bluuebunny/crossref_metadata_2025 huggingface dataset:
An apparent case of nonsymmetrical and sustained strand-specific hemimethylation in theDc8gene of carrot
Authors: Zhou Yuanxiang , Magill Clint W , Magill Jane M , Newton Ronald J
Published: April 2011

The Dc8 gene of carrot (Daucus carota L.) shows differential expression during embryo development. Changes in methylation patterns of a segment of about 500 bp (from base + 120 to base -446) of Dc8 allele 6 were investigated by treating genomic DNA, extracted from embryogenic callus at different stages of development, with sodium bisulfite to modify nonmethylated cytosines. Following asymmetric (strand-specific) amplification, base sequences for samples from each developmental stage were determined for each strand directly from the PCR products or from cloned PCR products. Different methylation patterns were detected in the two strands. The 5' to 3' sense (coding) strand was almost completely nonmethylated, whereas almost all the cytosines in the 3' to 5' (template) strand were methylated. By 71 days after transfer to embryo-inducing medium, few methylcytosines remained; those that were present were generally near the TATA box or in a region beyond -300. The cytosines that were methylated were not limited to CG or CNG sequences. The difference in the extent of methylation between the two complementary strands implies either that there is a mechanism for strand-specific methylation, or that complementary sequences can differ greatly in sensitivity to bisulfite treatment or PCR amplification.
H genome specific repetitive sequence, pEt2, of Elymus trachycaulus in part of Afa family of Triticeae
Authors: Nagaki Kiyotaka , Tsujimoto Hisashi , Sasakuma Tetsuo
Published: April 2011

The H genome specific repetitive sequence of Elymus trachycaulus, pEt2, consists of three units of a 337-339 bp repeat aligned in tandem. The sequence is homologous to Afa-family sequences that are widely distributed in the genomes of Triticeae (Gramineae) species.
Genome-specific repetitive DNA and RAPD markers for genome identification in Elymus and Hordelymus
Authors: Svitashev Sergei , Bryngelsson Tomas , Li Xiaomei , Wang Richard RC
Published: April 2011

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.
Patterns of DNase I sensitivity in the holocentric chromosomes of the aphid Megoura viciae
Authors: Manicardi Gian Carlo , Mandrioli Mauro , Bizzaro Davide , Bianchi Umberto
Published: April 2011

Using the in situ nick translation technique, we looked for the presence of DNase I sensitive sites in Megoura viciae chromosomes, to study the distribution of active or potentially active genes in aphids, a group of insects possessing holocentric chromosomes. Cytological preparations obtained by the spreading of embryo cells were treated in situ with increasing concentrations (ranging from 5 to 200 ng/mL) of DNase I. At DNase I concentrations below 50 ng/mL, only one hypersensitive site was observed, and this was located on a telomeric region of the X chromosome that contains transcriptionally active nucleolar organizing regions, as assayed by silver staining. Interestingly, at intermediate concentrations of DNase, the incorporation of biotinylated nucleotide occurred uniformly throughout all chromosomes, whereas at concentrations above 100 ng/mL, a C-like banding pattern was produced. Our data differ from results obtained with mammalian, frog, and grasshopper chromosomes, where it was found that DNase I nicking is concentrated at the distal regions of all chromosomes.Key words: aphids, holocentric chromosomes, DNase I sensitivity, nick translation.
Polymorphic microsatellites in Simulium damnosum s.l. and their use for differentiating two savannah populations: implications for epidemiological studies
Authors: Dumas Valérie , Herder Stéphane , Bebba Aïcha , Cadoux-Barnabé Cécile , Bellec Christian , Cuny Gérard
Published: April 2011

In West Africa, Onchocerca volvulus, the cause of human onchocerciasis, is transmitted by sibling species of the Simulium damnosum complex. Little is known about blackfly intraspecific variability and its consequences on vectorial capacity. This study reports the use of microsatellite markers for differentiating populations of S. damnosum s.l. Five microsatellite loci were characterized and used to analyze individuals from two savannah populations in Mali, 120 km apart. Four loci were highly polymorphic, having 8-12 alleles per locus and gene diversities ranging from 77.9 to 88.2%. A significant heterozygote deficiency was observed in the two populations. This may arise from inbreeding, population structure (the Walhund effect), or the presence of null alleles. To test this last hypothesis, new primers were designed for two loci and used to analyze homozygous individuals. After correcting for null alleles, heterozygote deficit persisted. Population subdivision in the two foci remains the most likely explanation. Our results indicate that microsatellite markers could differentiate fly populations, making them valuable tools for the study of population genetic structure.Key words: Simulium damnosum s.l., microsatellites, polymorphism, population structure, population genetics, null alleles.
Genome size and base composition of seven Quercus species: inter- and intra-population variation
Authors: Zoldos V , Papes D , Brown S C , Panaud O , Siljak-Yakovlev S
Published: April 2011

Seven Quercus species, four deciduous (Q. cerris, Q. petraea, Q. pubescens, andQ. robur) and three evergreen (Q. coccifera, Q. ilex, andQ. suber), were assessed for DNA content. Their genome sizes ranged from 1.88 to 2.00 pg/2C, namely an interspecific DNA content variation of 6%. In addition, the DNA content of several populations of Q. petraea andQ. robur with different geographical origins, French and Croatian, was estimated. DNA content did not vary among four populations of Q. robur, but did differ between two populations of Q. petraea, the French population having a higher 2C DNA value than the Croatian. The genome size of this French population showed important dispersion among 10 measured individuals. This was in accordance with subsequent cytogenetic data that revealed extra chromosomes in some individuals from this population. The percent GC varied little between the species; a GC content of 39.9% is established as typical for oak.Key words: Quercus, flow cytometry, genome size, GC percent, DNA content variations, extra chromosomes.
The physical mapping of microsatellite markers in wheat
Authors: Röder Marion S , Korzun Victor , Gill Bikram S , Ganal Martin W
Published: April 2011

Microsatellite markers represent a new class of genetic markers in plants. Such markers reveal a high level of polymorphism even in species with a narrow genetic base, such as hexaploid wheat (Triticum aestivum L.). We used a large set of such markers and 25 deletion stocks of 'Chinese Spring' in a deletion-mapping experiment to study the physical distribution of dinucleotide microsatellite markers in homoeologous group 2 chromosomes of hexaploid wheat. Thirty-one microsatellite markers identified 14 loci in chromosome 2A, 9 loci in chromosome 2B, and 10 loci in chromosome 2D. The microsatellite loci were evenly distributed along the chromosome length, marking 18 of 27 defined physical intervals, including centromeric, interstitial, and telomeric regions. The apparent random distribution indicates that microsatellite markers provide excellent coverage of the wheat genome.Key words: deletion stocks, group 2 homoeologues, microsatellites, wheat.
Biochemical and genetic characterisation of a D glutenin subunit encoded at the Glu-B3 locus
Authors: Nieto-Taladriz M T , Rodríguez-Quijano M , Carrillo J M
Published: April 2011

The SDS-PAGE pattern of reduced and alkylated glutenins from the bread wheat cultivar Prinqual presents a subunit (named d4) in the mobility zone of the omega -gliadins that only appears under reduced conditions. This subunit was isolated and characterised at the biochemical and genetic levels. Subunit d4 was shown to form disulphide aggregates with glutenins and had an acidic pI. These characteristics correspond to those of the D glutenin subunits. The N-terminal amino acid sequence of subunit d4 was coincident with the SRL sequence type characteristic of omega -gliadins encoded by genes on the 1B chromosome, and confirms the similarity between D glutenin subunits and omega -gliadins. The genetic study of subunit d4 was performed in the F2 progeny from the 'Prinqual' x 'Ablaca' cross, based on four prolamin loci: Glu-B1, Glu-B3, Gli-B1, and Gli-B5. The recombinants found between Glu-B3 and Gli-B1 demonstrated that subunit d4 was encoded at the Glu-B3 locus, and reinforces the hypothesis of the duplication of prolamin gene clusters in wheat. A preliminary study of the effect of subunit d4 on gluten strength showed that lines with the Glu-B3 allele from 'Prinqual', which includes subunit d4, had a significantly higher sedimentation volume than those with the allele from 'Ablaca'.Key words: wheat gluten proteins, D glutenin subunits, amino acid sequence, linkage mapping, complex loci duplication.
Thelightgene ofDrosophila melanogasterencodes a homologue ofVPS41, a yeast gene involved in cellular-protein trafficking
Authors: Warner T S , Sinclair DAR , Fitzpatrick K A , Singh M , Devlin R H , Honda B M
Published: April 2011

Mutations in a number of genes affect eye colour in Drosophila melanogaster; some of these "eye-colour" genes have been shown to be involved in various aspects of cellular transport processes. In addition, combinations of viable mutant alleles of some of these genes, such as carnation (car) combined with eitherlight (lt) or deep-orange (dor) mutants, show lethal interactions. Recently, dor was shown to be homologous to the yeast gene PEP3 (VPS18), which is known to be involved in intracellular trafficking. We have undertaken to extend our earlier work on the lt gene, in order to examine in more detail its expression pattern and to characterize its gene product via sequencing of a cloned cDNA. The gene appears to be expressed at relatively high levels in all stages and tissues examined, and shows strong homology to VPS41, a gene involved in cellular-protein trafficking in yeast and higher eukaryotes. Further genetic experiments also point to a role for lt in transport processes: we describe lethal interactions between viable alleles of lt and dor, as well as phenotypic interactions (reductions in eye pigment) between alleles of lt and another eye-colour gene, garnet (g),whose gene product has close homology to a subunit of the human adaptor complex, AP-3.Key words: vesicle transport, eye-colour gene, heterochromatin.
A genetic and molecular analysis of aninvectedDominantmutation inDrosophilamelanogaster
Authors: Simmonds A J , Bell J B
Published: April 2011

The invected gene of Drosophila melanogaster is a homeobox-containing gene that is closely related to engrailed. A dominant gain of function allele, invectedDominant, was derived from mutagenesis of a dominant allele of vestigial, In(2R)vgW. A careful analysis of the phenotype of invectedDominantshows that it is associated with a transformation of the anterior compartment of the wing to a posterior fate. This transformation is normally limited to the wing blade itself and does not involve the remaining tissues derived from the wing imaginal disc, including the wing hinge and dorsal thorax of the fly. The ectopic expression of invected protein associated with invectedDominantcorrelates spatially with the normal expression pattern of vestigial in the wing imaginal disc, suggesting that control elements of vestigial are driving ectopic invected expression. This was confirmed by sequence analysis that shows that the dominant vestigial activity was eliminated by a deletion that removes the 3' portion of the vestigial coding region. This leaves a gene fusion wherein the vestigial enhancer elements are still juxtaposed immediately 5' to the invected transcriptional start site, but with the vg sequences harboring an additional lesion. Unlike recessive invected alleles, the invectedDominantallele produces an observable phenotype, and as such, should prove useful in determining the role of invected in patterning the wing imaginal disc. Genetic analysis has shown that mutations of polyhomeotic, a gene involved in regulating engrailed expression, cause a reproducible alteration in the invectedDominantphenotype. Finally, the invectedDominantallele should prove valuable for identifying and characterizing genes that are activated within the posterior compartment. A screen using various lacZ lines that are asymmetrically expressed in an anterior-posterior manner in the wing imaginal disc isolated one line that shows posterior-specific expression within the transformed anterior compartment.Key words: Drosophila, development, dominant mutation, ectopic, wings.
More than one origin of hexaploid wheat is indicated by sequence comparison of low-copy DNA
Authors: Talbert L E , Smith L Y , Blake N K
Published: April 2011

Allohexaploid bread wheat is grown on more acreage than any other cereal crop, yet variation at the DNA level seems to be less than that observed in many diploid crop species. A common explanation for the small amount of DNA-level variation is that a severe bottleneck event resulted from the polyploidization events that gave rise to hexaploid wheat, whereby wheat was genetically separated from its progenitors. In this report, we test the extent of the bottleneck separating wheat from its D-genome progenitor, Triticum tauschii, by comparative DNA sequence analysis. Restriction site variation of low-copy DNA sequences amplified by PCR showed an average of 2.9 and 2.4 alleles per primer set in T. tauschii and wheat, respectively. Two different restriction patterns were present in T. tauschii for DNA amplified with a primer set for the A1 locus. Both alleles were also present in wheat. Alleles at the A1 locus were cloned and 527 bp of sequence obtained from 12 and 13 diverse accessions of wheat and T. tauschii, respectively. Average genetic distance among the wheat alleles was similar to that among the T. tauschii alleles (0.0127 and 0.0133, respectively). Nucleotide differences indicated that two distinct alleles existed in T. tauschii, both of which were present in wheat. These data suggest that hexaploid wheat formed at least twice, and that the bottleneck separating wheat from T. tauschii may be less constrictive than previously supposed.Key words: wheat, evolution, DNA.
Characterization and structure of the mitochondrial small rRNA gene of the entomopathogenic fungus Beauveria bassiana
Authors: Hegedus D D , Pfeifer T A , Mulyk D S , Khachatourians G G
Published: April 2011

The entire mitochondrial (mt) small ribosomal RNA (srRNA) gene from the entomopathogenic fungus Beauveria bassiana was sequenced. Alignment of the sequence to those of other filamentous fungi revealed gross length differences in their respective products. Construction of a secondary structural model showed that these differences were restricted to known variable srRNA subdomains. Several features were identified that were common only to the hyphomycetous fungi examined. Phylogenetic analysis indicated that the anamorph B. bassiana was more closely related to the pyrenomycete than to the plectomycete ascomycetous fungi. Based on our previous comparison of mt gene arrangement in filamentous fungi, this was unexpected. The possibility that the smaller mt genomes reflect the ancestral arrangement of genes is discussed.Key words: Beauveria bassiana, mitochondria, small ribosomal RNA, secondary structure, phylogeny.
Cytological and molecular characterization of repetitive DNA sequences of Solanum brevidens and Solanum tuberosum
Authors: Rokka V -M , Clark M S , Knudson D L , Pehu E , Lapitan NLV
Published: April 2011

The chromosomal distribution, copy numbers, and nucleotide sequences were determined for four repetitive DNA clones, pSB1 and pSB7 of Solanum brevidens and pST3 and pST10 of Solanum tuberosum. Using fluorescence in situ hybridization (FISH), pSB1 and pSB7 were localized near the telomeres and in some centromeric and interstitial sites of S. brevidens chromosomes, but not in S. tuberosum chromosomes, after high stringency washes. The clone pST3 showed signals in the telomeric areas of a few chromosomes in S. tuberosum, but signals were not detected in S. brevidens. All three repeated sequences (pSB1, pSB7, and pST3) were detected in chromosomal areas that are typically known to contain tandemly repeated sequences. The S. tuberosum clone pST10 did not show signals in either species even at low stringency conditions. The estimated copy numbers of the four clones were 1500, 6750, 300, and 400 for pSB1, pSB7, pST3, and pST10, respectively, in the corresponding haploid genomes (S. brevidens and S. tuberosum). The inserts of the four clones pSB1, pSB7, pST3, and pST10 were 322, 167, 845, and 121 bp, respectively. After sequencing, no significant sequence homologies were found among the four clones. A homology search in sequence data bases showed that pSB7 has variable homology (78-100%) with another repetitive sequence of S. brevidens Sb4/2 depending on its subrepeat. It also showed some homology with one repeat of tomato (pLEG15) and one repeat of Solanum circaeifolium (pSC15).Key words: chromosome, copy number, fluorescence in situ hybridization, FISH, nucleotide sequence, potato.
Characterisation and physical localisation of Ty1-copia-like retrotransposons in four Alstroemeria species
Authors: Kuipers Anja GJ , Heslop-Harrison Pat JS , Jacobsen Evert
Published: April 2011

The genus Alstroemeria contains species with large genomes (2C = 36.5-78.9 pg (17 600 - 38 000 Mb) in those species with 2n = 2x = 16). We investigated the diversity and genomic and chromosomal organisation of Ty1-copia-like retrotransposons in four Alstroemeria species. Analysis of 33 PCR-amplified sequences corresponding to a conserved domain of the Ty1-copia reverse transcriptase (rt) gene showed high heterogeneity among predicted amino acid sequences; no two sequences were identical, but most fell into one of five subgroups. Levels of inter- and intra-specific heterogeneity of sequences were similar. HaeIII-digested genomic DNA of various Alstroemeria species contained distinct bands upon hybridisation with individual rt gene fragments. Hybridisation with the heterogeneous PCR pool of rt fragments (retrotransposon pool) revealed additional bands; some minor bands were characteristic of either Brazilian or Chilean species. In situ hybridisation of the retrotransposon pool from three species to metaphase chromosomes from the same species showed a dispersed distribution of the retrotransposon pool with exclusion from rDNA and other chromosomal sites.Alstroemeria pelegrina, which is without major heterochromatic sites, showed some clustering and small negative bands. The retrotransposon pool was excluded from major DAPI-staining bands in Alstroemeria aurea, but in contrast, the sites of the major tandemly repeated sequences in Alstroemeria inodora showed a hybridisation signal similar to that in the rest of the chromosomes. The data are discussed in the context of the contribution of Ty1-copia-like retrotransposons to plant genome size, their evolution, and their value for phylogenetic and biodiversity studies.Key words: Alstroemeria, in situ hybridisation, genome organisation, retrotransposable elements, Ty1-copia.
The humanDENNgene: genomic organization, alternative splicing, and localization to chromosome 11p11.21-p11.22
Authors: Chow Vincent T , Lim K M , Lim Daniel
Published: April 2011

We have previously isolated and sequenced the cDNA of a novel gene, DENN, that exhibits differential mRNA expression in normal and neoplastic cells. The open reading frame of 4761 nucleotides encodes a putative hydrophilic protein of 1587 amino acids with a calculated molecular mass of 176 431 Da. Within DENN cDNA lies an alternative exon segment of 129 nucleotides encoding 43 amino acids, which may be excluded from some transcripts by alternative splicing. The serine- and leucine-rich DENN protein possesses a RGD cellular adhesion motif and a leucine-zipper-like motif associated with protein dimerization, and shows partial homology to the receptor binding domain of tumor necrosis factor alpha . DENN is virtually identical to MADD, a human MAP kinase-activating death domain protein that interacts with type I tumor necrosis factor receptor. DENN displays significant homology to Rab3 GEP, a rat GDP/GTP exchange protein specific for Rab3 small G proteins implicated in intracellular vesicle trafficking. DENN also exhibits strong similarity to Caenorhabditis elegans AEX-3, which interacts with Rab3 to regulate synaptic vesicle release. Composed of 15 exons (ranging in size from 73 to 1230 bp) and 14 introns (varying from about 170 bp to 5.3 kb), the DENN gene is estimated to span at least 28 kb. The alternative splicing event was traced to an alternative 5' donor site involving exon 7. DENN was mapped to chromosome region 11p11.21-p11.22 by FISH. Using polyclonal antibodies against a synthetic peptide, Western blotting of MOLT-4 T-lymphoblastic leukemic cell proteins and immunoblotting of subcellular fractions of MOLT-4 cells and PLC/PRF/5 liver cancer cells yielded data corroborating the alternative splicing mechanism that generates two variant isoforms of the DENN protein that display differential expression in cells of different lineages.Key words: human, DENN gene, genomic organization, alternative splicing, chromosomal localization.
Mitotic and polytene chromosome analyses in the Queensland fruit fly,Bactrocera tryoni(Diptera: Tephritidae)
Authors: Zhao J T , Frommer M , Sved J A , Zacharopoulou A
Published: April 2011

The Queensland fruit fly, Bactrocera tryoni, like the Mediterranean fruit fly, Ceratitis capitata, has a diploid complement of 12 chromosomes, including five pairs of autosomes and a XX/XY sex chromosome pair. Characteristic features of each chromosome are described. Chromosomal homology between B. tryoni and C. capitata has been determined by comparing chromosome banding pattern and in situ hybridisation of cloned genes to polytene chromosomes. Although the evidence indicates that a number of chromosomal inversions have occurred since the separation of the two species, synteny of the chromosomes appears to have been maintained.Key words: tephritid fruit fly, Bactrocera tryoni, polytene chromosomes, in situ hybridisation, chromosomal homology.
Organization and distribution of a Sau3A tandem repeated DNA sequence in Picea (Pinaceae) species
Authors: Brown Garth R , Newton Craig H , Carlson John E
Published: April 2011

Repeated DNA families contribute to the large genomes of coniferous trees but are poorly characterized. We report the analysis of a 142 bp tandem repeated DNA sequence identified by the restriction enzyme Sau3A and found in approximately 20 000 copies in Picea glauca. Southern hybridization indicated that the repeated DNA family is specific to the genus, was amplified early in its evolution, and has undergone little structural alteration over evolutionary time. Fluorescence in situ hybridization localized arrays of the Sau3A repeating element to the centromeric regions of different subsets of the metaphase chromosomes of P. glauca and the closely related Picea sitchensis, suggesting that mechanisms leading to the intragenomic movement of arrays may be more active than those leading to mutation of the repeating elements themselves. Unambiguous identification of P. glauca and P. sitchensis chromosomes was made possible by co-localizing the Sau3A tandem repeats and the genes encoding the 5S and 18S-5.8S-26S ribosomal RNAs.Key words: Picea, repeated DNA, in situ hybridization, centromere.
A pentamer-repeat-containing DNA sequence in Texas bluebonnet (Lupinus texensis Hook.)
Authors: MacRae Amy F
Published: April 2011

A 654-bp EcoRI restriction fragment called Lup4 was shotgun cloned from Texas bluebonnet (Lupinus texensis Hook.) nuclear genomic DNA that had been extracted from plant leaves. Its sequence was determined on both strands. Southern blot analysis of EcoRI-digested Texas bluebonnet DNA revealed clone hybridization throughout the ~1.0 to > 23 kb size range; the darkest hybridization was in the high molecular weight range (~6 to > 23 kb). Using dot blot analysis, the copy number of the 654-bp clone was estimated to be ~4.75 × 104 copies per haploid genome, and thus this repetitive sequence comprises 3.5-4.1% of the nuclear genome. Sequence analyses showed that this clone contains multiple repeats: mainly the ATTGG pentamer, but also derivative pentamers (e.g., GTTGG, TTTGG, ATAGG, and GGATT). Examination of DNA base occurrence revealed a strand bias in base composition. Data-base searches using the algorithm FASTA revealed no alignment with existing plant data base sequences, but showed sequence identity with several telomeric and satellite DNA sequences. The two highest-scoring alignments were with another pentamer-containing sequence from a telomeric region of the nematode Parascaris univalens. Key words: Texas bluebonnet, Lupinus, pentamer, repeat-containing sequence, repeated DNA, Tourist element motif.
Families of repeated DNA in the oomycete Phytophthora infestans and their distribution within the genus
Authors: Judelson Howard S , Randall Thomas A
Published: April 2011

The abundance, genomic organization, species distribution, and structure of 33 distinct families of repetitive DNA in Phytophthora are described. The families were identified by screening a library of Phytophthora infestans DNA for repetitive sequences. These were subsequently characterized within 26 species distributed within each of the six taxonomic groups traditionally defined within the genus. Some repeat elements were specific to P. infestans and its close relative, Phytophthora mirabilis, while other repeated sequences were present in most species. The distribution of the DNA families did not conform to the traditional taxonomic groups used for the genus. Characterization of the repeated sequences in P. infestans indicated that they included both dispersed and tandemly repeated elements, with copy numbers ranging from 70 to 8400 per haploid genome. In total, these repeats were estimated to represent 51% of the nuclear genome of P. infestans. Reverse transcriptase motifs were detected in seven of the repeat families that were widely distributed throughout the genus.Key words: chromosome structure, genome evolution, speciation, reverse transcriptase, transposable element.
Development of STS markers closely linked to the vrs1 locus in barley, Hordeum vulgare
Authors: Komatsuda T , Nakamura I , Takaiwa F , Oka S
Published: April 2011

Three random amplified polymorphic DNAs (RAPDs) closely linked to the vrs1 (formerly v) locus were sequenced and converted to sequence-tagged sites (STSs). Of the three STSs, two retained the RAPD polymorphism as dominant-recessive markers between 'Kanto Nakate Gold' (KNG; a two-rowed barley) and 'Azumamugi' (AZ; a six-rowed barley), while the other was co-dominant after digestion with restriction enzymes. Six restriction fragment length polymorphisms (RFLPs) linked to vrs1 were converted to six STSs. All six STSs were co-dominant between the two cultivars after digestion with restriction enzymes. A reliable protocol for small-scale DNA isolation from leaf tissue was developed. The STS markers and the small-scale DNA isolation protocol developed in this study are useful tools for mapping the vrs1 locus of barley.Key words: vrs1 locus (two-row vs. six-row), STSs, co-dominance, Hordeum vulgare.
Isolation and characterization of a satellite DNA family in the Saccharum complex
Authors: Alix Karine , Baurens Franc-Christophe , Paulet Florence , Glaszmann Jean-Christophe , D'Hont Angélique
Published: April 2011

EaCIR1, a 371-bp Erianthus-specific satellite DNA sequence, was cloned from TaqI restricted genomic DNA after agarose-gel electrophoresis. This sequence has 77% homology with a 365-bp satellite of Helictotrichon convolutum and 72% homology with a 353-bp tandem repeat sequence from Oryza sativa. PCR primers defined in the conserved regions of these repetitive sequences were used to isolate other satellite DNAs in different representatives of the Saccharum complex: SoCIR1 in Saccharum officinarum, SrCIR1 in Saccharum robustum, SsCIR1 and SsCIR2 in Saccharum spontaneum, and MsCIR1 in Miscanthus sinensis. EaCIR1 and SoCIR1 were localized to subtelomeric regions of the chromosomes by fluorescence in situ hybridization. Southern hybridization experiments, using two representatives of this repeat sequence family as probes, illustrated contrasting species-specificity and demonstrated the existence of similar repetitive elements in sorghum and maize.Key words: satellite DNA, sugarcane, Saccharum complex, Gramineae, fluorescence in situ hybridization, FISH.
Arabidopsis YAC restriction mapping
Authors: Morroll Shaun M , Wilson Zoe A
Published: April 2011

The approach of partial restriction mapping and vector hybridisation has been used to restriction map and align six yeast artificial chromosomes (YACs) corresponding to the top arm (~27.9 centiMorgans, cM) of Arabidopsis chromosome 5 and confirm the chimeric nature of a further four clones which map to this region. The restriction endonucleases Sma1 and Sfi1 which recognise rare-medium frequency sites in the Arabidopsis genome were used. This work has restriction mapped a 315 kb region that includes a number of genes implicated in floral development, namely PISTILLATA and TOUSLED, and a number of uncharacterised genes involved in male gametogenesis (e.g., Ms1 and Ms37). The information generated can be used to transcriptionally map genes to this contig and will provide data for the isolation of several uncharacterised floral development genes which lie in this region. This approach has demonstrated how large tracts of YAC DNA can be mapped and aligned to show the presence/absence of chimeric YAC clones and provide detailed restriction knowledge for a large genomic region to help facilitate the positional cloning of genes.Key words: yeast artificial chromosome, YAC, Arabidopsis thaliana, partial restriction mapping, floral development.
Disease-resistance related sequences in common bean
Authors: Rivkin M I , Vallejos C E , McClean P E
Published: April 2011

Primers based on a conserved nucleotide binding site (NBS) found in several cloned plant disease resistance genes were used to amplify DNA fragments from the genome of common bean (Phaseolus vulgaris). Cloning and sequence analysis of these fragments uncovered eight unique classes of disease-resistance related sequences. All eight classes contained the conserved kinase 2 motif, and five classes contained the kinase 3a motif. Gene expression was noted for five of the eight classes of sequences. A clone from the SB3 class mapped 17.8 cM from the Ur-6 gene that confers resistance to several races of the bean rust pathogen Uromyces appendiculatus. Linkage mapping identified microclusters of disease-resistance related sequence in common bean, and sequences mapped to four linkage groups in one population. Comparison with similar sequences from soybean (Glycine max) revealed that any one class of common bean disease-resistance related sequences was more identical to a soybean NBS-containing sequence than to the sequence of another common bean class.Key words: nucleotide binding sites, disease-resistance related sequences, Phaseolus vulgaris, Glycine max.
Desynapsis and spindle abnormalities leading to 2n pollen formation in Vaccinium darrowi
Authors: Qu Luping , Vorsa Nicholi
Published: April 2011

Cytological investigation revealed desynapsis in microsporogenesis of a wild diploid clone of Vaccinium darrowi. Expression of desynapsis appears variable among the pollen mother cells (PMCs). In the PMCs expressing desynapsis, all or most chromosomes appeared to be completely desynapsed before anaphase I (AI) since bivalents were rare at this stage. In some PMCs complete separation of chromatids was also observed before AI. Consequently, one or both meiotic divisions were lacking, which in turn suggests either a lack of spindle formation or function. Lack of spindle function was hypothesized from the observation that in PMCs with only separated chromatids (daughter chromosomes) before AI or anaphase II (AII), their subsequent movement to anaphase poles was not observed. Thus, spindle formation or function appears to be dependent on paired homologues (bivalents) or minimally joined sister chromatids (univalents) being present. Omission of meiosis II could lead to formation of fertile 2n pollen (~5%), since a balanced chromosome complement would be expected with an equational division of the entire chromosome complement at AI. The genetic constitution of the 2n gamete would be equivalent to first division restitution (FDR) origin. If chiasmata are lacking then recombination would be absent, and 100% transmission of parental heterozygosity would be expected with FDR 2n gametes. Because desynapsis may arise from the lack of effective chiasmata between the paired homologues, a high level of parental heterozygosity is expected to be retained in the 2n gametes. The potential usage of the 2n gametes in blueberry breeding was discussed.Key words: desynapsis, spindle abnormality, 2n pollen, blueberry.
Population cytogenetic studies on Simulium feuerborni Edwards (Diptera: Simuliidae) from northern Thailand
Authors: Kuvangkadilok Chaliow , Phayuhasena Suwannee , Baimai Visut
Published: April 2011

A standard photographic map of Simulium feuerborni (Diptera: Simuliidae) was constructed from larval salivary gland polytene chromosomes and is described herein. Analysis of polytene chromosomes was made from wild larvae collected from the four populations at Doi Inthanon National Park, Chiang Mai Province, northern Thailand. Simulium feuerborni has three pairs of chromosomes (2n = 6) which are arranged from the longest to the shortest. Chromosome I is metacentric while chromosomes II and III are submetacentric. A total of six simple paracentric inversions have been detected in these natural populations of S. feuerborni. These inversions (IS-1, IL-1, IIL-1, IIL-2, IIIS-1, IIIL-1) occurred in all chromosome arms except for the arm IIS. Significant deviation from Hardy-Weinberg equilibrium has been observed in inversion IIIL-1 at Hui Sai Luaeng suggesting the existence of two gene pools in this population. There is no indication of sex linkage associated with an inversion sequence in these populations. Thus, the X and Y chromosomes of S. feuerborni could not be recognized in this study.Key words: Simulium, polytene chromosome map, inversion polymorphisms
Induction of bicellular pollen by trifluralin treatment and occurrence of triploids and aneuploids after fertilization in maize
Authors: Kato Akio
Published: April 2011

By spraying tassels of maize (Zea mays L.) with a trifluralin solution before flowering, viable bicellular pollen grains (with one vegetative nucleus and one mitotically arrested diploid generative cell) were produced. Fertilization between a central cell (2n) of diploid plants and the mitotically arrested generative cell (2n) of the bicellular pollen induced by trifluralin treatment was detected by the presence of shriveled kernels on pollinated ears. A covered method (tassels covered with aluminum foil for 24 h after spraying) and a non-covered method were compared, and the non-covered treatment with 0.2-0.4% trefanocide solutions was the most effective treatment in producing viable bicellular pollen. About 40-50% of the kernels were shriveled on pollinated ears from the treatments. Chromosome counts on seedlings obtained from 0.3% non-covered treatment revealed 24% were triploid and 4% were aneuploid (2n = 19, 21, and 22).Key words: aneuploid, bicellular pollen, trifluralin, triploid, Zea mays L.
Molecular characterization of ribosomal gene variation within and among NORs segregating in specialized populations of chicken
Authors: Delany Mary E , Krupkin Alex B
Published: April 2011

The molecular organization of the 18S, 5.8S, and 28S ribosomal RNA gene repeat units, located at the single nucleolus organizer region (NOR) locus in the chicken, was investigated in genetically distinct populations of research and commercial chickens. Substantial gene repeat variation within and among NORs was documented. Intact ribosomal gene repeat size ranged from 11 kb to over 50 kb. Unique combinations of ribosomal genes, of different size, were specific to particular populations. It was determined that the basis for the ribosomal gene repeat size variation was intergenic spacer (IGS) length heterogeneity. Interestingly, in different populations, the location of the variation that contributes to length heterogeneity was specific to particular IGS subregions. In addition to IGS variation, an inbred line of Red Jungle Fowl exhibited coding region variation. Ribosomal gene copy number variation was also studied, and line averages ranged from 279 to 368. Average rDNA array size (a function of copy number and gene repeat length) was calculated for each of the populations and found to vary over a range of two megabases, from 5 to 7 Mb.Key words: rDNA, NOR, IGS, genetic variation, chicken.
Homogenization of 5S ribosomal genes on the noncoding strand of the rDNA units of two crustacean species
Authors: Drouin Guy
Published: April 2011

We amplified and cloned twelve 28S-18S ribosomal RNA gene intergenic regions from two crustacean species, the copepod Calanus finmarchicus and the euphausid Thysanoessa raschi. Hybridization of single-stranded and double-stranded versions of these clones with single-stranded oligonucleotide probes showed that at least one 5S ribosomal gene is present on the noncoding strand of all twelve 28S-18S intergenic regions from each species.Key words: concerted evolution, 5S ribosomal genes, 18S ribosomal genes, 28S ribosomal genes.
Comparative mapping of the wheat Vrn-AI region with the rice Hd-6 region
Authors: Kato K , Miura H , Sawada S
Published: April 2011

Although extensive synteny between hexaploid wheat and rice chromosomes has been demonstrated, synteny between the species breaks down in several regions of the wheat genome carrying agronomically important genes. A possible relationship between the wheat Vrn-A1, the vernalization response gene on chromosome 5A, and the rice Hd-6, a QTL controlling heading date by photoperiod response on chromosome 3, was investigated. Rice cDNA clones which had previously been mapped onto the Hd-6 region were screened for comparative genetic mapping of the Vrn-A1 region. Ten markers mapped to Hd-6 were assigned to wheat chromosome 5A by nullisomic-tetrasomic analysis. Of them, four cDNA markers, linked within 2.2 cM in the rice Hd-6 region, were mapped on the flanking region of the wheat Vrn-A1, with a complete correspondence of order, demonstrating a fine-scale genetic collinearity. These results gave evidence that the wheat Vrn-A1 region is in synteny with the rice Hd-6 region.Key words: wheat, rice, vernalization response gene, photoperiod response gene, synteny.
Arrays of repetitive DNA elements in the largest chromosomes of Toxoplasma gondii
Authors: Matrajt Mariana , Angel Sergio O , Pszenny Viviana , Guarnera Eduardo , Roos David S , Garberi Juan C
Published: April 2011

A novel tandemly repeated DNA structure of Toxoplasma gondii that meets the requirements assigned for satellital DNA was characterized. A DNA fragment of 1002 bp contains two different elements of repetitive DNA families named ABGTg7 and ABGTg8.2. Both repeats are members of a more complex tandem structure where ABGTg7-like monomers can be arranged either as direct tandems or flanked by other related or non-related repeats. Pulse-field gel electrophoresis analysis showed that these repeats hybridize with the largest T. gondii chromosomes. Bal31 sensitivity assays indicated that these elements are located near the telomeres and along other regions too. Five genomic lambda phages were isolated and two different completed clusters of the repeated structure were analyzed.Key words: Toxoplasma gondii, tandem repeat, satellite DNA, molecular karyotype, telomere.
FISH landmarks for barley chromosomes (Hordeum vulgare L.)
Authors: Brown Susan E , Stephens Janice L , Lapitan Nora LV , Knudson Dennis L
Published: April 2011

Barley metaphase chromosomes (2n = 14) can be identified by fluorescence in situ hybridization (FISH) and digital imaging microscopy using heterologous 18S rDNA and 5S rDNA probe sequences. When these sequences are used together, FISH landmark signals were seen so that all 7 chromosomes were uniquely identified and unambiguously oriented. The chromosomal location of the landmark signals was determined by FISH to a barley trisomic series using the 18S and 5S probes labeled with different fluorophores. The utility of these FISH landmarks for barley physical mapping was also demonstrated when an Amy-2 cDNA clone and a BAC clone were hybridized with the FISH landmark probes.Key words: Hordeum vulgare, barley, FISH, 5S, 18S, rDNA, landmarks, chromosome.
Euchromatic domains in plant chromosomes as revealed by H4 histone acetylation and early DNA replication
Authors: Vyskot Boris , Siroky Jiri , Hladilova Renata , Belyaev Nikolai D , Turner Bryan M
Published: April 2011

Using specific polyclonal antisera raised against acetylated isoforms of histone H4, we have analyzed their distribution in the dioecious plant Silene latifolia (syn.Melandrium album) possessing heteromorphic sex chromosomes. Our previous studies on this species have shown that one of the two X chromosomes in homogametic female cells is heavily methylated and late replicating, as a possible consequence of dosage compensation. Here we report that there are no detectable differences in intensity and distribution of H4 acetylation between these two X chromosomes. In S. latifolia only distal-subtelomeric chromosome regions, on both the sex chromosomes and autosomes, display strong signals of H4 acetylation at N-terminal lysines 5, 8, and 12. These acetylated domains correspond to the very early replicating distal chromosome regions as revealed by 5-bromodeoxyuridine pulses followed by the indirect immunofluorescence microscopy. The distribution of H4 acetylated at lysine 16 was uniform along the chromosomes. The unique distal-subtelomeric H4 acetylation signals were also observed in three other Silene species (S. vulgaris, S. pendula, andS. chalcedonica), but not in two non-related plant species tested (Allium cepa and Nicotiana tabacum). The presented data as well as our recent studies on the structure of S. latifolia chromosome ends indicate that Silene species possess the specific distal-subtelomeric location of euchromatin, gene-rich regions on chromosomes.Key words: histone H4 acetylation, DNA replication, euchromatin, immunofluorescence labeling, Silene spp.
Development of amplified consensus genetic markers (ACGM) inBrassica napusfromArabidopsis thalianasequences of known biological function
Authors: Brunel Dominique , Froger Nicole , Pelletier Georges
Published: April 2011

A method for the development of consensus genetic markers between species of the same taxonomic family is described in this paper. It is based on the conservation of the peptide sequences and on the potential polymorphism within non-coding sequences. Six loci sequenced from Arabidopsis thaliana, AG, LFY3, AP3, FAD7, FAD3, and ADH, were analysed for one ecotype of A. thaliana, four lines of Brassica napus, and one line for each parental species, Brassica oleracea and Brassica rapa. Positive amplifications with the degenerate primers showed one band for A. thaliana, two to four bands in rapeseed, and one to two bands in the parental species. Direct sequencing of the PCR products confirms their peptide similarity with the "mother" sequence. By comparison of intron sequences, the correspondence between each rapeseed gene and its homologue in one of the parental species can be determined without ambiguity. Another important result is the presence of a polymorphism inside these fragments between the rapeseed lines. This variability could generally be detected by differences of electrophoretic migration on long non-denaturing polyacrylamide gels. This method enables a quick and easy shuttle between A. thaliana and Brassica species without cloning.Key words: consensus genetics markers, PCR specific, Brassica, Arabidopsis, targeted markers, DSCP.
Rediscovery and further characterization of the aeroplane (ae) wing posture mutation in Drosophila melanogaster
Authors: Soanes Kelly H , Bell John B
Published: April 2011

In 1931, Theodore Quelprud characterized a novel spontaneous mutation in Drosophila melanogaster, which was named aeroplane (ae) based on its abnormal wing posture. Although the characterization of the original ae locus was minimal, it is very likely that another allele of this extinct mutation has now been identified. aeroplane-like (ae-l) was isolated as a by-product of a transformation experiment. The apparent wing paralysis is not caused by any obvious abnormalities in the thorax, wing, indirect flight muscles or direct flight muscles. Classical genetic complementation analyses of ae-l with other genes in the region suggest that it represents an allele of a novel locus. Unexpectedly, a molecular examination revealed that the physical lesion identified in the ae-l mutant is exceptionally close to the homeotic gene teashirt (tsh) and, indeed, may represent an unusual allele of teashirt.Key words: aeroplane, teashirt, wing posture, Drosophila, flight.
Two genes control aluminum tolerance in maize: Genetic and molecular mapping analyses
Authors: Sibov S T , Gaspar M , Silva M J , Ottoboni LMM , Arruda P , Souza A P
Published: April 2011

We have identified two loci linked to aluminum (Al) tolerance in the maize inbred line Cat-100-6 by means of restriction fragment length polymorphism (RFLP) and bulked segregant analysis (BSA). A segregating population F2was obtained from a cross between Cat-100-6 (Al tolerant) × S1587-17 (Al sensitive) parents. Subsequently two DNA bulks of individuals, displaying a contrasting Al tolerance trait were generated from F2. From a total of 158 markers used, 30 markers were identified showing polymorphism between parents and bulks. The segregation results derived from the hybridization from these 30 markers and 56 individuals from F2revealed 10 markers cosegregating with the Al tolerance which were located in two linkage groups. The linkage groups were composed of 6 and 4 markers, and they were mapped on the short arm of chromosomes 6 and 10, respectively. From these observations, we deduce that two loci are involved in this trait in Cat-100-6 line. QGENE software was used to study the correlation between these two loci and the trait for aluminum tolerance. The results indicate that the locus on chromosome 10 has the stronger effect, and it is responsible for the major part of the variability of the trait.Key words: maize, aluminum tolerance, molecular mapping, somaclonal variation.