucleotide databases. The UTV86 clone from Ae. sharonensis corresponded to an interspersed low frequency repeated sequence and did not show any significant homology with reported sequences. Southern hybridization experiments, using the cloned sequences as probes, detected polymorphism in the restriction patterns of all the five Aegilops species in section sitopsis. Aegilops speltoides showed the most divergent hybridization pattern. A close relationship was detected between the S genome of Ae. speltoides and the G genome of the wild Triticum timopheevii. In situ hybridization revealed a telomeric and (or) subtelomeric location of the sequences UTV39 and UTV5.

ITS regions in diploids of Aegilops (Poaceae) and their phylogenetic implications

The nucleotide sequences of the internal transcribed spacer (ITS) of nuclear ribosomal DNA in nine diploid species representing six sections of Aegilops were determined by direct sequencing of PCR-amplified DNA fragments. These sequences were aligned with two ITS sequences of additional species from Genbank. Sequence divergences were estimated using Kimura two-parameter model, and the phylogenetic analyses were performed using the maximum parsimony (MP) and the neighbor-joining (NJ) methods with PAUP and PHYLIP, respectively. The sequence divergences between the diploid species varied from 0.5% to 4.68%. The resulting MP tree and NJ tree showed relatively congruent phylogenetic relationships among these species, except Ae. caudata. Particularly, Ae. speltoides was basal within the two trees. The paraphyletic relationships between Ae. speltoides and two species of Sect. Sitopsis, and between Ae. uniaristata and two species of Sect. Comopyrum were supported strongly. The ITS data suggest that currently recognized sections within Aegilops should be reconsidered.

Simultaneous identification of A, B, D and R genomes by genomic in situ hybridization in wheat-rye derivatives

Multicolour genomic in situ hybridization was carried out in wheat-rye hybrids and in a wheat-rye translocation line. Different hybridization conditions and mixture compositions were used, and A, B and D genomes of hexaploid wheat as well as the R genome of rye were distinguished simultaneously in somatic cells. Combination of genomic and rDNA probes in multicolour in situ hybridization was also performed to identify chromosomes within a specific genome.

Standard karyotype of Triticum searsii and its relationship with other S-genome species and common wheat

C-banding polymorphism was analyzed in 14 accessions of Triticum searsii from Israel, and a generalized idiogram of the species was established. One accession was homozygous for whole arm translocations T1S(s)S·4S(s)S and T1S(s)L·4S(s)L. C-banding analysis was also used to identify 7 T. aestivum cv 'Chinese Spring'-T. searsii disomic chromosome addition lines, 14 ditelosomic chromosome addition lines, 21 disomic whole chromosome, and 31 ditelosomic chromosome substitution lines. The identity of these lines was further confirmed by meiotic pairing analysis. Sporophytic and gametophytic compensation tests were used to determine the homoeologous relationships of the T. searsii chromosomes. The results show that the T. searsii chromosomes do not compensate well for their wheat homoeologues. The C-banding patterns of T. searsii chromosomes are distinct from those of other S-genome species and from the B-genome chromosomes of wheat, indicating that T. searsii is not a direct B-genome donor species of T. turgidum and T. aestivum.

Standard karyotype of Triticum umbellulatum and the characterization of derived chromosome addition and translocation lines in common wheat

A standard karyotype and a generalized idiogram of Triticum umbellulatum (syn. Aegilops umbellulata, 2n = 2x = 14) was established based on C-banding analysis of ten accessions of different geographic origin and individual T. umbellulatum chromosomes in T. aestivum - T. umbellulatum chromosome addition lines. Monosomic (MA) and disomic (DA) T. aestivum - T. umbellulatum chromosome addition lines (DA1U = B, DA2U = D, MA4U = F, DA5U = C, DA6U = A, DA7U = E = G) and telosomic addition lines (DA1US, DA1UL, DA2US, DA2UL, DA4UL, MA5US, (+ iso 5US), DA5UL, DA7US, DA7UL) were analyzed. Line H was established as a disomic addition line for the translocated wheat - T. umbellulatum chromosome T2DS·4US. Radiation-induced wheat - T. umbellulatum translocation lines resistant to leaf rust (Lr9) were identified as T40 = T6BL·6BS-6UL, T41 = T4BL·4BS-6UL, T44 = T2DS·2DL-6UL, T47 = 'Transfer' = T6BS·6BL-6UL and T52 = T7BL·7BS-6UL. Breakpoints and sizes of the transferred T. umbellulatum segments in these translocations were determined by in situ hybridization analysis using total genomic T. umbellulatum DNA as a probe.

Analysis of metaphase I chromosome association in species of the genus Aegilops

Metaphase-I chromosome associations in every diploid and polyploid species of the genus Aegilops were studied using C-banding in order to analyse the cytogenetic behaviour of the whole complement as well as of specific genomes in different polyploid species. Differences were observed in the frequency of associations per cell among different species of the same ploidic level and even between species sharing the same genomic constitution. Differences were also found between different genomes within the same polyploid species and between the same genome when present in several diploid and polyploid species. Several factors proposed as having an influence on the frequency of metaphase-I associations, such as chromosome morphology, C-heterochromatin content, genetic control and genome interactions, are discussed. Most of the polyploid Aegilops species showed a diploid-like behaviour at metaphase I although multivalents involving homoeologous associations were occasionally observed in Ae. biuncialis, Ae. juvenalis and Ae. crassa(6x); therefore, the Aegilops diploidising genetic system is not equally effective in all polyploid species.

C-banding pattern and polymorphism of Aegilops caudata and chromosomal constitutions of the amphiploid T. aestivum - Ae. caudata and six derived chromosome addition lines

C-banding patterns were analysed in 19 different accessions of Aegilops caudata (= Ae. markgrafii, = Triticum dichasians) (2n = 14, genomically CC) from Turkey, Greece and the USSR, and a generalized C-banded karyotype was established. Chromosome specific C-bands are present in all C-genome chromosomes, allowing the identification of each of the seven chromosome pairs. While only minor variations in the C-banding pattern was observed within the accessions, a large amount of polymorphic variation was found between different accessions. C-banding analysis was carried out to identify Ae. caudata chromosomes in the amphiploid Triticum aestivum cv 'Alcedo' - Ae. caudata and in six derived chromosome addition lines. The results show that the amphiploid carries the complete Ae. Caudate chromosome complement and that the addition lines I, II, III, IV, V and VIII carry the Ae. caudata chromosome pairs B, C, D, F, E and G, respectively. One of the two SAT chromosome pairs (A) is missing from the set. C-banding patterns of the added Ae. caudata chromosomes are identical to those present in the ancestor species, indicating that these chromosomes are not structurally rearranged. The results are discussed with respect to the homoeologous relationships of the Ae. caudata chromosomes.

C-banding pattern and powdery mildew resistance of Triticum ovatum and four T. aestivum-T. ovatum chromosome addition lines

C-banding patterns of T. ovatum (Ae. ovata) and four T. aestivum cv 'Poros'-T. ovatum chromosome addition lines are presented, and the added chromosomes of T. ovatum have been identified. Furthermore, nucleolar activity and powdery mildew resistance were analyzed in the 'Poros'-ovatum addition lines and compared to that of T. ovatum and T. aestivum cv 'Poros'. The addition lines II, III and IV and 'Poros' were highly susceptible to powdery mildew isolates nos. 8 and 9, whereas the addition lines VI1 and VI2 showed high resistance. Even for an Ml-k virulent isolate, these two lines were highly resistant. By combining the cytological results and those of the powdery mildew analysis, the added chromosomes of T. ovatum can be excluded from responsibility for the high powdery mildew resistance of the addition lines VI1 and VI2. The same is true for a modified chromosome 6B, which is present in the 'Poros'-ovataum addition lines II, III and VI. The high variation in C-banding pattern observed in the A-, B- and D-genome complement of the addition lines is believed to be the result of crossing different lines of T. aestivum instead of 'Poros' alone. Thus, we cannot trace the powdery mildew resistance back to a specific chromosome.

Location of genes coding isozyme markers on Aegilops umbellulata chromosomes adds data on homoeology among Triticeae chromosomes

Zymogram analysis was used to identify the Aegilops umbellulata chromosomes that carry the structural genes for particular isozymes. Wheat, Aegilops and wheat-Aegilops hybrid derivative lines (which contained identified Aegilops chromosomes) were tested by gel electrophoresis for isozymes of particular enzymes. It was found that Aegilops chromosome A (nomenclature according to G. Kimber 1967) carries a structural gene for 6-phosphogluconate dehydrogenase, Aegilops chromosome B carries structural genes for glucose phosphate isomerase and phosphoglucose mutase, Aegilops chromosome D carries genes for leaf peroxidases, Aegilops chromosome E carries structural genes for endosperm peroxidases, acid phosphatases and leaf esterases, Aegilops chromosome F carries a gene for embryo plus scutellum peroxidases and Aegilops chromosome G carries structural genes for endosperm alkaline phosphatases, leaf alkaline phosphatases and leaf esterases. The results obtained indicate that chromosome B is partially homoeologous of the wheat chromosomes of group 1 and 4, and chromosome E is partially homoeologous of wheat chromosomes of groups 7 and 4. Circumstantial evidence is also provided about the possible association between chromosomes C, D and A of A. umbellulata respectively with chromosomes 5, 2 and 1 of wheat.

Nucleolus organizer competition in Triticum aestivum - Aegilops umbellulata chromosome addition lines

The nucleolar organizer activity of wheat (Triticum aestivum, AABBDD) and Aegilops umbellulata (UU) chromosomes have been analyzed in the complete set of the chromosome addition lines by using a highly reproducible silver-staining procedure. Chromosomes 1U and 5U produce the partial inactivation of wheat nucleolar organizer chromosomes 6B, 1B and 5D. The chromosomes D and G from Ae. umbellulata, which are not SAT-chromosomes, seem to specifically influence the activity of wheat NORs. The predominant status of the U genome with respect to nucleolar competition in the Triticeae is confirmed.

Meiotic behaviour of Un, D and R genomes in the amphiploid Aegilops ventricosa -Secale cereale and the parental species

Meiotic pairing frequencies of the Un and D genomes of Ae. ventricosa and the R of S. cereale could be easily established at metaphase I in Aegilops ventricosa - Secale cereale amphiploid plants as well as in its parental species by using the C-banding technique procedure. The results show a high diminution of chromosome pairing for all genomes in the amphiploid with respect to its parental species probably due to C-heterochromatin content and/or genotypic or cryptic interactions between the three genomes.

Intraspecific variation in C-banded chromosomes of Aegilops comosa and Ae. speltoides

Intraspecific variation in C-banding patterns can be used to differentiate subspecies of Ae. comosa, i.e. eu-comosa and heldrechii, but not those belonging to Ae. speltoides. Among the eu-comosa accessions, comosa E appears to possess a totally different karyotype as well as banding pattern. Two contrasting types of polymorphic changes were found. The first and more common type, observed in the 2 subspecies of Ae. speltoides and 2 accessions of Ae. comosa ssp. eucomosa, involved variation in C-band size and presence or absence of interstitial, terminal and proximal bands within a basic recognisable pattern. The second type involved complete repatterning of C-bands and could be seen in Ae. comosa where the ssp. eu-comosa has predominantly interstitial C-bands in contrast to centromeric and telomeric bands in the other ssp. heldrechii. Furthermore, the extent of polymorphic variation was found to vary between chromosomes of Ae. speltoides. That polymorphic changes have occurred without loss of fertility in hybrids between subspecies of each of the 2 species confirms that these sorts of changes have no effect on chromosome pairing or fertility. Polymorphic changes appear to be widespread within and between diploid Aegilops species and their non-random distribution seem to suggest that these changes could perhaps be intimately associated with the processes of speciation and subspeciation.