A molecular description of telometic heterochromatin in secale species

Cytogenetics in the age of molecular genetics

From the beginning of the 20th Century, we have seen tremendous advances in knowledge and understanding in almost all biological disciplines, including genetics, molecular biology, structural and functional genomics, and biochemistry. Among these advances, cytogenetics has played an important role. This paper details some of the important milestones of modern cytogenetics. Included are the historical role of cytogenetics in genetic studies in general and the genetics stocks produced using cytogenetic techniques. The basic biological questions cytogenetics can address and the important role and practical applications of cytogenetics in applied sciences, such as in agriculture and in breeding for disease resistance in cereals, are also discussed. The goal of this paper is to show that cytogenetics remains important in the age of molecular genetics, because it is inseparable from overall genome analysis. Cytogenetics complements studies in other disciplines within the field of biology and provides the basis for linking genetics, molecular biology and genomics research.

Molecular cytogenetic analyses of hexaploid lines spontaneously appearing in octoploid Triticale

Genome characterization of 14 hexaploid lines that spontaneously appeared in octoploid Triticales was carried out by sequential genomic in situ hybridization and fluorescence in situ hybridization, high molecular weight glutenin subunits and SSR marker analyses. All of the lines showed a chromosome constitution of complete A and B genomes, and a composite genome consisting of the chromosomes of D and R genomes. The composite genome of the 11 lines consisted of chromosomes 1R, 2D, 3R, 4R, 5R, 6R and 7R, that of the two lines were 1D, 2D, 3R, 4R, 5R, 6R and 7R, and that of one line was 1R, 2D, 3R, 4R, 5R, 6D and 7R. The incompatibility of the D and R genomes in common wheat genetic background, preferential retention of chromosome 2D and importance of these lines for the development of hexaploid Triticale are discussed in this report.

Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B

Bread wheat (Triticum aestivum) is one of the most important crops worldwide. However, because of its large, hexaploid, highly repetitive genome it is a challenge to develop efficient means for molecular analysis and genetic improvement in wheat. To better understand the composition and molecular evolution of the hexaploid wheat homoeologous genomes and to evaluate the potential of BAC-end sequences (BES) for marker development, we have followed a chromosome-specific strategy and generated 11 Mb of random BES from chromosome 3B, the largest chromosome of bread wheat. The sequence consisted of about 86% of repetitive elements, 1.2% of coding regions, and 13% remained unknown. With 1.2% of the sequence length corresponding to coding sequences, 6000 genes were estimated for chromosome 3B. New repetitive sequences were identified, including a Triticineae-specific tandem repeat (Fat) that represents 0.6% of the B-genome and has been differentially amplified in the homoeologous genomes before polyploidization. About 10% of the BES contained junctions between nested transposable elements that were used to develop chromosome-specific markers for physical and genetic mapping. Finally, sequence comparison with 2.9 Mb of random sequences from the D-genome of Aegilops tauschii suggested that the larger size of the B-genome is due to a higher content in repetitive elements. It also indicated which families of transposable elements are mostly responsible for differential expansion of the homoeologous wheat genomes during evolution. Our data demonstrate that BAC-end sequencing from flow-sorted chromosomes is a powerful tool for analysing the structure and evolution of polyploid and highly repetitive genomes.

Advanced resources for plant genomics: a BAC library specific for the short arm of wheat chromosome 1B

Common wheat (Triticum aestivum L., 2n = 6x = 42) is a polyploid species possessing one of the largest genomes among the cultivated crops (1C is approximately 17 000 Mb). The presence of three homoeologous genomes (A, B and D), and the prevalence of repetitive DNA make sequencing the wheat genome a daunting task. We have developed a novel 'chromosome arm-based' strategy for wheat genome sequencing to simplify this task; this relies on sub-genomic libraries of large DNA inserts. In this paper, we used a di-telosomic line of wheat to isolate six million copies of the short arm of chromosome 1B (1BS) by flow sorting. Chromosomal DNA was partially digested with HindIII and used to construct an arm-specific BAC library. The library consists of 65 280 clones with an average insert size of 82 kb. Almost half of the library (45%) has inserts larger than 100 kb, while 18% of the inserts range in size between 75 and 100 kb, and 37% are shorter than 75 kb. We estimated the chromosome arm coverage to be 14.5-fold, giving a 99.9% probability of identifying a clone corresponding to any sequence on the short arm of 1B. Each chromosome arm in wheat can be flow sorted from an appropriate cytogenetic stock, and we envisage that the availability of chromosome arm-specific BAC resources in wheat will greatly facilitate the development of ready-to-sequence physical maps and map-based gene cloning.

Diversity of a major repetitive DNA sequence in diploid and polyploid Triticeae

About 90 members of a major tandemly repeated DNA sequence family originally described in rye as pSc119.2 have been isolated from 11 diploid and polyploid Triticeae species using primers from along the length of the sequence for PCR amplification. Alignment and similarity analysis showed that the 120-bp repeat unit family is diverse with single nucleotide changes and few insertions and deletions occurring throughout the sequence, with no characteristic genome or species-specific variants having developed during evolution of the extant genomes. Fluorescent in situ hybridization showed that each of the large blocks of the repeat at chromosomal sites harboured many variants of the 120-bp repeat. There were substantial copy number differences between genomes, with abundant sub-terminal sites in rye, interstitial sites in the B genome of wheat, and relatively few sites in the A and D genome. We conclude that sequence homogenization events have not been operative in this repeat and that the common ancestor of the Triticeae tribe had multiple sequences of the 120-bp repeat with a range of variation not unlike that seen within and between species today. This diversity has been maintained when sites are moved within the genome and in all species since their divergence within the Triticeae.

Organization and evolution of highly repeated satellite DNA sequences in plant chromosomes

A major component of the plant nuclear genome is constituted by different classes of repetitive DNA sequences. The structural, functional and evolutionary aspects of the satellite repetitive DNA families, and their organization in the chromosomes is reviewed. The tandem satellite DNA sequences exhibit characteristic chromosomal locations, usually at subtelomeric and centromeric regions. The repetitive DNA family(ies) may be widely distributed in a taxonomic family or a genus, or may be specific for a species, genome or even a chromosome. They may acquire large-scale variations in their sequence and copy number over an evolutionary time-scale. These features have formed the basis of extensive utilization of repetitive sequences for taxonomic and phylogenetic studies. Hybrid polyploids have especially proven to be excellent models for studying the evolution of repetitive DNA sequences. Recent studies explicitly show that some repetitive DNA families localized at the telomeres and centromeres have acquired important structural and functional significance. The repetitive elements are under different evolutionary constraints as compared to the genes. Satellite DNA families are thought to arise de novo as a consequence of molecular mechanisms such as unequal crossing over, rolling circle amplification, replication slippage and mutation that constitute "molecular drive".

Chromosome sorting in tetraploid wheat and its potential for genome analysis

This study evaluates the potential of flow cytometry for chromosome sorting in durum wheat (Triticum turgidum Desf. var. durum, 2n = 4x = 28). Histograms of fluorescence intensity (flow karyotypes) obtained after the analysis of DAPI-stained chromosomes consisted of three peaks. Of these, one represented chromosome 3B, a small peak corresponded to chromosomes 1A and 6A, and a large peak represented the remaining 11 chromosomes. Chromosomes sorted onto microscope slides were identified after fluorescence in situ hybridization (FISH) with probes for GAA microsatellite, pSc119.2, and Afa repeats. Genomic distribution of these sequences was determined for the first time in durum wheat and a molecular karyotype has been developed for this crop. Flow karyotyping in double-ditelosomic lines of durum wheat revealed that the lines facilitated sorting of any arm of the wheat A- and B-genome chromosomes. Compared to hexaploid wheat, flow karyotype of durum wheat is less complex. This property results in better discrimination of telosomes and high purities in sorted fractions, ranging from 90 to 98%. We have demonstrated that large insert libraries can be created from DNA purified using flow cytometry. This study considerably expands the potential of flow cytogenetics for use in wheat genomics and opens the possibility of sequencing the genome of this important crop one chromosome arm at a time.

Chromosomal distribution of telomeric and telomeric-associated sequences in Hordeum chilense by in situ hybridization

The chromosomal distribution of telomeric repeat pAtT4 from Arabidopsis thaliana and telomeric associated repetitive sequence HvT01 from Hordeum vulgare have been studied by FISH (fluorescence in situ hybridization) in two accessions (H1 and H7) of Hordeum chilense. The telomeric sequence pAtT4 is present at the end of all chromosome arms in H1 and H7 accessions. In contrast, the telomeric associated sequence homologous to HvT01 showed variability for size, intensity and position of the signals for each line. In H1, HvT01 was present in every chromosome whereas only four chromosomes were labeled in H7 accession. Physical distribution of GAA-satellite sequence on both H1 and H7 metaphase chromosomes was also studied. Polymorphism for hybridization signals between the two accessions for GAA-banding pattern was also found. Based on differences in position and intensity of the hybridization signals found for both GAA and HvT01-homologous sequences, karyotypes for the in situ hybridization patterns are presented for H1 and H7 accessions of H. chilense.

Simultaneous painting of three genomes in hexaploid wheat by BAC-FISH

Fluorescence in situ hybridization (FISH) is widely used in the physical mapping of genes and chromosome landmarks in plants and animals. Bacterial artificial chromosomes (BACs) contain large inserts, making them amenable for FISH mapping. In our BAC-FISH experiments, we selected 56 restriction fragment length polymorphism (RFLP)-locus-specific BAC clones from the libraries of Triticum monococcum and Aegilops tauschii, which are the A- and D-genome donors of wheat (Triticum aestivum, 2n = 6x = 42), respectively. The BAC clone 676D4 from the T. monococcum library contains a dispersed repeat that preferentially hybridizes to A-genome chromosomes, and two BAC clones, 9I10 and 9M13, from the Ae. tauschii library contain a dispersed repeat that preferentially hybridizes to the D-genome chromosomes. These repeats are useful in simultaneously discriminating the three different genomes in hexaploid wheat, and in identifying intergenomic translocations in wheat or between wheat and alien chromosomes. Sequencing results show that both of these repeats are transposable elements, indicating the importance of transposable elements, especially retrotransposons, in the genome evolution of wheat.Key words: bacterial artificial chromosome (BAC), fluorescence in situ hybridization (FISH), transposable elements (TEs), wheat, Triticum aestivum.

Genomic distribution of three repetitive DNAs in cultivated hexaploid Diospyros spp. (D. kaki and D. virginiana) and their wild relatives

To understand the genomic organization of Diospyros species with different ploidy levels, we cloned three different repetitive DNAs and compared their genomic distributions in ten Diospyros species, including hexaploid D. kaki and D. virginiana. Genomic Southern hybridization demonstrated that the EcoRV-repetitive DNA was present in tandem in the genomes of D. glandulosa (2n=2x=30), D. oleifera (2n=2x=30), D. lotus (2n=2x=30), D. virginiana (2n=6x=90) and D. kaki (2n=6x=90). All of these species except D. virginiana also contained the HincII-repetitive DNA in tandem. Fluorescent in situ hybridization showed that the EcoRV- and HincII-repetitive DNAs were predominantly located at the proximal or centromeric regions of chromosomes. The DraI-repetitive sequence cloned from D. ehretioides (2n=2x=30) was not found in the other Diospyros species tested. This suggests that D. ehretioides has a genomic organization different from that of the other Diospyros species. Speciation of hexaploid Diospyros species is also discussed with respect to the genomic distribution of the three repetitive DNAs cloned.

Diverse patterns of the tandem repeats organization in rye chromosomes

Although the monomer size, nucleotide sequence, abundance and species distribution of tandemly organized DNA families are well characterized, little is known about the internal structure of tandem arrays, including total arrays size and the pattern of monomers distribution. Using our rye specific probes, pSc200 and pSc250, we addressed these issues for telomere associated rye heterochromatin where these families are very abundant. Fluorescence in situ hybridization (FISH) on meiotic chromosomes revealed a specific mosaic arrangement of domains for each chromosome arm where either pSc200 or pSc250 predominates without any obvious tendency in order and size of domains. DNA of rye-wheat monosomic additions studied by pulse field gel electrophoresis produced a unique overall blot hybridization display for each of the rye chromosomes. The FISH signals on DNA fibres showed multiple monomer arrangement patterns of both repetitive families as well as of the Arabidopsis-type telomere repeat. The majority of the arrays consisted of the monomers of both families in different patterns separated by spacers. The primary structure of some spacer sequences revealed scrambled regions of similarity to various known repetitive elements. This level of complexity in the long-range organization of tandem arrays has not been previously reported for any plant species. The various patterns of internal structure of the tandem arrays are likely to have resulted from evolutionary interplay, array homogenization and the generation of heterogeneity mediated by double-strand breaks and associated repair mechanisms.

Analysis and sorting of rye (Secale cereale L.) chromosomes using flow cytometry

Procedures for chromosome analysis and sorting using flow cytometry (flow cytogenetics) were developed for rye (Secale cereale L.). Suspensions of intact chromosomes were prepared by mechanical homogenization of synchronized root tips after mild fixation with formaldehyde. Histograms of relative fluorescence intensity obtained after the analysis of DAPI-stained chromosomes (flow karyotypes) were characterized and the chromosome content of the DNA peaks was determined. Chromosome 1R could be discriminated on a flow karyotype of S. cereale 'Imperial'. The remaining rye chromosomes (2R-7R) could be discriminated and sorted from individual wheat-rye addition lines. The analysis of lines with reconstructed karyotypes demonstrated a possibility of sorting translocation chromosomes. Supernumerary B chromosomes could be sorted from an experimental rye population and from S. cereale 'Adams'. Flow-sorted chromosomes were identified by fluorescence in situ hybridization (FISH) with probes for various DNA repeats. Large numbers of chromosomes of a single type sorted onto microscopic slides facilitated detection of rarely occurring chromosome variants by FISH with specific probes. PCR with chromosome-specific primers confirmed the identity of sorted fractions and indicated suitability of sorted chromosomes for physical mapping. The possibility to sort large numbers of chromosomes opens a way for the construction of large-insert chromosome-specific DNA libraries in rye.

Mapping of Rym14Hb, a gene introgressed from Hordeum bulbosum and conferring resistance to BaMMV and BaYMV in barley

Hordeum bulbosum represents the secondary gene pool of barley and constitutes a potential source of various disease resistances in barley breeding. Interspecific crosses of H. vulgare x H. bulbosum resulted in recombinant diploid-barley progeny with immunity to BaMMV after mechanical inoculation. Tests on fields contaminated with different viruses demonstrated that resistance was effective against all European viruses of the soil-borne virus complex (BaMMV, BaYMV-1, -2). Genetic analysis revealed that resistance was dominantly inherited. Marker analysis in a F5 mapping family was performed to map the introgression in the barley genome and to estimate its size after several rounds of recombination. RFLP anchor-marker alleles indicative of an H. bulbosum introgression were found to cover an interval 2.9 cM in length on chromosome 6HS. The soil-borne virus resistance locus harboured by this introgressed segment was designated Rym14(Hb). For marker-assisted selection of Rym14(Hb) carriers, a diagnostic codominant STS marker was derived from an AFLP fragment amplified from leaf cDNA of homozygous-resistant genotypes inoculated with BaMMV.

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.

A centromeric tandem repeat family originating from a part of Ty3/gypsy-retroelement in wheat and its relatives

From a wild diploid species that is a relative of wheat, Aegilops speltoides, a 301-bp repeat containing 16 copies of a CAA microsatellite was isolated. Southern blot and fluorescence in situ hybridization revealed that approximately 250 bp of the sequence is tandemly arrayed at the centromere regions of A- and B-genome chromosomes of common wheat and rye chromosomes. Although the DNA sequence of this 250-bp repeat showed no notable homology in the databases, the flanking or intervening sequences between the repeats showed high homologies (>82%) to two separate sequences of the gag gene and its upstream region in cereba, a Ty3/gypsy-like retroelement of Hordeum vulgare. Since the amino acid sequence deduced from the 250 bp with seven CAAs showed some similarity ( approximately 53%) to that of the gag gene, we concluded that the 250-bp repeats had also originated from the cereba-like retroelements in diploid wheat such as Ae. speltoides and had formed tandem arrays, whereas the 300-bp repeats were dispersed as a part of cereba-like retroelements. This suggests that some tandem repeats localized at the centromeric regions of cereals and other plant species originated from parts of retrotransposons.

Identification of wheat-barley translocations by sequential GISH and two-colour FISH in combination with the use of genetically mapped barley SSR markers

Five wheat-barley translocations in a wheat background were characterized through the combination of cytogenetic and molecular genetic approaches. The wheat chromosome segments involved in the translocations were identified using sequential GISH and two-colour FISH with the probes pSc119.2 and pAs1. The barley chromatin in these lines was identified using SSR markers. A total of 45 markers distributed over the total barley genome were selected from a recently published linkage map of barley and tested on the translocation lines. The following translocations were identified: 2DS.2DL-1HS, 3HS.3BL, 6BS.6BL-4HL, 4D-5HS, and 7DL.7DS-5HS. Wheat-barley disomic and ditelosomic addition lines for the chromosomes 3HS, 4H, 4HL, 5H, 5HL, and 6HS were used to determine the correct location of 21 markers and the position of the centromere. An intragenomic translocation breakpoint was detected on the short arm of the barley chromosome 5H with the help of SSR marker analysis. Physical mapping of the SSR markers on chromosomes 1H and 5H was carried out using the intragenomic and the interspecific translocation breakpoints, as well as the centromere, as physical landmarks.

Genus-specific localization of the TaiI family of tandem-repetitive sequences in either the centromeric or subtelomeric regions in Triticeae species (Poaceae) and its evolution in wheat

The TaiI family sequences are classified as tandem repetitive DNA sequences present in the genome of tribe Triticeae, and are localized in the centromeric regions of common wheat, but in the subtelomeric heterochromatic regions of Leymus racemosus and related species. In this study, we investigated the chromosomal distribution of TaiI family sequences in other Triticeae species. The results demonstrated a centromeric localization in genera Triticum and Aegilops and subtelomeric localization in other genera, thus showing a genus-dependent localization of TaiI family sequences in one or the other region. The copy numbers of TaiI family sequences in species in the same genus varied greatly, whether in the centromeric or subtelomeric regions (depending on genus). We also examined the evolution of TaiI family sequences during polyploidization of hexaploid common wheat. A comparison of chromosomal locations of the major TaiI family signals in common wheat and in its ancestral species suggested that the centromeric TaiI family sequences in common wheat were inherited from its ancestors with little modification, whereas a mixed origin for the B genome of common wheat was indicated.

High resolution FISH to delineate contiguous and small DNA sequences

Somatic and meiotic metaphase, and pachytene chromosomes were subjected to DNA: DNA in situ hybridization to elucidate relative resolution of FISH signals for weak/contiguous hybridization sites. Hybridization with a '350 family' rye repetitive DNA probe pSc 200 characteristically differentiated the rye chromosome 5 from the rest of the complement on account of two small terminal homologous sites in the long arm, resolution of which is substantially improved using pachytene. Higher resolution of the two weak hybridization sites; a very small distal and a small proximal, is unequivocally demonstrated in the FISH painted 5RL examined at pachytene in the 5AS/5RL wheat background. Additionally this probe exhibits a large block of distal telomeric hybridization site in 5RS, followed by a more prominent proximal site homologous to '610 family' rye repetitive probe pSc 250. Precise denaturation - hybridization incubation and post hybridization stringency washing facilitates spatial resolution of contiguous repetitive rye probes pSc 200 and pSc 250, and physical localisation of small RFLP probe xpr 115 of wheat on barley chromosomes.

Loss of chromosomes 2R and 5RS in octoploid triticale selected for agronomic traits

The advanced lines of octoploid triticale which have been bred for nearly a half century in China show significant improvements in agronomic traits such as plant height, fertility, threshability, maturity and seed plumpness, although no intentional cytological selection had been performed. In this study, eight primary and six advanced lines were analyzed by fluorescence and genomic in situ hybridization to elucidate their chromosome constitutions. In the advanced lines, about 70% of the plants examined had 2n = 56 chromosomes (range: 50 to 58). Almost all advanced lines, however, had lost rye chromosome 2R and the short arm of 5R (5RS). The exceptions were lines Y1005 and Y4683: The former had lost only the 2R chromosome and the latter only 5RS. The reduction of rye chromosomes was compensated by an extra pair of 2D or A-genome (possibly 2A) chromosomes in plants with 2n = 56. This suggests that the loss of 2R and 5RS chromosomes contributes to the improvement of octoploid triticale. Since the plants with chromosome 2R are non-free threshing and chromosome 2D of synthetic wheat is known to carry the Tg (tenacious glumes) gene, it is possible that chromosome 2R carries a gene affecting the threshability, and we carried out selection to remove it. We also discuss the possible relationshipbetween 5RS and the genetic stability of octoploid triticale.

Identification and chromosomal organization of two rye genome-specific RAPD products useful as introgression markers in wheat

Two rye genome-specific random amplified polymorphic DNA (RAPD) markers were identified for detection of rye introgression in wheat. Both markers were amplified in all of the tested materials that contained rye chromatin such as rye, hexaploid triticale, wheat-rye addition lines, and wheat varieties with 1BL.1RS translocation. Two cloned markers, designated pSc10C and pSc20H, were 1012 bp and 1494 bp, respectively. Sequence analysis showed that both pSc10C and pSc20H fragments were related to retrotransposons, ubiquitously distributed in plant genomes. Using fluorescence in situ hybridization (FISH), probe pSc10C was shown to hybridize predominantly to the pericentromeric regions of all rye chromosomes, whereas probe pSc20H was dispersed throughout the rye genome except at telomeric regions and nucleolar organizing regions. The FISH patterns showed that the two markers should be useful to select or track all wheat-rye translocation lines derived from the whole arms of rye chromosomes, as well as to characterize the positions of the translocation breakpoints generated in the proximal and distal regions of rye arms.

Comparative genomic in situ hybridization (cGISH) analysis on plant chromosomes revealed by labelled Arabidopsis DNA

A new approach for comparative cytogenetic banding analysis of plant chromosomes has been established. The comparative GISH (cGISH) technique is universally applicable to various complex genomes of Monocotyledonae (Triticum aestivum, Agropyron elongatum, Secale cereale, Hordeum vulgare, Allium cepa, Muscari armenaticum and Lilium longiflorum) and Dicotyledonae (Vicia faba, Beta vulgaris, Arabidopsis thaliana). Labelled total genomic DNA of A. thaliana generates signals at conserved chromosome regions. The nucleolus organizing regions (NORs) containing the majority of tandemly repeated rDNA sequences, N-band regions containing satellite DNA, conserved homologous sequences at telomeres and additional chromosome-characteristic markers were detected in heterologous FISH experiments. Multicolour FISH analysis with repetitive DNA probes simultaneously revealed the chromosome assignment of 56 cGISH signals in rye and 61 cGISH signals in barley. Further advantages of this technique are: (1) the fast and straightforward preparation of the probe; (2) the generation of signals with high intensity and reproducibility even without signal amplification; and (3) no requirement of species-specific sequences suitable for molecular karyotype analysis. Hybridization can be performed without competitive DNA. Signal detection without significant background is possible under low stringency conditions. The universal application of this fast and simple one-step fluorescence banding technique for plant cytogenetic and plant genome evolution is discussed.

Introgression of rye chromatin on chromosome 2D in the Portuguese wheat landrace 'Barbela'

The old Portuguese wheat landrace aggregate known as 'Barbela' shows good productivity under the low-fertility conditions often associated with acid soils. The use of genomic rye DNA, in combination with 45S rDNA and the repetitive sequences dpTa1 and pSc119.2 as probes, in two sequential in situ hybridization steps enabled the identification of all chromosomes in the 'Barbela' wheat lines and the detection of the introgression of rye-origin chromatin onto wheat chromosome arm 2DL in two of the lines. Amplification of microsatellite loci using published primer pairs showed that the distal segment of wheat chromosome 2DL, which was involved in the rye translocation, was deleted. The identification and characterization of small recombinant chromosome segments in wheat–rye lines may allow their use in plant breeding programmes. Their presence in farmer-maintained material demonstrates the importance of maintaining, characterizing, and collecting landrace material before valuable genetic combinations are lost as uniform commercial crops are introduced.Key words: biodiversity, in situ hybridization, microsatellites, plant breeding, recombination, alien chromosomes, marker selection.

Identification and characterization of two genes encoding the eukaryotic initiation factor 4A in rice

A cDNA encoding eukaryotic translation initiation factor 4A (eIF4A) was isolated from a cDNA library of rice (Oryza sativa L.). Based on this DNA sequence, a 414-amino acid protein exhibiting 67, 64 and 59% homology to the mouse, Schizosaccharomyces pombe and Saccharomyces cerevisiae eIF4A, respectively, was predicted. The deduced amino acid sequence contains the characteristic motifs shared by the DEAD box supergene family. Another cDNA of rice eIF4A was reported previously. Comparison of the coding sequences of the two rice eIF4As showed 85% homology in the nucleotide sequence and 90% homology in the amino acid sequence. The genomic clones corresponding to the two rice eIF4A cDNAs were also isolated from a genomic library of rice (Oryza sativa L.). It was found that the two genes have common patterns of exon-intron boundaries. Their coding regions are split into four exons, and there is an additional exon in the 5'-non coding region.

Identification and characterization of the gene encoding the mitochondrial elongation factor G in rice

A plant nuclear gene coding for a mitochondrial elongation factor G (mEF-G) was cloned from a cDNA library and genomic library of rice (Oryza sativa L.). This DNA sequence predicts a 757-amino-acid protein exhibiting 79%, 55% and 49% homology to Arabidopsis thaliana, Saccharomyces cerevisiae and rat mEF-G respectively, 53% homology to the elongation factor G in Escherichia coli and 43% homology to soybean chloroplast elongation factor G. The deduced amino acid sequence contains the characteristic motifs shared by all GTP binding proteins. Comparison of the sequence of the genomic clone to that of the cDNA clone revealed that this gene is split nineteen times by introns, although the gene of Arabidopsis is split seventeen times by introns. Some of the introns found in the rice genome are relatively long and they result in a long gene with a size of approximately 15 kb.

Physical arrangement of retrotransposon-related repeats in centromeric regions of wheat

Cereal centromeres commonly contain many repetitive sequences that are derived from Ty3/gypsy retrotransposon. FISH analysis using a large DNA insert library of wheat identified a 67-kb clone (R11H) that showed strong hybridization signals on the centromeres. The R11H clone contains Ty3/gypsy retrotransposon-related sequences; both integrase and CCS1 family sequences were identified. Subsequently, we isolated additional 23 large-insert clones which also contained the integrase and CCS1 sequences. Based on the number of the integrase repeats in the clones determined by DNA gel blot analysis, we concluded that the retrotransposon-like sequences are tandemly repeated in wheat centromeres in ca. 55-kb interval on average. This conclusion is consistent with the results of FISH analysis on the extended DNA fibers.

Organization of highly repeated sequences in surface-spread pachytene chromosomes of rye

A method of preparing two-dimensional surface spreads of plant synaptonemal complexes (SCs) associated with fluorescence in situ hybridization (FISH) has been applied to analyze the location and organization of five different highly repeated DNA sequences in rye. Our observations indicate that, depending on the type of sequence, the chromatin displays different types of organization. Telomeric sequences were seen tightly associated with the SC while other repetitive DNA sequences were found to form loops that are associated with SCs only at their bases. On the contrary, the FISH signal of a centromeric satellite had a granular appearance, reflecting that the hybridization occurs only with parts of the chromatin loops.Key words: fluorescence in situ hybridization, meiosis, repetitive DNA, rye, synaptonemal complex.

Widely separated multiple transgene integration sites in wheat chromosomes are brought together at interphase

We have investigated the organization of transgenes delivered by particle bombardment into the wheat genome, combining conventional molecular analysis with fluorescence in situ hybridization (FISH) and three-dimensional confocal microscopy. We selected a representative population of transformed wheat lines and carried out molecular and expression analysis. FISH on metaphase chromosomes showed that transgene integration sites were often separated by considerable lengths of genomic DNA (>1 Mbp), or could even be on opposite chromosome arms. Plants showing multiple integration sites on a single chromosome were selected for three-dimensional confocal analysis of interphase nuclei in root and embryo tissue sections. Confocal microscopy revealed that these sites lay in close physical proximity in the interphase nuclei. Our results clearly show that multiple transgenes physically separated by large intervening regions of endogenous DNA at metaphase can be brought together at interphase. This may reflect the original physical organization of the endogenous DNA at the moment of transformation, with DNA strand breaks introduced into several co-localized DNA loops by the intruding gold particles. Alternatively, the transgenes may be brought together after transformation, either by an ectopic homologous pairing mechanism, or by recruitment to a common transcription site.

CEREAL CHROMOSOME STRUCTURE, EVOLUTION, AND PAIRING

▪ Abstract  The determination of the order of genes along cereal chromosomes indicates that the cereals can be described as a single genetic system. Such a framework provides an opportunity to combine data generated from the studies on different cereals, enables chromosome evolution to be traced, and sheds light on key structures involved in cereal chromosome pairing. Centromeric and telomeric regions have been highlighted as important in these processes.

Isolation and characterization of copia-type retrotransposons in Arabidopsis thaliana

We isolated two copia-type retrotransposons from Arabidopsis thaliana. We named these elements AtRE1 (Arabidopsis thaliana Retro Element 1) and AtRE2. Nucleotide sequence analysis revealed that both elements have long terminal repeats (LTRs), and that their internal sequences include one large open reading frame that could encode Gag protein, protease, integrase, reverse transcriptase, and RNaseH. The deduced amino acids sequences contain several domains that are conserved among a large family of retrotransposons. The primer binding site for first-strand DNA synthesis and the polypurine tract for second-strand DNA synthesis existed at corresponding positions. A 5bp target site duplication (TSD) sequence was also found in the flanking region of LTRs. Southern hybridization and sequence determination of the flanking region demonstrated that AtREs exist at different loci in the two A. thaliana ecotypes Columbia and Landsberg erecta. Moreover, AtRE2 exists at two loci in Landsberg erecta, in contrast to the existence of only one copy in Columbia. These findings suggest that AtREs were recently transfected via some mediators or that AtREs were transposed after differentiation of the two ecotypes. One cDNA clone derived from the transcripts of AtRE1 was isolated, and the nucleotide sequence showed that this RNA was transcribed in the antisense direction. RT-PCR analysis revealed that AtRE1 was transcribed in both directions. This result suggests that the antisense RNA controls the expression of AtRE1 at the post-transcriptional level.

Exclusive localization of tandem repetitive sequences in subtelomeric heterochromatin regions of Leymus racemosus (Poaceae, Triticeae)

Two kinds of tandem repetitive sequences were isolated from Leymus racemosus (Lam.) Tzvelev. One of them was classified in the 350-bp family originally isolated from Secale. The other was a novel repetitive sequence family, named 'TaiI family', which consisted of a repeat unit of 570 bp. Fluorescence in-situ hybridization of the chromosomes of L. racemosus indicated that both families were located in subtelomeric heterochromatin and that the 350-bp family and TaiI family occupied different heterochromatin regions. In addition, even homologous chromosomes did not show the same patterns of TaiI and 350-bp families. The combination of these two families of repetitive sequences, together with Afa-family sequences and rDNAs, helps to identify the ten homologous chromosome pairs of L. racemosus. From these data, we proposed a karyotype of L. racemosus and compared it with other karyotypes already reported.

Physical mapping of wheat-Aegilops longissima breakpoints in mildew-resistant recombinant lines using FISH with highly repeated and low-copy DNA probes

Fluorescence in situ hybridization (FISH) with multiple probes, consisting of highly repeated DNA sequences (pSc119.2 and pAs1) and of a low-copy, 3BS-specific RFLP sequence (PSR907), enabled determination of the physical position of the wheat-alien breakpoints (BPs) along the 3BS and 3DS arms of common wheat recombinant lines. These lines harbour 3SlS Aegilops longissima segments containing the powdery mildew resistance gene Pm13. In all 3B recombinants, the wheat-Aegilops longissima physical BPs lie within the interval separating the two most distal of the three pSc119.2 3BS sites. In all such recombinants a telomeric segment, containing the most distal of the pSc119.2 3BS sites, was in fact replaced by a homoeologous Ae. longissima segment, marked by characteristic pSc119.2 hybridization sites. Employment of the PSR907 RFLP probe as a FISH marker allowed to resolve further the critical region in the various 3B recombinant lines. Three of them, like the control common wheat, exhibited between the two most distal pSc119.2 sites a single PSR907 FISH site, which was missing in a fourth recombinant line. The amount of alien chromatin can thus be estimated to represent around 20% of the recombinant arm in the three former lines and a maximum of 27% in the latter. A similar physical length was calculated for the alien segment contained in three 3D recombinants, all characterized by the presence of the Ae. longissima pSc119.2 sites distal to the nearly telomeric pAs1 sites of normal 3DS. Comparison between the FISH-based maps and previously developed RFLP maps of the 3BS-3SlS and 3DS-3SlS arms revealed substantial differences between physical and genetic map positions of the wheat-alien BPs and of molecular markers associated with the critical chromosomal portions.Key words: wheat-alien recombinants, chromosome engineering, fluorescence in situ hybridization, highly repeated and low-copy DNA probes, physical versus genetic maps.

Rye chromosome variability in wheat-rye addition and substitution lines

In a study of polymorphism and stability in rye chromosomes, three rye varieties and the sets of wheat-rye addition and substitution lines were compared using two non-homologous highly repetitive DNA families, pSc200 and pSc250. The rye varieties, Petkus, Imperial and Onohoiskaya, showed polymorphism for the presence and the size of the pSc200 in-situ hybridization signals on chromosome pairs, 2R, 4R and 7R, and the pSc250 signals on chromosomes, 5R, 6R and 7R. Chromosome 1R was heteromorphic within the Onohoiskaya variety. Differences in the distribution of chromosome polymorphisms imply that intervarietal changes to these highly repetitive DNA families occurred independently, despite their juxtaposition or even overlapping locations in subtelomeric heterochromatic regions. In the set of Saratovskaya 29 wheat/Onohoiskaya substitution lines, only chromosome 2R was altered relative to its counterpart in the parental rye variety due to amplification of the pSc250 signal on the long arm, although this did not exceed intervarietal polymorphism. In the set of Chinese Spring wheat/Imperial addition lines, only two Imperial chromosomes, 4R and 6R, were unchanged. We detected the loss of one or both rye homologous chromosomes, the loss of one arm, and the deletion of subtelomeric heterochromatin accompanied by the loss of the pSc200 signal. The results show that Saratovskaya 29/Onohoiskaya chromosome substitution lines possess increased chromosome stability compared with Chinese Spring/Imperial addition lines.

Molecular cytogenetic analysis ofAegilops cylindrica Host

The genomic constitution of Aegilops cylindrica Host (2n = 4x = 28, DcDcCcCc) was analyzed by C-banding, genomic in situ hybridization (GISH), and fluorescence in situ hybridization (FISH) using the DNA clones pSc119, pAs1, pTa71, and pTA794. The C-banding patterns of the Dc- and Cc-genome chromosomes of Ae. cylindrica are similar to those of D-and C-genome chromosomes of the diploid progenitor species Ae. tauschii Coss. and Ae. caudata L., respectively. These similarities permitted the genome allocation and identification of the homoeologous relationships of the Ae. cylindrica chromosomes. FISH analysis detected one major 18S-5.8S-25S rDNA locus in the short arm of chromosome 1Cc. Minor 18S-5.8S-25S rDNA loci were mapped in the short arms of 5Dc and 5Cc. 5S rDNA loci were identified in the short arm of chromosomes 1Cc, 5Dc, 5Cc, and 1Dc. GISH analysis detected intergenomic translocation in three of the five Ae. cylindrica accessions. The breakpoints in all translocations were non-centromeric with similar-sized segment exchanges.Key words: Aegilops cylindrica, C-banding, GISH, FISH, genome evolution.

A novel repetitive sequence, termed the JNK repeat family, located on an extra heterochromatic region of chromosome 2R of Japanese rye

Among cultivated rye, Seccale cereale L., collected in Japan, we found an extra heterochromatin on the long-arm interstitial region of chromosome 2R. This extra heterochromatin was polymorphic in the population. The plants with the extra heterochromatin showed a specific DNA fragment of 1.2 kb in digests prepared with the restriction enzyme Dral. The fragment was cloned and used as a probe for fluorescent in-situ hybridization (FISH). The clone, pScJNK1, showed a hybridization signal at the extra heterochromatic region. The segregation of the number of signals corresponded to the number of the extra heterochromatin of the 2R chromosome, indicating that the sequence might construct the heterochromatin. Southern hybridization using the clone as a probe showed a ladder pattern, suggesting that the sequence was a tandem repeat. Three sequences homologous to pScJNK1 were isolated; these were 1192 1232 bp, 44.7-45.9% in GC content, highly homologous (> 93%) with each other, and did not show any significant homology to other sequences in a DNA database. Slot blot hybridization using pScJNK1 as a probe indicated that there were about 4000 copies of the sequence in the haploid genome carrying the extra heterochromatin, whereas less than 20 copies existed in the genome without the heterochromatin. Southern hybridization using MspI and HapII indicated that all of the second cytosine nucleotides in CCGG sites in the sequence were methylated in the extra heterochromatin.

Molecular cytogenetic analysis of tetraploid and hexaploid Aegilops crassa

The distribution of highly repetitive DNA sequences on chromosomes of tetraploid and hexaploid cytotypes of Aegilops crassa (Dcr1Xcr and Dcr1XcrDcr2 genomes) was studied using C-banding and in situ hybridization analyses with the pSc119, pAs1 and pTa794 DNA clones. In total, 14 tetraploid and five hexaploid accessions were examined. All chromosomes can be identified by their C-banding and ISH pattern with the pAs1 DNA clone. Only a few pSc119 hybridization sites were observed in the telomeric regions of several chromosomes. We found a high level of C-banding polymorphism and only minor variations in labeling patterns. The position of C-bands generally coincided with the location of the pAs1 sequence. Three 5S rDNA loci were detected in tetraploid Ae. crassa, whereas five pTa794 ISH sites were observed in 6x Ae. crassa. All the hexaploid accessions differed from the tetraploids by a reciprocal non-centromeric translocation involving chromosomes A and N. Three additional translocations were detected in the accessions analyzed. The Dcr1 genome of 4x Ae. crassa is highly modified compared with the D genome of the progenitor species Ae. tauschii. Because of the large amount of chromosomal rearrangements, the origin of the Xcr genome remains unknown. The second Dcr2 genome of 6x Ae. crassa is different from the Dcr1 genome but is similar to the D-genome chromosomes of Ae. tauschii, indicating that no additional large rearrangements occurred at the hexaploid level.

Isolation and characterisation of repeated DNA sequences from Erianthus spp. (Saccharinae: Andropogoneae)

Four anonymous noncoding sequences were isolated from Erianthus arundinaceus. The four sequences were selected because they were specific to the genusErianthus section Ripidium, relative to Saccharum spp. These sequences, designated Eracsi 294, 228, 153, and 34, showed various degrees of repetitiveness and different patterns of distribution. Eracsi 34 and 153 were low- and medium-copy repeated sequences, respectively, and appeared to be present at discrete locations in the Erianthus genome. By contrast, Eracsi 294, also a low-copy sequence, appeared to be more dispersed in location, with some tandem arrays identified. Eracsi 228 was highly repeated and dispersed. The location of Eracsi 228 was more precisely determined by FISH and was found to be distributed along the length of, but not at the telomeres of, most chromosomes in two Erianthus species. The distribution of the four sequences was investigated in a sample of 65 Erianthus (representing 9 species) and 14 Saccharum (2 species) accessions. The usefulness of these sequences for phylogenetic and genome organisation studies in sugarcane and for assessing the genetic structure of Saccharum x Erianthus intergeneric hybrids is discussed.Key words: Erianthus, FISH, repetitive sequences, Saccharum, sugarcane.

A method for fluorescence in situ hybridization against synaptonemal complex-associated chromatin of plant meiocytes

An improved method of preparing two-dimensional surface spreads of plant synaptonemal complexes (SCs) associated with fluorescent in situ hybridization is described. This technique produces clear preparations of SCs and, in addition, consistently reveals the organization and location of different repetitive DNA sequences in plant meiotic prophase chromosomes.

Genome-specific repetitive DNA and RAPD markers for genome identification in Elymus and Hordelymus

We have developed RFLP and RAPD markers specific for the genomes involved in the evolution of Elymus species, i.e., the St, Y, H, P, and W genomes. Two P genome specific repetitive DNA sequences, pAgc1 (350 bp) and pAgc30 (458 bp), and three W genome specific sequences, pAuv3 (221 bp), pAuv7 (200 bp), and pAuv13 (207 bp), were isolated from the genomes of Agropyron cristatum and Australopyrum velutinum, respectively. Attempts to find Y genome specific sequences were not successful. Primary-structure analysis demonstrated that pAgc1 (P genome) and pAgc30 (P genome) share 81% similarity over a 227-bp stretch. The three W genome specific sequences were also highly homologous. Sequence comparison analysis revealed no homology to sequences in the EMBL- GenBank databases. Three to four genome-specific RAPD markers were found for each of the five genomes. Genome-specific bands were cloned and demonstrated to be mainly low-copy sequences present in various Triticeae species. The RFLP and RAPD markers obtained, together with the previously described H and St genome specific clones pHch2 and pPlTaq2.5 and the Ns genome specific RAPD markers were used to investigate the genomic composition of a few Elymus species and Hordelymus europaeus, whose genome formulas were unknown. Our results demonstrate that only three of eight Elymus species examined (the tetraploid species Elymus grandis and the hexaploid speciesElymus caesifolius and Elymus borianus) really belong to Elymus.

Characterization and genomic organization of Ty1-copia group retrotransposons in rye (Secale cereale)

The genomic organisation of the Ty1-copia retrotransposons in rye (Secale cereale) has been studied. We have used the polymerase chain reaction (PCR) to amplify sequences from a conserved domain of the reverse transcriptase gene of the Ty1-copia retrotransposons in this species. Sequence analysis of 26 of these PCR products shows them to be a highly heterogeneous population, a feature that is common in plants. Slot blot analysis shows that there are about 100,000 individual Ty1-copia retrotransposons in rye. In situ hybridization of a heterogeneous probe, representing the whole population of rye Ty1-copia retrotransposon sequences, to chromosome spreads of triticale (xTriticosecale), a rye-wheat hybrid, shows that these sequences are present throughout all the rye chromosomes but absent from the centromeric regions and, in particular, from the terminal heterochromatin. Southern analysis of oat, barley, wheat, and rye, using as a probe R9, one of the rye sequences that is closely similar to the BARE-1 element of barley, shows that close relatives of this retrotransposon subgroup are present in all these species in high copy number. Northern analysis on RNAs from seedlings shows that the BARE-1 subgroup is transcribed in all these cereal plants but in variable amounts: high in barley, moderate in wheat and rye, and extremely low in oat.

A complex arrangement of genes at a starch branching enzyme I locus in the D-genome donor of wheat

Genomic DNA fragments from Triticum tauschii (D-genome donor to wheat) carrying starch branching enzyme I (SBE I) type genes have been characterized. One fragment contains one complete gene and two partial genes in 16 kb of DNA. One of the partial genes is oriented in the opposite strand to the other two. The gene that is complete was sequenced. Its structure corresponds closely to that of rice in that exons 3-8 are retained at similar sizes and spacings. A cDNA closely corresponding to the complete gene was isolated and characterized; it codes for a putative protein that represents a novel type of SBE I, as it is shorter at the 3' end than the forms reported so far in other plants. A second genomic fragment contains a different SBE I gene. There appear to be approximately 10 copies of SBE I type genes in wheat (approximately 5 in T. tauschii) and most of them have been assigned to group 7 chromosomes. In situ hybridization indicates that a major locus for the genes is located at the distal end of the short arm of chromosome 7D.

Multiple repetitive DNA sequences in the paracentromeric regions of Arabidopsis thaliana L

Nine repetitive DNA sequences, present in the haploid Arabidopsis thaliana genome in 7-300 copies, were hybridized in situ to metaphase and interphase chromosomes. Every sequence was detected on all five chromosome pairs, but was not evenly dispersed over the genome. Clusters of signals were found in particular regions of the centromeric heterochromatin, and each sequence showed a characteristic distribution pattern. Some sequences hybridized more strongly on different chromosomes, reflecting chromosome-specific amplification or the presence of homologous sequences. No hybridization signals could be detected on euchromatic regions. In situ hybridization on extended chromatin fibres showed that the pAL1 repeats are interrupted by another repetitive DNA sequence. A cosmid subclone (74A) contained a (GA)38 microsatellite motif, and hybridization with a (GA) oligonucleotide revealed that most of the hybridization sites of 74A correspond to the distribution of this microsatellite motif. The results show that the paracentromeric heterochromatin of A. thaliana chromosomes is composed not only of the tandemly arranged 180-bp repeat family pAL1/pAtMr, but also of some other repetitive sequences, thus giving a better understanding of the organization of sequences at the centromeres of A. thaliana.

Distribution of highly repeated DNA sequences in species of the genus Secale

The presence and distribution of the most important highly repetitive DNA sequences of rye in cultivated and wild species of the genus Secale were investigated using fluorescence in situ hybridization. Accurate identification of individual chromosomes in the most commonly recognized species or subspecies of the genus Secale (S. cereale, S. ancestrale, S. segetale, S. afghanicum, S. dighoricum, S. montanum, S. montanum ssp. kuprijanovii, S. africanum, S. anatolicum, S. vavilovii, and S. silvestre) was achieved using three highly repetitive rye DNA sequences (probes pSc119.2, pSc74, and pSc34) and the 5S ribosomal DNA sequence pTa794. It is difficult to superimpose trends in the complexity of repetitive DNA during the evolution of the genus on conclusions from other cytogenetic and morphological assays. However, there are two clear groups. The first comprises the self-pollinated annuals S. silvestre and S. vavilovii that have few repeated nucleotide sequences of the main families of 120 and 480 bp. The second group presents amplification and interstitialization of the repeated nucleotide sequences and includes the perennials S. montanum, S. anatolicum, S. africanum, and S. kuprijanovii, as well as the annual and open-pollinated species S. cereale and its related weedy forms. The appearance of a new locus for 5S rRNA in S. cereale and S. ancestrale suggests that cultivated ryes evolved from this wild weedy species.

Nucleolar dominance in triticales: control by unlinked genes

Hybrid plants and animals often show suppression of activity of ribosomal genes (rDNA) originating from one of the parental or ancestral species. In the wheat x rye amphiploid triticale, containing 28 chromosomes of wheat origin and 14 from rye, rDNA of rye origin (on chromosome 1R) is not normally expressed, while the 1B- and 6B-origin rDNA from wheat shows strong expression. Expression of rDNA can be accurately assessed by the silver staining method, which stains both interphase nucleoli and metaphase rDNA sites that were actively expressed at the previous interphase. We show here that substitution of another rye chromosome, 2R, by a chromosome from hexaploid wheat, 2D (triticale-2D(2R)), prevents suppression of the rye-origin rDNA, and leads to activity of all six major rDNA loci. These results were found in two different triticales and supported by rDNA behaviour in wheat-rye chromosomal addition lines. Models for chromosomal interactions leading to control of rDNA expression are presented.

Nuclear instability and its manipulation in plant breeding

Nuclear instability occurs spontaneously in a typically very small proportion of cells of every individual, even in crop varieties. Of greatest interest to the cereal breeder are instabilities in the germ line, which produce off-types among progeny, or in the endosperm, which reduce grain quality. Nuclear instabilities in crop plants merit cytological investigation for several reasons: first, to ensure that biologically possible standards of genetical purity are set for varieties in agriculture; secondly, because once understood, nuclear instability may be usefully applied in plant breeding; thirdly, because nuclear instability is thought to have played a major role in crop plant evolution - understanding the past may help in predicting which new genome combinations will be successful crop species; fourthly, because failure to achieve adequate nuclear stability has played a major role in preventing so many potentially useful plants from becoming crops. These points are illustrated mainly by reference to three different nuclear instabilities, namely: (1) haploid barley production by genome elimination in some Hordeum vulgare x H. bulbosum crosses; (2) the action of the tri gene in barley to produce about 50% diploid embryo sacs; (3) aberrant endosperm development in hexaploid triticale. Improved seed type in triticale has been achieved by a controlled reduction in rye telomeric heterochromatin. This approach may open the way for a new type of plant breeding, selecting for nucleotypic variation in the amount of non-coding DNA sequences. Understanding the cellular mechanisms responsible for nuclear stability (or instability) is essential if controlled plant modification based on precise nuclear engineering is to become possible. This understanding can come only from sustained fundamental research.

Nuclear DNA amounts in angiosperms

Nuclear DNA amounts have been estimated for more than 200 angiosperm species since the last collected list of such values for about 750 species was published by Bennett & Smith in 1976 ( Phil. Trans. R. Soc. Lond. B 274, 227- 274). These new estimates are either scattered in a wide range of scientific journals or, in many cases, unpublished; so they are not readily accessible. A publication, collecting these data in a single list is required. This paper contains a supplementary list of absolute DNA values, including estimates for 240 angiosperm species not listed by Bennett & Smith in 1976, as well as additional estimates for 41 species already listed by them. These data are assembled primarily for reference purposes. Consequently, the species are listed in alphabetical order, as this was felt to be more helpful to cyto- and biochemists, who it is anticipated will be among the major users.

Distribution and complex organization of satellite DNA sequences in Aveneae species

Distribution, organization, and molecular analysis of four unrelated satellite DNA components in Aveneae species are described. Highly repeated DNA elements were cloned from Helictotrichon convolutum (CON1 and CON2) and Helictotrichon compressum (COM1 and COM2). The lengths of the repeat monomers are 365 bp (CON1), 562 bp (CON2), 346 bp (COM1), and 476 bp (COM2). Similar repeats were detected by dot blots, Southern blots, and by DNA sequencing in other species of the genus Helictotrichon, in Aveneae species, and in species of the tribes Andropogoneae and Oryzeae. All four satellite DNAs are differently distributed in the taxonomic groups mentioned above. Remarkably, the longer elements are built up in a complex pattern of either shorter subrepeats arranged in tandem (COM2) or by duplications inserted into an original 369-bp element (CON2). Shorter representatives, 190 bp, similar to CON1 elements occur in Holcus species. In Koeleria species, COM1-related repeats are only 180 bp in length. No similarity was found among the sequences CON2, COM1, and COM2 or with sequences of other repetitive DNA elements of the grasses, but CON1 shows sequence similarity to an A genome specific repetitive DNA of Oryza (rice).

Identification and characterization of two tandem repeat sequences (TrsB and TrsC) and a retrotransposon (RIRE1) as genome-general sequences in rice

Three kinds of DNA sequences (here called TrsB, TrsC and RIRE1) have been previously reported to be those repeated in tandem specifically in the wild rice species with FF, CC or EE genome, respectively. To characterize these genome type-specific sequences, we carried out PCR using a pair of primers, which hybridize to a restricted region in the repeating unit sequence and prime DNA synthesis in both directions. Gel electrophoresis and DNA sequencing revealed that PCR using primers for TrsB (or TrsC) amplified the fragments with an integral series of a unit length not only from total DNA of the rice strain with FF (or CC) genome, but also from those of the rice strains with non-FF (or non-CC) genome. TrsB or TrsC was, however, found to be repeated in an extraordinary number of copies in the species with FF or CC genome, respectively, in which the TrsB (or TrsC) sequence has been originally identified. PCR using primers for RIRE1 produced various sizes of fragments from total DNA of the rice strains with EE genome. The fragments, however, showed no progression at interval of the unit length characteristic for tandem repeats. Nucleotide sequencing of the amplified fragments revealed that they were not the sequences repeated in tandem, but were those interspersed as an element having partial homology with the LTR sequences of retrotransposons, Wis-2-1A in wheat and BARE-1 in barley. RIRE1 was present in the rice species with any types of genomes, but in the species with EE genome in an extraordinary number of copies.

Molecular diversification of tandemly organized DNA sequences and heterochromatic chromosome regions in some Triticeae species

The subtelomeric heterochromatin of rye (Secale cereale) chromosomes makes up 12-18% of the genome and consists largely of a small number of tandemly organized DNA sequence families. The genomic organization, chromosomal locations and the structural organization of monomer units of the major DNA sequences from these regions were investigated and compared in other Triticeae species from the genera Secale, Agropyron, Dasypyrum, Triticum and Hordeum. Southern hybridization and polymerase chain reaction analysis established that all studied species preserve the tandem type of sequence organization but the copy number is altered drastically between species. In the pSc200 family, a fraction of the tandem arrays is present with a head-to-head orientation of dimers in S. cereale and S. montanum. Members of the same family are more heterogeneous and present as head-to-head monomers in the Dasypyrum species and A. cristatum. In situ hybridization demonstrates different organization of the sequence families in the various species: pSc200 and pSc250 are concentrated in major blocks at the ends of most rye chromosome arms, whereas they are more dispersed and in smaller blocks in Dasypyrum and Agropyron, indicating that accumulation is not simply due to the sequence itself. In contrast to rye, D. villisum has large blocks of only pSc200 whereas D. breviaristatum shows greater amplification of pSc250. These data indicate that each repetitive family is an independent unit of evolution, and suggest that the two Dasypyrum species are not closely related. The data are discussed in terms of existing evolutionary models for repetitive DNA sequences. The contribution of random events, through molecular drive and selection, to the evolution of heterochromatic regions is considered.