Detection of ribosomal DNA sites in lentil and chickpea by fluorescent in situ hybridization

Critical review on karyotype diversity in lentil based on classical and molecular cytogenetics

Lentil is an annual protein rich valuable edible crop with only one cultivated and six wild taxa. Keeping in mind its narrow gene pool, the genus deserves critical assessment of genomic diversity at the chromosomal level. Genetic diversity represents the heritable variation within and between populations of organisms. Over the decades classical and molecular cytogenetics have played an immense role in the field of crop improvement. Lentil, though grown in different countries, country-wise chromosomal information is inadequate. Critical evaluation of more than seven decades chromosomal information has revealed unique karyotype diversity within the landraces of different countries. Application of fluorescent banding and fluorescent in situ hybridization (FISH) has helped to segregate cultivars based on cultivar specific chromosomal markers and landmarks. Selection of cultivated and wild cultivars based on qualitative and diseases related morpho-traits and new information from this critical review especially on molecular cytogenetics may provide more options for crop improvement. More research in the field of molecular cytogenetics from country specific species and cultivars are needed to enrich the repository of gene pool. Alien gene introgression from extended gene pool through the advanced genomics and biotechnological tools could facilitate the path of sustainable improvement of this crop.

Comparative chromosome studies in species of subtribe Orchidinae (Orchidaceae)

In our study, FISH mapping using 18S-5.8S-25S rDNA and 5S rDNA sequences was performed for the first time on Ophrystenthredinifera Willdenow, 1805, Serapiasvomeracea (Burman f., 1770) Briquet, 1910 and Himantoglossumhircinum (Linnaeus, 1753) Sprengel, 1826. A detailed study was also performed on O.tenthredinifera using Giemsa-staining, silver-staining, CMA fluorescence banding and fluorescence in situ hybridisation (FISH) with rDNA probes. We analysed two subspecies, i.e. O.tenthrediniferasubsp.neglecta (Parlatore, 1860) E.G. Camus, 1908 and O.tenthrediniferasubsp.grandiflora (Tenore, 1819) Kreutz, 2004 by the traditional Feulgen method and constructed the karyotype. The cytotaxonomic implications for both taxa are also discussed. In Himantoglossumhircinum, FISH and silver staining highlighted differences in the number of two rDNA families (35S and 5S) with respect to Barliarobertiana (Loiseleur-Deslongchamps, 1807) Greuter, 1967. In addition, fluorescence in situ hybridisation was also applied to diploid (2n = 2x = 36) and triploid (2n = 3x = 54) Anacamptismorio (Linnaeus, 1753) R.M. Bateman, Pridgeon et M.W. Chase, 1997. As far as we are aware, this is the first case of autotriploidy observed in A.morio.

A Tale of Two Families: Whole Genome and Segmental Duplications Underlie Glutamine Synthetase and Phosphoenolpyruvate Carboxylase Diversity in Narrow-Leafed Lupin (Lupinus angustifolius L.)

Narrow-leafed lupin (Lupinus angustifolius L.) has recently been supplied with advanced genomic resources and, as such, has become a well-known model for molecular evolutionary studies within the legume family—a group of plants able to fix nitrogen from the atmosphere. The phylogenetic position of lupins in Papilionoideae and their evolutionary distance to other higher plants facilitates the use of this model species to improve our knowledge on genes involved in nitrogen assimilation and primary metabolism, providing novel contributions to our understanding of the evolutionary history of legumes. In this study, we present a complex characterization of two narrow-leafed lupin gene families—glutamine synthetase (GS) and phosphoenolpyruvate carboxylase (PEPC). We combine a comparative analysis of gene structures and a synteny-based approach with phylogenetic reconstruction and reconciliation of the gene family and species history in order to examine events underlying the extant diversity of both families. Employing the available evidence, we show the impact of duplications on the initial complement of the analyzed gene families within the genistoid clade and posit that the function of duplicates has been largely retained. In terms of a broader perspective, our results concerning GS and PEPC gene families corroborate earlier findings pointing to key whole genome duplication/triplication event(s) affecting the genistoid lineage.

Comparative chromosomal localization of 45S and 5S rDNAs and implications for genome evolution in Cucumis

Ribosomal DNAs are useful cytogenetic markers for chromosome analysis. Studies investigating site numbers and distributions of rDNAs have provided important information for elucidating genome organization and chromosomal relationships of many species by fluorescence in situ hybridization. But relevant studies are scarce for species of the genus Cucumis, especially in wild species. In the present study, FISH was conducted to investigate the organization of 45S and 5S rDNA among 20 Cucumis accessions, including cultivars and wild accessions. Our results showed that the number of 45S rDNA sites varied from one to five pairs in different accessions, and most of these sites are located at the terminal regions of chromosomes. Interestingly, up to five pairs of 45S rDNA sites were observed in C. sativus var. sativus, the species which has the lowest chromosome number, i.e., 2n = 14. Only one pair of 5S rDNA sites was detected in all accessions, except for C. heptadactylus, C. sp, and C. spp that had two pairs of 5S rDNA sites. The distributions of 5S rDNA sites showed more variation than 45S rDNA sites. The phylogenetic analysis in this study showed that 45S and 5S rDNA have contrasting evolutionary patterns. We find that 5S rDNA has a polyploidization-related tendency towards the terminal location from an interstitial location but maintains a conserved site number, whereas the 45S rDNA showed a trend of increasing site number but a relatively conserved location.

Integration of Lupinus angustifolius L. (narrow-leafed lupin) genome maps and comparative mapping within legumes

Narrow-leafed lupin (Lupinus angustifolius L.) has recently been considered a reference genome for the Lupinus genus. In the present work, genetic and cytogenetic maps of L. angustifolius were supplemented with 30 new molecular markers representing lupin genome regions, harboring genes involved in nitrogen fixation during the symbiotic interaction of legumes and soil bacteria (Rhizobiaceae). Our studies resulted in the precise localization of bacterial artificial chromosomes (BACs) carrying sequence variants for early nodulin 40, nodulin 26, nodulin 45, aspartate aminotransferase P2, asparagine synthetase, cytosolic glutamine synthetase, and phosphoenolpyruvate carboxylase. Together with previously mapped chromosomes, the integrated L. angustifolius map encompasses 73 chromosome markers, including 5S ribosomal DNA (rDNA) and 45S rDNA, and anchors 20 L. angustifolius linkage groups to corresponding chromosomes. Chromosomal identification using BAC fluorescence in situ hybridization identified two BAC clones as narrow-leafed lupin centromere-specific markers, which served as templates for preliminary studies of centromere composition within the genus. Bioinformatic analysis of these two BACs revealed that centromeric/pericentromeric regions of narrow-leafed lupin chromosomes consisted of simple sequence repeats ordered into tandem repeats containing the trinucleotide and pentanucleotide simple sequence repeats AGG and GATAC, structured into long arrays. Moreover, cross-genus microsynteny analysis revealed syntenic patterns of 31 single-locus BAC clones among several legume species. The gene and chromosome level findings provide evidence of ancient duplication events that must have occurred very early in the divergence of papilionoid lineages. This work provides a strong foundation for future comparative mapping among legumes and may facilitate understanding of mechanisms involved in shaping legume chromosomes.

The use of double fluorescence in situ hybridization to physically map the positions of 5S rDNA genes in relation to the chromosomal location of 18S-5.8S-26S rDNA and a C genome specific DNA sequence in the genus Avena

A physical map of the locations of the 5S rDNA genes and their relative positions with respect to 18S-5.8S-26S rDNA genes and a C genome specific repetitive DNA sequence was produced for the chromosomes of diploid, tetraploid, and hexaploid oat species using in situ hybridization. The A genome diploid species showed two pairs of rDNA loci and two pairs of 5S loci located on both arms of one pair of satellited chromosomes. The C genome diploid species showed two major pairs and one minor pair of rDNA loci. One pair of subtelocentric chromosomes carried rDNA and 5S loci physically separated on the long arm. The tetraploid species (AACC genomes) arising from these diploid ancestors showed two pairs of rDNA loci and three pairs of 5S loci. Two pairs of rDNA loci and 2 pairs of 5S loci were arranged as in the A genome diploid species. The third pair of 5S loci was located on one pair of A-C translocated chromosomes using simultaneous in situ hybridization with 5S rDNA genes and a C genome specific repetitive DNA sequence. The hexaploid species (AACCDD genomes) showed three pairs of rDNA loci and six pairs of 5S loci. One pair of 5S loci was located on each of two pairs of C-A/D translocated chromosomes. Comparative studies of the physical arrangement of rDNA and 5S loci in polyploid oats and the putative A and C genome progenitor species suggests that A genome diploid species could be the donor of both A and D genomes of polyploid oats. Key words : oats, 5S rDNA genes, 18S-5.8S-26S rDNA genes, C genome specific repetitive DNA sequence, in situ hybridization, genome evolution.

Chromatin characterization by banding techniques, in situ hybridization, and nuclear DNA content in Cicer L. (Leguminosae)

The karyotypes of three accessions, one each from three annual species of the genus Cicer, namely Cicer arietinum, Cicer reticulation, and Cicer echinospermum, were examined and compared using C-banding, the fluorochromes chromomycin A3, DAPI, and Hoechst 33258, in situ hybridization of the 18S-5.8S-25S and 5S rDNA sequences, and silver staining. The nuclear DNA content of the three species and the amount of heterochromatin were also determined. The results suggest an evolutionary pathway in which C. reticulatum is the ancestral species from which both C. arietinum and C. echinospermum are derived with the loss of one pair of satellites; subsequently, C. echinospermum further differentiated by the accumulation of chromosomal rearrangement(s) that gave rise to a hybrid sterility barrier. Key words : Cicer, C-banding, fluorochromes, Ag staining, rRNA genes.

Integration of genetic and physical maps of the chickpea (Cicer arietinum L.) genome using flow-sorted chromosomes

Cultivated chickpea is the third most important legume after field bean and garden pea worldwide. Despite considerable breeding towards improved yield and resistance to biotic and abiotic stresses, the production of chickpea remained stagnant, but molecular tools are expected to increase the impact of current improvement programs. As a first step towards this goal, various genetic linkage maps have been established and markers linked to resistance genes been identified. However, until now, only one linkage group (LG) has been assigned to a specific chromosome. In the present work, mitotic chromosomes were sorted using flow cytometry and used as template for PCR with primers designed for genomic regions flanking microsatellites. These primers amplify sequence-tagged microsatellite site markers. This approach confirmed the assignment of LG8 to the smallest chromosome H. For the first time, LG5 was linked to the largest chromosome A, LG4 to a medium-sized chromosome E, while LG3 was anchored to the second largest chromosome B. Chromosomes C and D could not be flow-sorted separately and were jointly associated to LG6 and LG7. By the same token, chromosomes F and G were anchored to LG1 and LG2. To establish a set of preferably diagnostic cytogenetic markers, the genomic distribution of various probes was verified using FISH. Moreover, a partial genomic bacterial artificial chromosome (BAC) library was constructed and putative single/low-copy BAC clones were mapped cytogenetically. As a result, two clones were identified localizing specifically to chromosomes E and H, for which no cytogenetic markers were yet available.

Comparative study of chromosome morphology and C-banding patterns in several genotypes of Lens culinaris

Karyotype and C-banding patterns of mitotic chromosomes in 10 cultivars and landraces of lentil were studied. Aceto-iron-hematoxilin staining and Giemsa C-banding techniques were used to staining choromosomes and banding patterns analysis, respectively. Chromosome characteristics including long arm, short arm and chromosome lengths, total length of chromosome set, arm ratio index, relative chromosome length, the width and position of each band, heterochromatin percent per chromosome and per chromosome set were measured using Micromeasure software. The results of this study revealed that the genome of this species consisted of four pairs of metacentric and three pairs of submetacentric chromosomes. Chromosome 4 had a secondary constriction near centromeric region of its long arm. Arm ratio index of chromosomes ranged from 1.24 in chromosome 3 to 2.38 in chromosomes 6. Each chromosome, having a distinctive banding pattern, was recognizable. Karyological characteristics and banding patterns of all materials studied were similar to each other, however, some polymorph C-bands were observed on chromosome arms.

5S rDNA genome regions of Lens species

The length variability of the nontranscribed spacer (NTS) of the 5S rDNA repeats was analyzed in species of the genus Lens by means of PCR amplification. The NTS ranged from approximately 227 to approximately 952 bp. The polymorphism detected was higher than previous NTS polymorphisms described in this genus. Three NTS length variants from Lens culinaris subsp. culinaris and 2 from Lens culinaris subsp. orientalis were sequenced. The culinaris NTS fragment lengths were 239, 371, and 838 bp, whereas the orientalis ones were 472 bp and 506 bp, respectively. As a result of sequence similarities, 2 families of sequences were distinguished, 1 including the sequences of 838 and 506 bp, and others with the sequences of 239, 371, and 472 bp. The 1st family was characterized by the presence of a repeated sequence designated A, whereas the 2nd family showed a single A sequence and other repeated sequences designated B, C, and D. The presence of an (AT)n microsatellite was also observed in the 2nd family of sequences. The fragments, which included the 239-bp and 838-bp NTS sequences, as well as the intergenic spacer (IGS) of the 18S-5.8S-26S ribosomal DNA also from L. culinaris subsp. culinaris, were used to localize the nucleolar organizer region (NOR) and the 5S rDNA loci in the chromosomes of several species of the genus Lens by means of fluorescence in situ hybridization (FISH). The selective hybridization of the 2 NTS probes allowed us to distinguish between different 5S rDNA chromosomal loci.

Distribution of highly repeated DNA sequences in species of the genus Lens Miller

Multiple-target fluorescence in situ hybridization (FISH) was applied on mitotic chromosomes of seven Lens taxa using two highly repetitive sequences (pLc30 and pLc7) isolated from the cultivated lentil and the multigene families for the 18S-5.8S-25S (pTa71) and 5S rRNA (pTa794) from wheat simultaneously as probes. The number and location of pLc30 and pLc7 sites on chromosomes varied markedly among the species, whereas the hybridization pattern of 5S rDNA and 18S-5.8S-25S rDNA was less variable. In general, each species showed a typical FISH karyotype and few differences were observed among accessions belonging to the same species, except for the accessions of Lens odemensis. The most similar FISH karyotype to the cultivated lentil is that of Lens culinaris subsp. orientalis, whereas Lens nigricans and Lens tomentosus are the two species that showed the most divergent FISH patterns compared with all taxa for number and location of pLc30 and 18S-5.8S-25S rDNA sites.

Development of flow cytogenetics and physical genome mapping in chickpea (Cicer arietinum L.)

Procedures for flow cytometric analysis and sorting of mitotic chromosomes (flow cytogenetics) have been developed for chickpea (Cicer arietinum). Suspensions of intact chromosomes were prepared from root tips treated to achieve a high degree of metaphase synchrony. The optimal protocol consisted of a treatment of roots with 2 mmol/L hydroxyurea for 18 h, a 4.5-h recovery in hydroxyurea-free medium, 2 h incubation with 10 micromol/L oryzalin, and ice-water treatment overnight. This procedure resulted in an average metaphase index of 47%. Synchronized root tips were fixed in 2% formaldehyde for 20 min, and chromosome suspensions prepared by mechanical homogenization of fixed root tips. More than 4 x 10(5) morphologically intact chromosomes could be isolated from 15 root tips. Flow cytometric analysis of DAPI-stained chromosomes resulted in histograms of relative fluorescence intensity (flow karyotypes) containing eight peaks, representing individual chromosomes and/or groups of chromosomes with a similar relative DNA content. Five peaks could be assigned to individual chromosomes (A, B, C, G, H). The parity of sorted chromosome fractions was high, and chromosomes B and H could be sorted with 100% purity. PCR on flow-sorted chromosome fractions with primers for sequence-tagged microsatellite site (STMS) markers permitted assignment of the genetic linkage group LG8 to the smallest chickpea chromosome H. This study extends the number of legume species for which flow cytogenetics is available, and demonstrates the potential of flow cytogenetics for genome mapping in chickpea.

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.

Identification of Lens culinaris ssp. culinaris chromosomes by physical mapping of repetitive DNA sequences

We describe the characterisation and the chromosomal localisation of two repeated DNA sequences, named pLc30 (466 bp long, 64% AT residues) and pLc7 (408 bp long, 61% AT residues), isolated from lentil (Lens culinaris ssp. culinaris) genomic DNA. The pLc30 family is characterised by four internal repeats organised in a head-to-tail orientation, whereas the pLc7 contains many short direct subrepeats. The two families do not share significant sequence similarity. The distribution of these repetitive sequences in different Lens species and in other legumes was investigated. pLc30 is present in all Lens species investigated but absent from other genera examined. In contrast, pLc7 is present also in the genome of other legumes. As determined by FISH, the pLc30 sequence hybridises on six out of seven lentil chromosome pairs, while pLc7 hybridises on one only. The distribution of the nine different hybridisation sites of pLc30 allows the discrimination of all seven chromosome pairs and the construction of a karyotype of L. culinaris ssp. culinaris. Additionally, the combination of simultaneous and successive FISH with pLc7, 5S rRNA, 18S-5.8S-25S rRNA genes, and a telomeric sequence allowed the assembly of a physical map based on lentil karyotype.