Chromosomal locations of four minor rDNA loci and a marker microsatellite sequence in barley

Comparative Cytogenetic of the 36-Chromosomes Genera of Orchidinae Subtribe (Orchidaceae) in the Mediterranean Region: A Summary and New Data

This article provides a summary of the current knowledge on the cytogenetics of four genera, which are all composed of 36 chromosomes, within the Orchidinae subtribe (Orchidaceae). Previous classical studies have revealed differences in karyomorphology among these genera, indicating genomic diversity. The current study includes an analysis of the current knowledge with an update of the karyotype of 47 species with 36 chromosomes from the genera Anacamptis, Serapias, Himantoglossum, and Ophrys. The study discusses comparisons of karyotypes among these genera that used traditional techniques as well as karyotype asymmetry relationships with various asymmetry indices. Additionally, the study reports new findings on polyploidy in Anacamptis pyramidalis and Serapias lingua, which were observed through karyotype and meiotic metaphase analyses in EMC. Moreover, the study detected B chromosomes for the first time in A. papilionacea and A. palustris. The article also describes the use of fluorescent in situ hybridization in some specimens of A. papilionacea and A. collina to locate different sites of the 18S-5.8S-25S rDNA and 5S rDNA ribosomal complexes on chromosomes. The information derived from these cytogenetic analyses was used to refine the classification of these orchids and identify evolutionary relationships among different species and genera.

Physical localization of 45S rDNA in Cymbopogon and the analysis of differential distribution of rDNA in homologous chromosomes of Cymbopogon winterianus

Cymbopogon, commonly known as lemon grass, is one of the most important aromatic grasses having therapeutic and medicinal values. FISH signals on somatic chromosome spreads off Cymbopogon species indicated the localization of 45S rDNA on the terminal region of short arms of a chromosome pair. A considerable interspecific variation in the intensity of 45S rDNA hybridization signals was observed in the cultivars of Cymbopogon winterianus and Cymbopogon flexuosus. Furthermore, in all the varieties of C. winterianus namely Bio-13, Manjari and Medini, a differential distribution of 45S rDNA was observed in a heterologous pair of chromosomes 1. The development of C. winterianus var. Manjari through gamma radiation may be responsible for breakage of fragile rDNA site from one of the chromosomes of this heterologous chromosome pair. While, in other two varieties of C. winterianus (Bio-13 and Medini), this variability may be because of evolutionary speciation due to natural cross among two species of Cymbopogon which was fixed through clonal propagation. However, in both the situations these changes were fixed by vegetative method of propagation which is general mode of reproduction in the case of C. winterianus.

The Hordeum bulbosum 25S-18S rDNA region: comparison with Hordeum vulgare and other Triticeae

Hordeum vulgare and Hordeum bulbosum are two closely related barley species, which share a common H genome. H. vulgare has two nucleolar organizer regions (NORs), while the NOR of H. bulbosum is only one. We sequenced the 2.5 kb 25S-18S region in the rDNA of H. bulbosum and compared it to the same region in H. vulgare as well as to the other Triticeae. The region includes an intergenic spacer (IGS) with a number of subrepeats, a promoter, and an external transcribed spacer (5'ETS). The IGS of H. bulbosum downstream of 25S rRNA contains two 143-bp repeats and six 128-bp repeats. In contrast, the IGS in H. vulgare contains an array of seven 79-bp repeats and a varying number of 135-bp repeats. The 135-bp repeats in H. vulgare and the 128-bp repeats in H. bulbosum show similarity. Compared to H. vulgare, the 5'ETS of H. bulbosum is shorter. Additionally, the 5'ETS regions in H. bulbosum and H. vulgare diverged faster than in other Triticeae genera. Alignment of the Triticeae promoter sequences suggests that in Hordeum, as in diploid Triticum, transcription starts with guanine and not with adenine as it is in many other plants.

Molecular cytogenetic and morphological characterization of two wheat-barley translocation lines

Barley chromosome 5H, carrying important QTLs for plant adaptation and tolerance to abiotic stresses, is extremely instable in the wheat genetic background and is eliminated in the early generations of wheat-barley crosses. A spontaneous wheat-barley 5HS-7DS.7DL translocation was previously obtained among the progenies of the Mv9kr1 x Igri hybrid. The present work reports on the transfer of the 5HS-7DS.7DL translocation into a modern wheat cultivar, Mv Bodri, in order to use it in the wheat breeding program. The comparison of the hybridization bands of DNA repeats HvT01, pTa71, (GAA)n and the barley centromere-specific (AGGGAG)n in Igri barley and the 5HS-7DS.7DL translocation, together with the visualization of the barley chromatin made it possible to determine the size of the introgressed barley segment, which was approximately 74% of the whole 5HS. Of the 29 newly developed PCR markers, whose source ESTs were selected from the Genome Zipper of barley chromosome 5H, 23 were mapped in the introgressed 1-0.26 FL 5HS bin, three were located in the missing C-0.26 FL region, while three markers were specific for 5HL. The translocation breakpoint was flanked by markers Hv7502 and Hv3949. A comparison of the parental wheat cultivars and the wheat-barley introgression lines indicated that the presence of the translocation improved tillering ability in the Mv9kr1 and Mv Bodri genetic background. The similar or better yield components under high- or low-input cultivation environments, respectively, indicated that the 5HS-7DS.7DL translocation had little or no negative effect on yield components, making it a promising genotype to improve wheat genetic diversity. These results promise to accelerate functional genomic studies on barley chromosome 5H and to support pre-breeding and breeding research on wheat.

Addition of Manas barley chromosome arms to the hexaploid wheat genome

Background

Cultivated barley belongs to the tertiary genepool of hexaploid wheat. Genes of interest can be transferred from barley into wheat through wide hybridization. The application of wheat-barley introgression lines could provide an excellent tool for the transfer of earliness, favourable amino acid composition, biotic stress resistance, abiotic stress tolerance, or good tillering ability into wheat.

Results

A set of 10 wheat-barley ditelosomic addition lines (2HS, 2HL, 3HS, 3HL, 4HS, 4HL, 6HS, 6HL, 7HS and 7HL) was developed from the progenies of an Asakaze/Manas wheat-barley hybrid produced in Martonvásár, Hungary. The addition lines were selected from self-fertilized plants of the BC₂F₂-BC₂F₄ generations using genomic in situ hybridization (GISH) and were identified by fluorescence in situ hybridization (FISH) with repetitive DNA probes [HvT01, (GAA)₇ and centromere-specific (AGGGAG)₄ probes]. The cytogenetic identification was confirmed using barley arm-specific SSR and STS markers. The ditelosomic additions were propagated in the phytotron and in the field, and morphological parameters (plant height, tillering, length of the main spike, number of seeds/spike and seeds/plant, and spike characteristics) were described. In addition, the salt stress response of the ditelosomic additions was determined.

Conclusions

The six-rowed winter barley cultivar Manas is much better adapted to Central European environmental conditions than the two-rowed spring barley Betzes previously used in wheat-barley crosses. The production of wheat-barley ditelosomic addition lines has a wide range of applications both for breeding (transfer of useful genes to the recipient species) and for basic research (mapping of barley genes, genetic and evolutionary studies and heterologous expression of barley genes in the wheat background).

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-016-0393-2) contains supplementary material, which is available to authorized users.

Chromosomal detection of simple sequence repeats (SSRs) using nondenaturing FISH (ND-FISH)

Simple Sequence Repeats (SSRs) are known to be scattered and present in high number in eukaryotic genomes. We demonstrate that dye-labeled oligodeoxyribonucleotides with repeated mono-, di-, tri, or tetranucleotide motifs (15-20 nucleotides in length) have an unexpected ability to recognize SSR target sequences in non-denatured chromosomes. The results show that all these probes are able to invade chromosomes, independent of the size of the repeat motif, their nucleotide sequence, or their ability to form alternative B-DNA structures such as triplex DNA. This novel and remarkable property of binding SSR oligonucleotides to duplex DNA targets permitted the development of a non-denaturing fluorescence in situ hybridization method that quickly and efficiently detects SSR-enriched chromosome regions in mitotic, meiotic, and polytene chromosome spreads of different model organisms. These results have implications for genome analysis and for investigating the roles of SSRs in chromosome structure and function.

Bulbosum to Go: A Toolbox to Utilize Hordeum vulgare/bulbosum Introgressions for Breeding and Beyond

Hordeum bulbosum L., a wild relative of barley (Hordeum vulgare L.), has been considered as a valuable source of genetic diversity for barley improvement. Since the 1990s, a considerable number of barley/H. bulbosum introgression lines (IL)s has been generated, with segments introgressed from H. bulbosum harboring a diverse set of desirable traits. However, the efficient utilization of these ILs has been hampered, largely due to the lack of suitable molecular tools for their genetic characterization and highly reduced interspecific recombination frequencies in the region of the introgression. In the present study, we utilized genotyping-by-sequencing for the detailed molecular characterization of 145 ILs. Genotypic information allows the genetic diversity within the set of ILs to be determined and a strategy was outlined to tackle the obstacle of reduced recombination frequencies. Furthermore, we compiled exome capture re-sequencing information of barley and H. bulbosum and designed an integrated barley/H. bulbosum sequence resource with polymorphism information on interspecific and intraspecific sequence variations of both species. The integrated sequence will be valuable for marker development in barley/H. bulbosum ILs derived from any barley and H. bulbosum donors. This study provides the tools for the widespread utilization of barley/H. bulbosum ILs in applied barley breeding and academic research.

Improvement of the agronomic traits of a wheat-barley centric fusion by introgressing the 3HS.3BL translocation into a modern wheat cultivar

The 3HS.3BL spontaneous Robertsonian translocation obtained from the progenies of wheat-barley (Chinese Spring × Betzes) hybrids backcrossed with wheat line Mv9kr1 was transferred into the modern Martonvásár wheat cultivar Mv Bodri. The translocation was identified with molecular cytogenetic methods. The inheritance of the translocation was traced using genomic in situ hybridization. Fluorescence in situ hybridization using barley subtelomeric (HvT01) and centromere-specific [(AGGGAG)4] repetitive DNA probes confirmed that the complete barley chromosome arm was involved in the Robertsonian translocation. The wheat-specific repetitive DNA probes identified the presence of the whole wheat genome, except the short arm of the 3B chromosome. Genotypes homozygous for the centric fusion were selected, after which morphological analysis was performed on the plants and the yield components were measured in the field during two consecutive vegetative seasons. The introgression of the 3HS.3BL translocation into the modern wheat cultivar Mv Bodri significantly reduced the plant height due to the incorporation of the dwarfing allele RhtD1b. The presence of the 3HS.3BL translocation in the Mv9kr1 and Mv Bodri wheat background improved tillering and seeds per plant productivity in field experiments carried out in Martonvásár and Keszthely, Hungary.

Analysis of chromosomal polymorphism in barley (Hordeum vulgare L. ssp. vulgare) and between H. vulgare and H. chilense using three-color fluorescence in situ hybridization (FISH)

The aim of the present work was to study chromosomal polymorphism within cultivated barley (Hordeum vulgare ssp. vulgare) using three-color fluorescence in situ hybridization (FISH). The physical distribution of the most frequently used, highly repetitive DNA sequences (GAA)7 specific for pericentromeric heterochromatic regions, the ribosomal DNA clone pTa71, specific for the 45S rDNA, and the barley-specific telomere-associated sequence HvT01, was investigated to reveal genetic diversity in metaphase spreads of ten barley genotypes with diverse geographical origin, growth habit and row number. A wild relative of barley, Hordeum chilense was also studied in order to compare the polymorphism between and within Hordeum species. Significant differences in the hybridization patterns of all three DNA probes could be detected between the two related species, but only probes pTa71 and HvT01 showed variation in the intensity and/or position of hybridization sites among genotypes of H. vulgare ssp. vulgare. The extent of polymorphism was less than that earlier reported for molecular markers and was restricted to the long chromosome arms, with differences between the chromosomes. 1H and 3H proved to be the most variable chromosomes and 4H and 6H the most conserved.

Distribution of 45S rDNA sites in chromosomes of plants: structural and evolutionary implications

Background

45S rDNA sites are the most widely documented chromosomal regions in eukaryotes. The analysis of the distribution of these sites along the chromosome in several genera has suggested some bias in their distribution. In order to evaluate if these loci are in fact non-randomly distributed and what is the influence of some chromosomal and karyotypic features on the distribution of these sites, a database was built with the position and number of 45S rDNA sites obtained by FISH together with other karyotypic data from 846 plant species.

Results

In angiosperms the most frequent numbers of sites per diploid karyotype were two and four, suggesting that in spite of the wide dispersion capacity of these sequences the number of rDNA sites tends to be restricted. The sites showed a preferential distribution on the short arms, mainly in the terminal regions. Curiously, these sites were frequently found on the short arms of acrocentric chromosomes where they usually occupy the whole arm. The trend to occupy the terminal region is especially evident in holokinetic chromosomes, where all of them were terminally located. In polyploids there is a trend towards reduction in the number of sites per monoploid complement. In gymnosperms, however, the distribution of rDNA sites varied strongly among the sampled families.

Conclusions

The location of 45S rDNA sites do not vary randomly, occurring preferentially on the short arm and in the terminal region of chromosomes in angiosperms. The meaning of this preferential location is not known, but some hypotheses are considered and the observed trends are discussed.

Genetic characterization of a reciprocal translocation present in a widely grown barley variety

Artificially induced translocation stocks have been used to physically map the barley genome; however, natural translocations are extremely uncommon in cultivated genotypes. Albacete is a barley variety widely grown in recent decades in Spain and carrying a reciprocal translocation which obviously does not affect its agronomical fitness. This translocation has been characterized by a combination of cytological and molecular genetic approaches. Firstly, recombination frequencies between markers on chromosomes 1H and 3H were estimated to determine the boundaries of the reciprocal interchange. Secondly, 1H-3H wheat barley telosome addition lines were used to assign selected markers to chromosome arms. Thirdly, fluorescence in situ hybridization (FISH) with rDNA probes (5S and 18S-5.8S-26S) and microsatellite probes [(ACT)(5), (AAG)(5) and (CAG)(5)] was used to determine the locations of the translocation breakpoints more precisely. Fourthly, fine-mapping of the regions around the translocation breakpoints was used to increase the marker density for comparative genomics. The results obtained in this study indicate that the translocation is quite large with breakpoints located on the long arms of chromosomes 1H and 3H, between the pericentromeric (AAG)(5) bands and above the (ACT)(5) interstitial distal bands, resulting in the reciprocal translocation 1HS.1HL-3HL and 3HS.3HL-1HL. The gene content around the translocation breakpoints could be inferred from syntenic relationships observed among different species from the grass family Poaceae (rice, Sorghum and Brachypodium) and was estimated at approximately 1,100 and 710 gene models for 1H and 3H, respectively. Duplicated segments between chromosomes Os01 and Os05 in rice derived from ancestral duplications within the grass family overlap with the translocation breakpoints on chromosomes 1H and 3H in the barley variety Albacete.

Identification and phenotypic description of new wheat – six-rowed winter barley disomic additions

To increase the allelic variation in wheat–barley introgressions, new wheat–barley disomic addition lines were developed containing the 2H, 3H, 4H, 6H, and 7H chromosomes of the six-rowed Ukrainian winter barley ‘Manas’. This cultivar is agronomically much better adapted to Central European environmental conditions than the two-rowed spring barley ‘Betzes’ previously used. A single ‘Asakaze’ × ‘Manas’ wheat × barley hybrid plant was multiplied in vitro and one backcross plant was obtained after pollinating 354 regenerant hybrids with wheat. The addition lines were selected from the self-fertilized seeds of the 16 BC2 plants using genomic in situ hybridization. The addition lines were identified by fluorescence in situ hybridization using repetitive DNA probes (HvT01, GAA, pTa71, and Afa family), followed by confirmation with barley SSR markers. The addition lines were grown in the phytotron and in the field, and morphological parameters (plant height, fertility, tillering, and spike characteristics) were measured. The production of the disomic additions will make it possible to incorporate the DNA of six-rowed winter barley into the wheat genome. Addition lines are useful for genetic studies on the traits of six-rowed winter barley and for producing new barley dissection lines.

The chromosome number, karyotype and genome size of the desert plant diploid Reaumuria soongorica (Pall.) Maxim

Extreme drought and salt resistant plant Reaumuria soongorica is of great potential for revealing genetic bases unique to naturally stress-tolerant plants. A preliminary genome survey, including chromosome number, karyotype, chromosomal localization of 45S rDNA loci and genome size was conducted with R. soongorica collected from Lanzhou, China. Chromosome counting showed that R. soongorica is diploid with chromosome number of 22. Karyotypical analysis illustrated that the chromosomes size ranges from 3.38 to 5.51 μm, and the chromosomal formula is 2n = 2x = 22 = 4 m + 14sm + 4st. Fluorescence in situ hybridization revealed that four pairs of 45SrDNA signals were detected at the end of R. soongorica chromosomes. The flow cytometry analysis indicated that the mean C value of R. soongorica is 0.806 pg with predicted genome size of about 778 Mb. The results indicate that the extreme drought and salt resistance of R. soongorica was not attributed to a big and complicate genome and also offer some clues in resolving the problems of taxonomy and evolution in Tamaricaceae.

Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.)

Background

Chickpea (Cicer arietinum L.) is an economically important cool season grain legume crop that is valued for its nutritive seeds having high protein content. However, several biotic and abiotic stresses and the low genetic variability in the chickpea genome have continuously hindered the chickpea molecular breeding programs. STMS (Sequence Tagged Microsatellite Sites) markers which are preferred for the construction of saturated linkage maps in several crop species, have also emerged as the most efficient and reliable source for detecting allelic diversity in chickpea. However, the number of STMS markers reported in chickpea is still limited and moreover exhibit low rates of both inter and intraspecific polymorphism, thereby limiting the positions of the SSR markers especially on the intraspecific linkage maps of chickpea. Hence, this study was undertaken with the aim of developing additional STMS markers and utilizing them for advancing the genetic linkage map of chickpea which would have applications in QTL identification, MAS and for de novo assembly of high throughput whole genome sequence data.

Results

A microsatellite enriched library of chickpea (enriched for (GT/CA)_n and (GA/CT)_n repeats) was constructed from which 387 putative microsatellite containing clones were identified. From these, 254 STMS primers were designed of which 181 were developed as functional markers. An intraspecific mapping population of chickpea, [ICCV-2 (single podded) × JG-62 (double podded)] and comprising of 126 RILs, was genotyped for mapping. Of the 522 chickpea STMS markers (including the double-podding trait, screened for parental polymorphism, 226 (43.3%) were polymorphic in the parents and were used to genotype the RILs. At a LOD score of 3.5, eight linkage groups defining the position of 138 markers were obtained that spanned 630.9 cM with an average marker density of 4.57 cM. Further, based on the common loci present between the current map and the previously published chickpea intraspecific map, integration of maps was performed which revealed improvement of marker density and saturation of the region in the vicinity of sfl (double-podding) gene thereby bringing about an advancement of the current map.

Conclusion

An arsenal of 181 new chickpea STMS markers was reported. The developed intraspecific linkage map defined map positions of 138 markers which included 101 new locations.Map integration with a previously published map was carried out which revealed an advanced map with improved density. This study is a major contribution towards providing advanced genomic resources which will facilitate chickpea geneticists and molecular breeders in developing superior genotypes with improved traits.

High-density fluorescence in situ hybridization signal detection on barley (Hordeum vulgare L.) chromosomes with improved probe screening and reprobing procedures

The barley ( Hordeum vulgare L.) genome was screened to identify sequences that could be used for fluorescence in situ hybridization (FISH). From 2000 transformed bacterium colonies carrying barley clones, 56 colonies were selected on the basis of the patterns that their PCR products produced when subjected to agarose gel electrophoresis. Among them, 42 (75%) exhibited fluorescent signals on barley chromosomes after in situ hybridization using the directly labeled PCR products. Sequencing revealed seven clones, pHv-365, pHv-177, pHv-1112, pHv-689, pHv-1476, pHv-1889, and pHv-1972, to be newly identified FISH-positive sequences. The remainder possess previously described sequences such as 5S, GAA microsatellite, centromere repeats, HVT01, and pHvMWG2315 (324 bp repeat). It is shown here that a combination of five probes, which produce strong signals on barley chromosomes, pHv-38 (5S), pHv-365, pHv-961 (HVT01), GAA, and TAG microsatellites, offer unequivocal recognition of each chromosome. The combination of three probes, i.e., pHv-1123 (barley 324 bp repeat), GAA, and TAG, decorated entire chromosomes with fine dotted signals and was useful for detecting the break points of aberrant chromosomes. The signals’ distributions of pHv-177, pHv-1112, and TAG were highly polymorphic. An improved reprobing procedure and its usefulness are also discussed.

Distribution of 45S and 5S rDNA sites in 23 species of Eleocharis (Cyperaceae)

Studies of rDNA location in holocentric chromosomes of the Cyperaceae are scarce, but a few reports have indicated the occurrence of multiple 45S rDNA sites at terminal positions, and in the decondensed state of these regions in prometaphase/metaphase. To extend our knowledge of the number 45S and 5S rDNA sites and distribution in holocentric chromosomes of the Cyperaceae, 23 Brazilian species of Eleocharis were studied. FISH showed 45S rDNA signals always located in terminal regions, which varied from two (E. bonariensis with 2n = 20) to ten (E. flavescens with 2n = 10 and E. laeviglumis with 2n = 60). 5S rDNA showed less variation, with 16 species exhibiting two sites and 7 species four sites, preferentially at terminal positions, except for four species (E. subarticulata, E. flavescens, E. sellowiana and E. geniculata) that showed interstitial sites. The results are discussed in order to understand the predominance of terminal rDNA sites, the mechanisms involved in the interstitial positioning of 5S rDNA sites in some species, and the events of amplification and dispersion of 45S rDNA terminal sites.

[Analysis of the chromosomes of S. bicolor x S. propinquum and S. dochna x S. propinquum by FISH]

By means of fluorescence in situ hybridization (FISH), we located and analyzed the sites of the 45S rDNA on the F1 hybrids of S. bicolor x S. propinquum and S. dochnaxS.propinquum. Two signals of 45S rDNA were mapped on the mitotic metaphase chromosomes in the F1 hybrids, respectively, and one signal was present on a bivalent during meiotic of synaptene, diakinesis, and metaphase I. We inferred that the two mitotic chromosomes carrying 45S rDNA were homologous pairs. Considering the signals of 45S rDNA location during meiotic process, chromosome pairing of these two F1 hybrids was normal with an average pairing configuration of 2n=2x=20 (10 II). Our results indicated that 45S rDNA could provide a landmark for identification of individual chromosome during meiosis indirectly.

A transgenomic cytogenetic sorghum (Sorghum propinquum) bacterial artificial chromosome fluorescence in situ hybridization map of maize (Zea mays L.) pachytene chromosome 9, evidence for regions of genome hyperexpansion

A cytogenetic FISH map of maize pachytene-stage chromosome 9 was produced with 32 maize marker-selected sorghum BACs as probes. The genetically mapped markers used are distributed along the linkage maps at an average spacing of 5 cM. Each locus was mapped by means of multicolor direct FISH with a fluorescently labeled probe mix containing a whole-chromosome paint, a single sorghum BAC clone, and the centromeric sequence, CentC. A maize-chromosome-addition line of oat was used for bright unambiguous identification of the maize 9 fiber within pachytene chromosome spreads. The locations of the sorghum BAC-FISH signals were determined, and each new cytogenetic locus was assigned a centiMcClintock position on the short (9S) or long (9L) arm. Nearly all of the markers appeared in the same order on linkage and cytogenetic maps but at different relative positions on the two. The CentC FISH signal was localized between cdo17 (at 9L.03) and tda66 (at 9S.03). Several regions of genome hyperexpansion on maize chromosome 9 were found by comparative analysis of relative marker spacing in maize and sorghum. This transgenomic cytogenetic FISH map creates anchors between various maps of maize and sorghum and creates additional tools and information for understanding the structure and evolution of the maize genome.

The nonrandom distribution of long clusters of all possible classes of trinucleotide repeats in barley chromosomes

This paper is the first to report the long-range organization of all possible classes of trinucleotide motifs in a higher plant genome. Fluorescent in situ hybridization (FISH), employing the synthetic oligonucleotides (AAC)5, (AAG)5, (AAT)5, (AGG)5, (CAC)5, (CAT)5, (CAG)5, (ACT)5, (ACG)5 and (GCC)5, was used to characterize the nonrandom and motif-dependent distribution of tandem arrays of trinucleotide repeats in the metaphase chromosomes and interphase nuclei of barley (Hordeum vulgare L.). This provided detailed information on the sequence content of barley chromatin and allowed the saturation of the physical map of all barley chromosomes. The following conclusions were also drawn: (1) Except for (AAT)5 and (GCC)5, the studied repetitive motifs have a characteristic pattern of distribution in terms of their in situ FISH signals. Some permit the accurate identification of individual chromosomes. (2) (CAG)5, (CAT)5 and (ACT)5 are not found in all barley chromosomes. (3) With the exception of (ACT)5, the remaining trinucleotide repeats occur predominantly in the heterochromatin and are largely absent from the euchromatic regions. Moreover, (CAC)5, (ACG)5 and (CAG)5 are exclusively concentrated in the centromeres. The employment of simple synthetic probes for the identification of chromosomes and genomic characterization, and their importance in studies on genome organization, function and evolution, are discussed.

A simple chromosomal marker can reliably distinguishes Poncirus from Citrus species

Several chromosome types have been recognized in Citrus and related genera by chromomycin A(3 )(CMA) banding patterns and fluorescent in situ hybridization (FISH). They can be used to characterize cultivars and species or as markers in hybridization and backcrossing experiments. In the present work, characterization of six cultivars of P. trifoliata ("Barnes", "Fawcett", "Flying Dragon", "Pomeroy", "Rubidoux", "USDA") and one P. trifoliata x C. limonia hybrid was performed by sequential analyses of CMA banding and FISH using 5S and 45S rDNA as probes. All six cultivars showed a similar CMA(+) banding pattern with the karyotype formula 4B + 8D + 6F. The capital letters indicate chromosomal types: B, a chromosome with one telomeric and one proximal band; D, with only one telomeric band; F, without bands. In situ hybridization labeling was also similar among cultivars. Three chromosome pairs displayed a closely linked set of 5S and 45S rDNA sites, two of them co-located with the proximal band of the B type chromosomes (B/5S-45S) and the third one co-located with the terminal band of a D pair (D/5S-45S). The B/5S-45S chromosome has never been found in any citrus accessions investigated so far. Therefore, this B chromosome can be used as a marker to recognize the intergeneric Poncirus x Citrus hybrids. The intergeneric hybrid analyzed here displayed the karyotype formula 4B + 8D + 6F, with two chromosome types B/5S-45S and two D/5S-45S. The karyotype formula and the presence of two B/5S-45S chromosomes clearly indicate that the plant investigated is a symmetric hybrid. It also demonstrates the suitability of karyotype analyses to differentiate zygotic embryos or somatic cell fusions involving trifoliate orange germplasm.

Ancestry of American polyploid Hordeum species with the I genome inferred from 5S and 18S-25S rDNA

BACKGROUND AND AIMS

The genus Hordeum exists at three ploidy levels (2x, 4x and 6x) and presents excellent material for investigating the patterns of polyploid evolution in plants. Here the aim was to clarify the ancestry of American polyploid species with the I genome. *

METHODS

Chromosomal locations of 5S and 18S-25S ribosomal RNA genes were determined by fluorescence in situ hybridization (FISH). In both polyploid and diploid species, variation in 18S-25S rDNA repeated sequences was analysed by the RFLP technique. *

KEY RESULTS

Six American tetraploid species were divided into two types that differed in the number of rDNA sites and RFLP profiles. Four hexaploid species were similar in number and location of both types of rDNA sites, but the RFLP profiles of 18S-25S rDNA revealed one species, H. arizonicum, with a different ancestry. *

CONCLUSIONS

Five American perennial tetraploid species appear to be alloploids having the genomes of an Asian diploid H. roshevitzii and an American diploid species. The North American annual tetraploid H. depressum is probably a segmental alloploid combining the two closely related genomes of American diploid species. A hexaploid species, H. arizonicum, involves a diploid species, H. pusillum, in its ancestry; both species share the annual growth habit and are distributed in North America. Polymorphisms of rDNA sites detected by FISH and RFLP analyses provide useful information to infer the phylogenetic relationships of I-genome Hordeum species because of their highly conserved nature during polyploid evolution.

Chromatin techniques for plant cells

A large number of recent studies have demonstrated that many important aspects of plant development are regulated by heritable changes in gene expression that do not involve changes in DNA sequence. Rather, these regulatory mechanisms involve modifications of chromatin structure that affect the accessibility of target genes to regulatory factors that can control their expression. The central component of chromatin is the nucleosome, containing the highly conserved histone proteins that are known to be subject to a wide range of post-translational modifications, which act as recognition codes for the binding of chromatin-associated factors. In addition to these histone modifications, DNA methylation can also have a dramatic influence on gene expression. To accommodate the burgeoning interest of the plant science community in the epigenetic control of plant development, a series of methods used routinely in our laboratories have been compiled that can facilitate the characterization of putative chromatin-binding factors at the biochemical, molecular and cellular levels.

Ribosomal ITS sequences and plant phylogenetic inference

One of the most popular sequences for phylogenetic inference at the generic and infrageneric levels in plants is the internal transcribed spacer (ITS) region of the 18S-5.8S-26S nuclear ribosomal cistron. The prominence of this source of nuclear DNA sequence data is underscored by a survey of phylogenetic publications involving comparisons at the genus level or below, which reveals that of 244 papers published over the last five years, 66% included ITS sequence data. Perhaps even more striking is the fact that 34% of all published phylogenetic hypothesis have been based exclusively on ITS sequences. Notwithstanding the many important contributions of ITS sequence data to phylogenetic understanding and knowledge of genome relationships, a number of molecular genetic processes impact ITS sequences in ways that may mislead phylogenetic inference. These molecular genetic processes are reviewed here, drawing attention to both underlying mechanism and phylogenetic implications. Among the most prevalent complications for phylogenetic inference is the existence in many plant genomes of extensive sequence variation, arising from ancient or recent array duplication events, genomic harboring of pseudogenes in various states of decay, and/or incomplete intra- or inter-array homogenization. These phenomena separately and collectively create a network of paralogous sequence relationships potentially confounding accurate phylogenetic reconstruction. Homoplasy is shown to be higher in ITS than in other DNA sequence data sets, most likely because of orthology/paralogy conflation, compensatory base changes, problems in alignment due to indel accumulation, sequencing errors, or some combination of these phenomena. Despite the near-universal usage of ITS sequence data in plant phylogenetic studies, its complex and unpredictable evolutionary behavior reduce its utility for phylogenetic analysis. It is suggested that more robust insights are likely to emerge from the use of single-copy or low-copy nuclear genes.

Karyotypes of Elymus scabrifolius (Poaceae: Triticeae) from South America studied by banding techniques and in situ hybridization

Karyotypes of 4 accessions of Elymus scabrifolius (2n = 4x = 28) were investigated by Giemsa C- and N-banding, GAA-banding (one accession), AgNO3-staining and in situ hybridization with the rDNA probe pTa71. Two additional accessions were studied in less detail. The chromosomes were large (9-14 microns). The complements included 11 pairs of metacentrics, one with conspicuous satellites on the short arms, and 3 pairs of submetacentrics. Two of 4 accessions from Eastern Argentina and Uruguay had minute or small satellites on a submetacentric pair. No such satellites were observed in the other two accessions. In two accessions from the Cordoba province, a non-homologous submetacentric pair had very long satellites. AgNO3-staining established the presence of 4 nucleoli, two larger and two small ones, in 5 accessions. The C-banding patterns comprised from one to 12 conspicuous bands per chromosome at no preferential positions. The amount of constitutive heterochromatin (19-21%) was the highest hitherto established in the Triticeae. Similarities in banding patterns and chromosome morphology identified homologous and discriminated between non-homologous chromosomes within and, except for two chromosomes, between plants. Heteromorphic chromosome pairs were identified in satellite-carrying chromosomes only. N-banding produced conspicuous bands overall at the same positions as C-banding. GAA-banding patterns were similar to N-banding patterns. The rDNA probe hybridized to chromosome segments at nucleolar constrictions only. The production of C- and N-banding patterns in both genomes of E. scabrifolius suggests the presence of two H genomes and the absence of the pivotal St genome of Elymus. On account of the uncertain identity of one genome, and the overall similar gross morphology of E. scabrifolius and other tetraploid South American species referred to Elymus, E. scabrifolius is retained in Elymus.

Physical mapping of 45S and 5S rDNA on maize metaphase and sorted chromosomes by FISH

Physical locations of 45S and 5S rDNA were detected in maize by fluorescence in situ hybridization (FISH). The FISH results on metaphase chromosome spreads showed the 45S rDNA was located just at the nucleolus organizer region (NOR) on 6S (the short arm) of chromosome 6) as expected, and 5S rDNA at the distal region of 2L (the long arm of chromosome 2). No signals were detected on the other maize chromosomes for these two probes. The precision of the chromosomal position of a hybridization site is related to the number of measurements. We also mapped the location of 5S rDNA at the same sites on 2L by FISH on sorted chromosomes. We could calculate more precisely the percentage distance of hybridization signals since we had large numbers of target chromosomes on a small spot on the slide by flow sorting. The percentage distance from centromere to the hybridization site was 85% for 5S rDNA on 2L. The physical location of 5S rDNA was inconsistent with its genetic site, which was positioned in the middle of genetic linkage group 2. A FISH procedure for mapping genes on sorted plant chromosomes is described and occurrence of only one 45S or 5S rDNA site on maize genome is discussed.

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.

Physical locations of 5S and 18S-25S rDNA in Asian and American diploid Hordeum species with the I genome

The physical locations of 5S and 18S-25S rDNA sequences in 15 diploid Hordeum species with the I genome were examined by double-target in situ hybridization with pTa71 (18S-25S rDNA) and pTa794 (5S rDNA) clones as probes. All the three Asian species had a species-specific rDNA pattern. In 12 American species studied, eight different rDNA types were found. The type reported previously in H. chilense (the 'chilense' type) was observed in eight American species. The chilense type had double 5S rDNA sites - two sites on one chromosome arm separated by a short distance - and two pairs of major 18S-25S rDNA sites on two pairs of satellite chromosomes. The other seven types found in American species were similar to the chilense type and could be derived from the chilense type through deletion, reduction or addition of a rDNA site. Intraspecific polymorphisms were observed in three American species. The overall similarity in rDNA patterns among American species indicates the close relationships between North and South American species and their derivation from a single ancestral source. The differences in the distribution patterns of 5S and 18S-25S rDNA between Asian and American species suggest differentiation between the I genomes of Asian and American species. The 5S and 18S-25S rDNA sites are useful chromosome markers for delimiting Asian species, but have limited value as a taxonomic character in American species. On the basis of rDNA patterns, karyotype evolution and phylogeny of the I-genome diploid species are discussed.

Comparative physical mapping of the 18S-5.8S-26S rDNA in three sorghum species

The physical locations of the 18S-5.8S-26S rDNA sequences were examined in three sorghum species by fluorescence in situ hybridization (FISH) using biotin-labeled heterologous 18S-5.8S-26S rDNA probe (pTa71). Each 18S-5.8S-26S rDNA locus occurred at two sites on the chromosomes in Sorghum bicolor (2n = 20) and S. versicolor (2n = 10), but at four sites on the chromosomes of S. halepense (2n = 40) and the tetraploid S. versicolor (2n = 20). Positions of the rDNA loci varied from the interstitial to terminal position among the four accessions of the three sorghum species. The rDNA data are useful for investigation of chromosome evolution and phylogeny. This study excluded S. versicolor as the possible progenitor of S. bicolor.Key words: Sorghum bicolor, Sorghum versicolor, Sorghum halepense, 18S-5.8S-26S rDNA, fluorescence in situ hybridization.

Number and sites of rDNA loci of Guizotia abyssinica (L. f.) Cass. as determined by fluorescence in situ hybridization

Fluorescence in situ hybridization (FISH) was employed on somatic chromosome preparations of Guizotia abyssinica using a DNA probe of the 18S-5.8S-26S rRNA genes including the transcribed and non-transcribed spacer sequences. A maximum of six major and two minor signal sites of rDNA was observed. However, the minor signals were not persistently detected. The positions of the FISH signals coincided with the sites of the nucleolar organizer regions and their adjacent C-banded heterochromatin when present.

Flow karyotyping and sorting of mitotic chromosomes of barley (Hordeum vulgare L.)

A high-yield method for isolation of barley chromosomes in suspension, their analysis and sorting using flow cytometry is described. To accumulate meristem root tip cells at metaphase, actively growing roots were subjected to subsequent treatment with 2 mmol/L hydroxyurea for 18 h, 2.5 micromol/L amiprophos methyl for 2 h, and ice water (overnight). This treatment resulted in metaphase indices exceeding 50%. Synchronized root tips were fixed in 2% formaldehyde for 20 min and chromosomes were released into a lysis buffer by mechanical homogenization, producing, on average, 5 x 10(5) chromosomes from 50 root tips. The isolated chromosomes were morphologically intact and suitable for flow cytometric analysis and sorting. While it was possible to discriminate and sort only one chromosome from a barley cultivar with standard karyotype, up to three chromosomes could be sorted in translocation lines with morphologically distinct chromosomes. The purity of chromosome fractions, estimated after PRINS with primers specific for GAA microsatellites, reached 97%. PCR with chromosome-specific primers confirmed the purity and suitability of flow-sorted chromosomes for physical mapping of DNA sequences.

Long tomato microsatellites are predominantly associated with centromeric regions

Microsatellites as genetic markers are used in many crop plants. Major criteria for their usability as molecular markers include that they are highly polymorphic and evenly spread throughout a genome. In tomato, it has been reported that long arrays of tetranucleotide microsatellites containing the motif GATA are highly clustered around the centromeres of all chromosomes. In this study, we have isolated tomato microsatellites containing long arrays (> 20 repeats) of the dinucleotide motifs GA, GT, AT, as well as GATA, assessed their variability within Lycopersicon esculentum varieties and mapped them onto a genetic map of tomato. The investigated microsatellite markers exhibited between 1 and 5 alleles in a diverse set of L. esculentum lines. Mapping of the microsatellites onto the genetic map of tomato demonstrates that, as previously shown, GATA microsatellites are highly clustered in the regions of the tomato centromeres. Interestingly, the same centromeric location was now found for long dinucleotide microsatellite markers. Because of this uneven distribution, genetic mapping of the entire tomato genome using long dinucleotide microsatellites will be very difficult to achieve and microsatellite markers with shorter arrays of microsatellites could be more suitable for mapping experiments albeit their lower level of polymorphism. Some microsatellite markers described in this study might provide a useful tool to study the molecular structure of tomato centromeric regions and for variety identification.Key words: molecular marker, Lycopersicon esculentum, genetic variability, genetic map, simple sequence repeats.

Short communication: the cell cycle dependent phosphorylation of histone H3 is correlated with the condensation of plant mitotic chromosomes

Mitotically dividing cells of Secale cereale, Hordeum vulgare and Vicia faba were studied by indirect immunofluorescence using an antibody recognizing phosphorylated histone H3. The study revealed the following features: (i) the H3 phosphorylation starts at prophase and ends at telophase in the pericentromeric chromatin, is associated with the condensation of mitotic chromosomes and is independent of the distribution of late replicating heterochromatin. (ii) Compared with other chromosome regions, the pericentromeric chromatin is histone H3 hyperphos- phorylated. (iii) The study of a semi-dicentric chromo- some revealed that only at intact centromeres is the chromatin hyperphosphorylated at H3.

Characterization of chromosomes and genome organization of Thapsia garganica L. by localizations of rRNA genes using fluorescent in situ hybridization

The karyotype (2n = 22) of Thapsia garganica L. (Apiaceae, Apioideae, Laserpitieae) was constructed using molecular cytogenetics. The size of the 22 chromosomes ranged between 5 and 10 microns. Two chromosomes had satellites on the short arms. The 18S-5.8S-26S rDNA genes were located to the two satellites by fluorescent in situ hybridization (FISH). The 5S rDNA repeat unit was amplified and located by FISH to one pair of the non-satellited chromosomes. Sequencing 5S rDNA of T. garganica revealed two classes of genes based on distinct intergenic spacer regions of 191/193-bp and 181-bp. respectively. The ITS1 and ITS2 of the 18S-5.8S-26S repeats were also amplified and phylogenetic analysis placed T. garganica in a distinct clade from the Daucus clade containing Laserpitium sp. The organization of T. garganica L. genome is tentatively divided in group A of 14 chromosomes with median centromere and of which one pair (q/p 1.22) contains single 5S rDNA locus on the long arm. Group B consists of six chromosomes with subterminal centromeres (q/p between 4.23 and 7.92) and finally group C with the satellited chromosome pair containing the 18S-5.8S-26S rDNA locus at the secondary constriction.

Multiple locations of the rDNA sites in holocentric chromosomes of Rhynchospora (Cyperaceae)

Several cytogenetic studies have shown that representatives of the family Cyperaceae have holocentric chromosomes. Despite their interesting chromosome morphology, the chromosome organization has not been studied. This paper reports on the number and distribution of 18S-5.8S-26S ribosomal RNA sites by fluorescence in situ hybridization in eight Brazilian species of Rhynchospora. The signal of the rDNA probe was always localized in the telomeric regions. A high degree of variation was observed in the number of labelled sites, ranging from 4-8 in karyotypes with 2n = 10 to 30 sites in a karyotype with 50 chromosomes. It is possible that the same mechanism involved in the multiplication of these regions in organisms with monocentric chromosomes also plays a role in the polymorphism observed in holocentric chromosomes of Rhynchospora. An interesting feature of most hybridization sites was their diffuse state observed through to early metaphase. The decondensed state probably reflects the later transcription of this region during the cell cycle.

Chromosomal localization and distribution of simple sequence repeats and the Arabidopsis-type telomere sequence in the genome of Cicer arietinum L

We used fluorescence in situ hybridization to probe the physical organization of five simple sequence repeat motifs and the Arabidopsis-type telomeric repeat in metaphase chromosomes and interphase nuclei of chickpea (Cicer arietinum L.). Hybridization signals were observed with the whole set of probes and on all chromosomes, but the distribution and intensity of signals varied depending on the motif. On root-tip metaphase chromosomes, CA and GATA repeats were mainly restricted to centromeric areas, with additional GATA signals along some chromosomes. TA, A and AAC repeats were organized in a more dispersed manner, with centromeric regions being largely excluded. In interphase nuclei of the inner integument, CA and GATA signals predominantly occurred in the heterochromatic endochromocentres, whereas the other motifs were found both in eu- and heterochromatin. The distribution of the Arabidopsis-type telomeric repeat (TTTAGGG)n on metaphase chromosomes was found to be quite exceptional. One major cluster of repeats was spread along the short arm of chromosome B, whereas a second, weaker signal occurred interstitially on chromosome A. Only faint and inconsistent hybridization signals were visualized with the same probe at the chromosomal termini.

Physical localization of rRNA genes by two-colour fluorescent in-situ hybridization and sequence analysis of the 5S rRNA gene in Phalaris coerulescens

The 18S-5.8S-26S rDNA and 5S rDNA loci have been mapped physically by fluorescent in-situ hybridization to the chromosomes of Phalaris coerulescens. The biotin-labelled heterologous 18S-5.8S-26S rRNA probe (pTa71) detected one locus, which corresponded to the secondary constriction (nucleolar organizer) on the long arm of the satellited chromosome II. The homologous 5S rDNA probe (Bam2.12) detected two pairs of 5S rRNA gene clusters which were localized at two different non-satellited chromosomes, one near the telomere on the short arm of the chromosome I, which is the largest chromosome of the complement, and the other about 42% out on the long arm of the chromosome III. A BamHI fragment containing the 5S rRNA gene, has been isolated and characterized. The 5S rDNA repeat unit is 309 bp in length, consisting of 121 bp highly conserved coding region and 188 bp variable spacer region. The karyotype of Phalaris coerulescens is characterized by the similar size of chromosomes within the group 2, group 3, or group 4. This study represents the first step towards the understanding the genome organization of Phalaris coerulescens and provides reliable markers for chromosome identification in this grass, an important species as a model system for the study of self-incompatibility in grasses.

Identification of the entire chromosome complement of bread wheat by two-colour FISH

Using the Aegilops tauschii clone pAs1 together with the barley clone pHvG38 for two-colour fluorescence in situ hybridization (FISH) the entire chromosome complement of hexaploid wheat was identified. The combination of the two probes allowed easy discrimination of the three genomes of wheat. The banding pattern obtained with the pHvG38 probe containing the GAA-satellite sequence was identical to the N-banding pattern of wheat. A detailed idiogram was constructed, including 73 GAA bands and 48 pAs1 bands. Identification of the wheat chromosomes by FISH will be particularly useful in connection with the physical mapping of other DNA sequences to chromosomes, or for chromosome identification in general, as an alternative to C-banding.Key words: Triticum aestivum, chromosome identification, fluorescence in situ hybridization, repetitive DNA sequences.