bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular characterization and chromosome location of repeated DNA sequences in Hordeum species and in the amphiploid tritordeum (×Tritordeum Ascherson et Graebner)
Authors: Ferrer Esther , Loarce Yolanda , Hueros Gregorio
Published: May 2008

Genomic DNA from 19 species and subspecies representing the four basic genomes (H, I, X, and Y) of Hordeum was restricted with HaeIII and hybridized with two repeated DNA sequences of Hordeum chilense. The potential use of repeated sequences in ascertaining genomic affinities within the genus Hordeum was studied by comparing restriction fragment patterns. The study demonstrated the following: (i) species that shared a basic genome showed more similar hybridization fragment patterns than species with different genomes, whether with pHchl or pHch3; (ii) hybridization with pHchl revealed the presence of certain fragments limited to the species with a H genome; and (iii) the alloploid nature of species like H. jubatum was confirmed. The chromosomal distribution of the two repeated sequences was studied in species representing each basic genome and in the amphiploid tritordeum using fluorescent in situ hybridization. No interspecific differences were found between the diploid species. In situ experiments indicated the alloploid nature of H. depressum. Both sequences allow H. chilense chromatin to be distinguished from wheat chromosomes in tritordeum.Key words: repeated DNA sequences; in situ hybridization, Hordeum, tritordeum.
Improved electroporation buffer enhances transient gene expression in Arachis hypogaea protoplasts
Authors: Li Zhijian , Cheng Ming , Demski James W. , Jarret Robert L.
Published: May 2008

An electroporation medium containing 50 mM glycine or 10 mM glycylglycine (glygly), 70 mM potassium glutamate, and 0.4 M mannitol was evaluated for its ability to improve transient β-glucuronidase (GUS) expression in immature cotyledonary protoplasts of Arachis hypogaea L. GUS activity in electroporated protoplasts was 8- to 430-fold greater than that obtained using any of other four commonly employed poration media. Analysis of viability and histochemical staining of protoplasts indicated that electroporation using the glycine- or glygly-based poration medium resulted in increased protoplast viability and GUS expression when compared with other poration media. Replacement of glygly with MES or HEPES buffers significantly reduced the level of GUS expression in electroporated protoplasts.Key words: transient expression, electroporation, Arachis, protoplasts, GUS.
C-banding plus fluorochrome staining shows differences in C-, G-, and R-bands in human and mouse metaphase chromosomes
Authors: Bella J. L. , Gosálvez J. , Fernández J. L.
Published: May 2008

C-banded slides stained with DAPI or chromomycin A3 show different banding patterns between human and L929 mouse cell line metaphase chromosomes, which are also different from those obtained with standard Giemsa C-banding or fluorochrome staining. Human metaphase chromosomes pretreated for C-banding and stained with DAPI show simultaneous C– and DA–DAPI banding patterns, whilst the mouse metaphase chromosomes show both C-banding and G/Q banding like patterns. However, the chromomycin A3 staining of pre-C-banded metaphase chromosomes reveals conspicuous R-banding in man that is absent in mouse. Chromatin species-specific structural factors would explain these results, which prevent simple comparisons of R-, G-, and C-bands among different organisms. The markers induced by this technique may be of practical use for chromosome identification in human–mouse somatic cell hybridization cultures.Key words: mammalian cytogenetics, chromosome structure, chromosome banding, fluorochrome staining.
Nonrandom chromosome variation and morphogenic potential in cell lines of bread wheat (Triticum aestivum L.)
Authors: Winfield M. O. , Karp A. , Schmitt M. , Lörz H. , Davey M. R.
Published: May 2008

A cytogenetical analysis of 18 cell lines, 9 microspore derived, 6 anther derived, and 3 immature-embryo derived, of bread wheat (Triticum aestivum L.) varying in their morphogenic potential was undertaken. Chromosome variation, both structural and numerical, was detected in all lines studied. Variation was present and, in some cases quite extensive, in the earliest samples taken (only 12 weeks after initiation of the suspensions). Within any culture, the pattern and extent of variation changed throughout the course of the study and cells with a euploid constitution generally decreased in frequency with culture age. Among the nine microspore-derived suspensions, morphogenic lines generally showed a more restricted range of chromosome numbers and higher proportions of euploid cells than nonmorphogenic lines. The patterns of distribution of chromosome numbers among the anther-derived cultures were similar to those of the microspore-derived lines but the correspondence between instability and regenerative capacity was less. The immature embryo derived lines, which were neither regenerable nor morphogenic, were all unstable. The anther-derived lines were sampled over several months to determine whether loss of morphogenic potential was related to changes in chromosome instability of specific lines. Analysis of the "elite" line Fl.7, initially capable of regenerating green plants, showed that substantial decreases in the frequencies of normal euploid cells (from 45 to 5%) occurred over the period when morphogenic capacity was lost. However, whether the chromosome instability resulted in loss of morphogenicity or vice versa was not clarified. C-banding analyses of lines Fl.7 and C82d indicated that instability was not random with respect to the three genomes (A, B, and D) of wheat nor to the different chromosomes within the genomes. Chromosomes of the B genome were most often lost or involved in rearrangements, with breakpoints located at, or near, the heterochromatic blocks. Because of the heterogeneity of the cell lines, extensive analyses of large numbers of cells would be required before it would be possible to determine whether loss of morphogenic potential arises as a result of specific chromosome loss(es).Key words: somaclonal variation, wheat, chromosomes, heterochromatin, cell cultures.
Genome flux in tomato auto- and auxo-trophic cell clones cultured in different auxin/cytokinin equilibria. I. DNA multiplicity and methylation levels
Authors: Bogani Patrizia , Simoni Alessandra , Bettini Priscilla , Mugnai Maria , Pellegrini M. Gabriella , Buiatti Marcello
Published: May 2008

An analysis of the effect of changing physiological conditions on genetic stability, in terms of epigenetic changes, such as DNA, methylation patterns, and multiplicity of repetitive DNA, was carried out on tomato cell clones grown on media supplemented with different auxin/cytokinin ratios. The effect of endogenous variation in phytohormone equilibria was also indirectly analysed through a comparison of auxotrophic or habituated (autotrophic) cell clones and the differentiated leaf tissue. The data obtained showed significant variation in methylation and multiplicity levels both between clones and between treatments, clearly suggesting a contemporary influence of exogenous hormonal treatments and of the initial/endogenous physiological state of the treated tissue on both phenomena studied.Key words: tomato clones, somaclonal variation, methylation, DNA amplification.
Two permanent linear chains of sex chromosomes in Neotermes fulvescens and karyotypes of two other neotropical Kalotermitidae species (Insecta, Isoptera)
Authors: Martins Vanderlei Geraldo , Mesa Alejo
Published: May 2008

Meiosis and (or) mitosis of males and females of Cryptotermes brevis, Eucryptotermes wheeleri, and Neotermes fulvescens, all of them from the neotropical region, were analyzed. Cryptotermes brevis showed a similar karyotype to that obtained by other authors for specimens of the neartic and Australian regions (2n = 36 for females and 2n = 37 for males, with XX and XYY sex mechanisms, respectively). Eucryptotermes wheeleri, the only species that has been described in this genus, showed the lowest number of chromosomes reported for Isoptera (2n = 22) until now. The male meiosis of this species presents a linear chain of six sex chromosomes, three of them being X and three of them Y chromosomes. Neotermes fulvescens showed a diploid number of 40 for males and 42 for females and, in the first male meiosis, two linear chains of chromosomes, both related to sex. One of the chains, named A, presented nine chromosomes and the other, named B, seven chromosomes. Hypotheses to explain these mechanisms are formulated in this paper and putative ancestral relationships with other species of Kalotermitidae are presented.Key words: termite, Neotermes, two linear chains, translocations, South American.
Mapping of digested and undigested random amplified microsatellite polymorphisms in barley
Authors: Becker Jörg , Heun Manfred
Published: May 2008

The broad use of microsatellites as a tool for constructing linkage maps in plants has been limited by the need for sequence data to detect the underlying simple sequence repeats. Therefore, random amplified microsatellite polymorphisms (RAMPs) were studied as an alternative approach for barley mapping. Labelled (GA)nsimple sequence repeat primers were combined with RAPD primers of different length and sequence to generate RAMPs. To get additional polymorphisms (called dRAMPs), the obtained products were also analysed after digestion with MseI. There were 0–11 polymorphisms found per primer combination. Sixty RAMPs/dRAMPs identifying 40 new loci were mapped onto a barley RFLP map. The new DNA markers are found on all chromosomes and they increased the length of the barley map by 174 cM to a total of 1270 cM. Interestingly, the RAMPs/dRAMPs caused stretching effects in genome areas where stretching was also observed for AFLPs.Key words: barley, microsatellite, mapping, RAMP, RFLP.
Comparison of methods for the detection of in situ restriction enzyme – nick translation using fluorochromes and confocal microscopy
Authors: Stuppia L. , Cinti C. , Santi S. , Peila R. , Maraldi N. M. , Calabrese G. , Palka G. , Sumner A. T.
Published: May 2008

A series of experiments was carried out to determine the most efficient methods for detecting incorporated nucleotides in the "in situ" restriction enzyme – nick translation technique. Different methods were tested on fixed human metaphase chromosomes using confocal microscopy for the demonstration of the patterns produced. Of the various techniques tested, that using DIG-dUTP in conjunction with FITC-labelled anti-DIG appears to show the greatest sensitivity and specificity. The use of biotinylated nucleotides with FITC-avidin gives rather less sensitivity, while direct labelling with fluorescein-dUTP produces results more rapidly with better chromosome morphology but at the cost of reduced sensitivity. Resorufin-labelled dUTP was unusable, because of the low level of fluorescence and its very rapid fading. The successful fluorescence methods are more sensitive and faster than using horseradish peroxidase or alkaline phosphatase for detection.Key words: restriction enzymes, nick translation, chromosomes, fluorochromes, confocal microscopy.
Assessment of inter- and intra-inbred line variability in sunflower (Helianthus annuus) by RFLPs
Authors: Zhang Y. X. , Gentzbittel L. , Vear F. , Nicolas P.
Published: May 2008

The restriction fragment length polymorphism (RFLP) between 26 sunflower inbred lines was evaluated with 81 probe–enzyme combinations involving 51 cDNA clones and 4 restriction enzymes (HindIII, EcoRI, EcoRV, and BglII). An average of 4.6 fragments and 4.9 profiles was detected per probe–enzyme combination, across all inbred lines. The RFLPs revealed were characterized by a high percentage (>70%) of multifragment profiles. Nei's average gene diversity was calculated to measure the genetic variability within cultivated sunflower; the average gene diversity computed with 81 probe–enzyme combinations was 0.59. The relationships between the 26 sunflower inbred lines were analysed by estimates of Nei's F index, which ranged from 0.50 to 0.91, as well as Nei's genetic distance, d, which varied from 0.05 to 0.41. A UPGMA (unweighted pair-group arithmetic average clustering) dendrogram was constructed using the genetic distance matrix; likewise, a principal component analysis was performed using the F matrix. The results obtained from the two clustering analyses allowed the separation of maintainer lines (females) from restorer lines (males). After partitioning the 26 lines into a pool of maintainer lines and a pool of restorer lines, the estimation of gene differentiations showed that the absolute difference (Dm) between females and males was only about 5%. Intraline variability was also examined in 4 sunflower inbred lines, using 30 probe–enzyme combinations. Heterogeneity at varying levels was detected in 3 of the 4 lines studied. The RFLPs detected by this set of selected clones in the 26 inbred lines suggests that RFLPs could be very useful descriptors for sunflower inbred line and variety studies.Key words: RFLPs, sunflower, inbred lines, genetic diversity.
First isolation of tandemly repeated DNA sequences in New World vultures and phylogenetic implications
Authors: Keyser C. , Pfitzinger H. , Montagnon D. , Schlee M. , Ludes B. , Mangin P.
Published: May 2008

A highly repeated DNA sequence composed of closely related subunits that ranged from 171 to 176 base pairs has been cloned and characterized in the king vulture (Sarcoramphus papa). Related sequences were also isolated in the black vulture (Coragyps atratus). This new family of avian repetitive DNA elements is here termed the "HaeIII family." Genomic DNAs from a number of avian species were probed with one of the king vulture restriction fragments. In the cathartids, the hybridization patterns showed no individual or sexual variations. A strong HaeIII ladder was present in the two aforementioned species as well as in the Andean condor (Vultur gryphus), but in the black vulture the bands of the ladder alternated in intensity. Weaker hybridization signals were obtained in two ciconids, the jabiru stork (Jabiru mycteria) and the white stork (Ciconia ciconia). The HaeIII repeat was not detected in accipitrid birds of prey, a Polyborinae falconid, pelecanids, and psittacids. Key words : satellite DNA, New World vulture, tandem repeat, Sarcoramphus papa, Coragyps atratus.
Genome and chromosome identification in cultivated barley and related species of the Triticeae (Poaceae) by in situ hybridization with the GAA-satellite sequence
Authors: Pedersen C. , Rasmussen S. K. , Linde-Laursen I.
Published: May 2008

The satellite sequence studied was primarily composed of GAA repeats organized in long tracts of heterochromatic DNA. Fluorescent in situ hybridization (FISH) with the GAA satellite (GAA banding) to the chromosomes of barley, wheat, rye, and other Triticeae species produced banding patterns similar to those obtained by N-banding. The GAA-banding patterns of barley are described in detail and those of 12 other Triticeae species are described briefly. In situ hybridization with the GAA-satellite sequence permits identification of all the chromosomes of barley. It is a valuable alternative to other banding techniques, especially in connection with physical gene mapping by FISH. The application of the GAA-satellite sequence for the characterization of genomes in phylogenetic studies of genera containing the sequence is discussed. Key words : Hordeum vulgare, Triticeae, GAA-satellite sequence, chromosome identification, genome differentiation.
Analysis ofHeterodera avenaepopulations by the random amplified polymorphic DNA technique
Authors: López-Braña I. , Delibes A. , Romero M. D.
Published: May 2008

Eleven populations of the Heterodera avenae complex (four Spanish, two British, two French, and three Swedish) were studied by random amplified polymorphic DNA analysis. From 5 to 11 fragments were obtained with each of 14 random primers, with fragment size ranging from 200 to 2200 bp. Cluster analysis of the 11 populations, using 108 scorable markers, separate these populations into two main groups. These groups coincide with what is known as the "true" H. avenae and the "Gotland strain" or "British pathotype 3" of H. avenae. The results also clarify the relationships among some members of the H. avenae complex established previously using morphological and biochemical criteria. Key words : cereal cyst nematode, CCN, Heterodera avenae, RAPD.
Comparative mapping of homoeologous group 1 regions and genes for resistance to obligate biotrophs inAvena,Hordeum, andZea mays
Authors: Yu Gong Xin , Bush Arla L. , Wise Roger P.
Published: May 2008

The colinearity of markers linked with resistance loci on linkage group A of diploid oat, on the homoeologous groups in hexaploid oat, on barley chromosome 1H, and on homoeologous maize chromosomes was determined. Thirty-two DNA probes from homoeologous group 1 chromosomes of the Gramineae were tested. Most of the heterologous probes detected polymorphisms that mapped to linkage group A of diploid oat, two linkage groups of hexaploid oat, barley chromosome 1H, and maize chromosomes 3, 6, and 8. Many of these DNA markers appeared to have conserved linkage relationships with resistance and prolamin loci in Avena, Hordeum, and Zea mays. These resistance loci included the Pca crown rust resistance cluster in diploid oat, the R203 crown rust resistance locus in hexaploid oat, the Mla powdery mildew resistance cluster in barley, and the rp3, wsm1, wsm2, mdm1, ht2, and htn1 resistance loci in maize. Prolamin encoding loci included Avn in diploid oat and Hor1 and Hor2 in barley. A high degree of colinearity was revealed among the common RFLP markers on the small chromosome fragments among these homoeologous groups. Key words : disease resistance, colinearity, Gramineae, cereals.
Complex arrangement of dispersed repeated DNA sequences in Oryza officinalis
Authors: Kiefer-Meyer M. C. , Reddy A. S. , Delseny M.
Published: May 2008

A 525-bp BglII fragment was isolated from Oryza officinalis DNA (accession W1278) and shown to correspond to a new dispersed repetitive DNA sequence with specificity restricted to a subset of the wild rice with a C genome. The sequence of the fragment was determined but it does not correspond to any sequence already present in databases. It contains several imperfect palindromes. Larger genomic clones (12–18 kbp) were isolated and all contain sequences homologous to the BglII element. Analysis of these clones confirms that the BglII element is dispersed in the O. officinalis genome. From one genomic clone, the sequences adjacent to the BglII element were subcloned and used as probes to demonstrate that the sequences flanking the BglII element are variable in different genomic clones and that some of them are also dispersed repetitive sequences. The genomic specificity of two of these dispersed repeats was evaluated and shown to be different from that of the initial BglII element. This analysis revealed a complex arrangement of various dispersed repeated sequences. Key words : wild rice, genome specificity, repeated DNA sequences.
Identification, mapping, and application of polymorphic DNA associated with resistance gene Pm21 of wheat
Authors: Qi Lili , Cao Mingshu , Chen Peidu , Li Wanlong , Liu Dajun
Published: May 2008

A new powdery mildew resistance gene designated Pm21, from Haynaldia villosa, a relative of wheat, has been identified and incorporated into wheat through an alien translocation line. Cytogenetic and biochemical analyses showed that chromosome arms 6VS and 6AL were involved in this translocation. Random amplified polymorphic DNA (RAPD) analysis was performed on recipient wheat cultivar Yangmai 5, the translocation line, and H. villosa with 180 random primers. Eight of the 180 primers amplified polymorphic DNA in the translocation line, and the same results were obtained in four replications. Furthermore, RAPD analysis was reported for substitution line 6V, seven addition lines (1V–7V), and the F1, as well as F2 plants of (translocation line × 'Yangmai 5'), using two of the eight random primers. One RAPD marker, specific to chromosome arm 6VS, OPH17-1900, could be used as a molecular marker for the detection of gene Pm21 in breeding materials with powdery mildew resistance introduced from H. villosa. Key words : RAPD analysis, 6VS-specific marker, Pm21, Erysiphe graminis f.sp. tritici, Triticum aestivum – Haynaldia villosa translocation.
Direct FISH of 5S rDNA on tomato pachytene chromosomes places the gene at the heterochromatic knob immediately adjacent to the centromere of chromosome 1
Authors: Xu Jie , Earle E. D.
Published: May 2008

We describe a molecular cytogenetic procedure for high resolution physical mapping of DNA markers, an essential step toward construction of an integrated molecular–classical–cytological map. Tomato was selected as material because its pachytene chromosomes are amenable for study and because detailed molecular, classical, and cytological maps are available. Karyotyping of acetocarmine-stained pachytene chromosomes showing detailed cytogenetic landmarks was combined with direct FISH of the 5S rDNA gene. This enabled us to pinpoint the 5S rDNA gene to the first heterochromatic knob immediately adjacent to the centromere in the short arm of chromosome 1. Thus the position of the 5S rDNA gene on the molecular map was related to the position of the 5S rDNA on the cytogenetic map. The results also provide conclusive evidence of the location of a functional gene in the pericentric heterochromatic region, a rare event to date in plants. We conclude that karyotyping of pachytene chromosomes can be combined with FISH to map a DNA sequence to a cytogenetically defined region and to determine the chromatin origin of an expressed gene. Key words : direct fluorescence in situ hybridization, 5S rDNA, pachytene chromosomes, heterochromatic gene.
Generation of expressed sequence tags and sequence-tagged sites as physical landmarks in the mosquito, Aedes aegypti, genome
Authors: Severson D. W. , Zhang Y.
Published: May 2008

Twenty-three clones were developed as expressed sequence tags (ESTs) and sequence-tagged sites (STSs) that provide broad coverage of the mosquito, Aedes aegypti, genome at an average spacing of about 7.2 cM. Each of these clones had been mapped previously as a restriction fragment length polymorphism (RFLP) marker. Nineteen of these clones represent anonymous cDNAs and 4 clones represent known genes. Forty-seven percent of the anonymous cDNAs showed significant deduced amino acid sequence similarity to previously described sequences from a wide variety of organisms. STSs developed from RFLPs will provide effective tools for rapid screening of YAC and cosmid libraries, and will therefore, provide anchor points for contig construction for any region in the A. aegypti genome. Also, they facilitate the simultaneous integration of physical and genetic mapping data for A. aegypti. Key words : STS, EST, RFLP, restriction fragment length polymorphisms, QTL, quantitative trait loci.
The molecular structure, chromosomal organization, and interspecies distribution of a family of tandemly repeated DNA sequences of Antirrhinum majus L.
Authors: Schmidt Thomas , Kudla Jörg
Published: May 2008

Monomers of a major family of tandemly repeated DNA sequences of Antirrhinum majus have been cloned and characterized. The repeats are 163–167 bp long, contain on average 60% A + T residues, and are organized in head-to-tail orientation. According to site-specific methylation differences two subsets of repeating units can be distinguished. Fluorescent in situ hybridization revealed that the repeats are localized at centromeric regions of six of the eight chromosome pairs of A. majus with substantial differences in array size. The monomeric unit shows no homologies to other plant satellite DNAs. The repeat exists in a similar copy number and conserved size in the genomes of six European species of the genus Antirrhinum. Tandemly repeated DNA sequences with homology to the cloned monomer were also found in the North American section Saerorhinum, indicating that this satellite DNA might be of ancient origin and was probably already present in the ancestral genome of both sections. Key words : Antirrhinum majus, satellite DNA, repetitive DNA, methylation, in situ hybridization.
Molecular genetic maps of the group 6 chromosomes of hexaploid wheat (Triticum aestivumL. em. Thell.)
Authors: Marino Celso L. , Tuleen Neal A. , Hart Gary E. , Nelson James C. , Sorrells Mark E. , Lu Yun Hai , Leroy Philippe , Lopes Catalina R.
Published: May 2008

Restriction fragment length polymorphism (RFLP) maps of chromosomes 6A, 6B, and 6D of hexaploid wheat (Triticum aestivum L. em. Thell.) have been produced. They were constructed using a population of F7–8recombinant inbred lines derived from a synthetic wheat × bread wheat cross. The maps consist of 74 markers assigned to map positions at a LOD ≥ 3 (29 markers assigned to 6A, 24 to 6B, and 21 to 6D) and 2 markers assigned to 6D ordered at a LOD of 2.7. Another 78 markers were assigned to intervals on the maps. The maps of 6A, 6B, and 6D span 178, 132, and 206 cM, respectively. Twenty-one clones detected orthologous loci in two homoeologues and 3 detected an orthologous locus in each chromosome. Orthologous loci are located at intervals of from 1.5 to 26 cM throughout 70% of the length of the linkage maps. Within this portion of the maps, colinearity (homosequentiality) among the three homoeologues is strongly indicated. The remainder of the linkage maps consists of three segments ranging in length from 47 to 60 cM. Colinearity among these chromosomes and other Triticeae homoeologous group 6 chromosomes is indicated and a consensus RFLP map derived from maps of the homoeologous group 6 chromosomes of hexaploid wheat, tetraploid wheat, Triticum tauschii, and barley is presented. Key words : RFLP, wheat, linkage maps, molecular markers.
Cloning and mapping of variety-specific rice genomic DNA sequences: amplified fragment length polymorphisms (AFLP) from silver-stained Polyacrylamide gels
Authors: Cho Yong Gu , Blair Matthew W. , Panaud Olivier , McCouch Susan R.
Published: May 2008

An efficient technique for cloning DNA from silver-stained denaturing Polyacrylamide gels was developed to allow the isolation of specific bands obtained from selective restriction fragment amplification (SRFA). This method proved as reliable as cloning radioactively labelled SRFA bands from the same gels. Rice DNA was used as a template, both with and without [32P]dCTP, using the same PCR profiles. Amplified products were separated using denaturing polyacryamide gel electrophoresis and visualized either by silver staining of gels or by autoradiography of32P-labelled products. We cloned specific polymorphic SRFA bands directly from the denaturing polyacrylamide gels with one round of PCR amplification and confirmed that the sequences of the bands from silver-stained gels were identical to the corresponding32P-labelled bands. The bands that were chosen represented amplified fragment length polymorphisms (AFLPs) between japonica and indica rice varieties. We studied the ability of two cloned AFLP bands to serve as heritable genetic markers by mapping them as RFLPs in an interspecific rice population and found that they represented single-copy DNA at unique loci in the rice genome. Key words : amplified fragment length polymorphism, AFLP, selective restriction fragment amplification, SRFA, PCR cloning, silver staining.
Comparison and integration of four barley genetic maps
Authors: Qi Xiaoquan , Stam Piet , Lindhout Pim
Published: May 2008

Barley (Hordeum vulgare L.) is one of the most extensively studied food crops in recent molecular research. More than 1000 molecular markers have been located on the barley genome by using five independent populations. For the present study, four segregation data sets, 'Proctor' × 'Nudinka', 'Igri' × 'Franka', 'Steptoe' × 'Morex', and 'Harrington' × TR306, were downloaded from the publicly available GrainGenes databank. Since 22% of the markers are common to at least two of the independent data sets, we were able to establish an integrated map using the computer package JOINMAP v2.0. The integrated map contains 898 markers, covers 1060 cM, and removes many large gaps present in the individual maps. Comparison of the integrated map with the individual maps revealed that the overall linear order of markers is in good agreement and that the integrated map is consistent with the component maps. No significant reordering of markers was found. This conservative property of the barley genome makes the integrated map reliable and successful. Except for chromosome 7 (5H), marker clustering was observed in the centromeric regions, probably owing to the centromeric suppression of recombination. Based on this integrated map, geneticists and breeders can choose their favourite markers in any region of interest of the barley genome. Key words : Hordeum vulgare, RFLP, integrated map.
Chromosomal and genomic organization of Ty1-copia-like retrotransposon sequences in the genus Avena
Authors: Katsiotis A. , Schmidt T. , Heslop-Harrison J. S.
Published: May 2008

A cloned repetitive sequence, pAvKB30, obtained from an Avena vaviloviana (AB genome) genomic library, along with two polymerase chain reaction products derived from the conserved region of the reverse transcriptase (RT) gene of retrotransposons, were characterized molecularly and cytologically. The cloned DNA fragment was a dispersed repeat present in all Avena species used in this study (A. strigosa, A. clauda, A. vaviloviana, A. magna, and A. sativa). The fragment was sequenced (210 bp) and found to be 69.5% homologous to part of WIS-2-1A, and 60.5% homologous to the leader sequence of BARE-1; both of these elements have been characterized as Ty1-copia-like retrotransposons in wheat and barley, respectively. In situ hybridization of pAvKB30 to diploid, tetraploid, and hexaploid oat species revealed that the probe is present on both arms of all chromosomes (A, B, C, and D genomes) but is excluded from their centromeric and nucleolar organizer regions. By using double in situ hybridization in hexaploid A. sativa (ACD genome), pAvKB30 was found to be present in lower copy numbers in C-genome chromosomes compared with A- and D-genome chromosomes. Furthermore, under low stringency conditions, pAvKB30 hybridized on Southern blots containing barley, wheat, rye, and Arrhenatherum DNA. However, under high stringency conditions, it hybridized only on Arrhenatherum DNA, which is considered to be the genus most closely related to Avena. All Avena species included in this study yielded a PCR product when the primers from the RT domain of retrotransposons were used. Two products, rtA, obtained by using A. strigosa (As genome) as template, and rtC, obtained by using A. clauda (Cp genome) as template, gave Southern and in situ hybridization results similar to pAvKB30, but each was more abundant in its genome of origin. Key words : genomes, oats, in situ hybridization, translocations, repetitive sequence.
DNA sequences of RAPD fragments in artiodactyls
Authors: Kostia Silja , Palo Jukka , Varvio Sirkka-Liisa
Published: May 2008

A bovine RAPD profile, generated by a 10-mer primer, was analysed by sequencing the major fragments. Three of four different fragments showed homologies to previously characterized mammalian sequences. One was 61–66% identical to LINE sequences and another was 78.5% identical to a human chromosome 2 sequence tagged site. The third fragment was 93.1% identical to the human type 2 inositol 1,4,5-trisphosphate receptor gene. This fragment had counterparts in white-tailed deer and reindeer; fragments of slightly different size in these species showed high sequence similarity and the size differences were due to varying numbers of dinucleotide microsatellite repeats inside the fragment. Key words : RAPD, artiodactyls, sequence similarity, microsatellites, type 2 inositol 1,4,5-trisphosphate receptor.
Heterochromatin heterogeneity in the holocentric X chromatin of Megoura viciae (Homoptera, Aphididae)
Authors: Manicardi G. C. , Bizzaro D. , Galli E. , Bianchi U.
Published: May 2008

Holocentric chromosomes, prepared by spreading embryo cells obtained from Megoura viciae parthenogenetic females, have been C-banded, enzymatically digested in situ using the specific endonucleases DdeI (C↓TNAG), DraI (TTT↓AAA), Tru9I (TT↓AA), and CfoI (GCG↓C), and subsequently stained with Giemsa, DAPI, CMA3, and AgNO3. We observed that the X chromosome had the best defined banding patterns. In the M. viciae X chromosome there is a certain amount of heterogeneity in heterochromatic DNA composition. In fact, the GC-rich NOR-associated heterochromatin differs from other heterochromatic bands that are characterized by AT-rich DNAs. Our data also indicate that, in M. viciae holocentric chromosomes, all heterochromatic blocks are accessible to in situ enzyme attack, the only limit to the digestion being the presence or absence of recognition targets. This is an interesting point, since, in monocentric chromosomes, it is well known that in situ endonuclease digestion is heavily affected not only by DNA base composition but also by chromatin compactness that may limit enzyme accessibility to their specific targets. Key words : heterochromatin, holocentric chromosomes, aphids.
Tomato chromosome 6: effect of alien chromosomal segments on recombinant frequencies
Authors: Liharska Tsvetana , Wordragen Monique van , Kammen Ab van , Zabel Pim , Koornneef Maarten
Published: May 2008

Variation in recombinant frequencies at two adjacent intervals on chromosome 6 of tomato (Lycopersicon esculentum Mill.) has been studied in seven lines that differ in the amount and origin of introgressed segments from wild species. These lines were all crossed to a genotype homozygous recessive for the markers tl, yv, and c, which define the centromere spanning region tl–yv and the long arm region yv–c. Recombinants were identified in large F2, populations consisting of over 30 000 plants in total. Application of molecular markers provided additional information on the distribution of crossover events within the centromere-containing interval tl–yv. A decrease in recombination at the marked intervals correlated with the presence of an alien segment. Suppression of recombination was up to sixfold in the centromere spanning interval tl–yv depending on the source and size of the introgression, and was restricted to the alien segments with no strong effect on the neighbouring intervals. Key words : recombinant frequency, Lycopersicon esculentum, morphological markers, introgressions, centromere.
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 genusAvena
Authors: Linares Concha , González Juan , Ferrer Esther , Fominaya Araceli
Published: May 2008

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.
A PCR assay for detection of a 2RL.2BS wheat–rye chromosome translocation
Authors: Lee J. H. , Kaeppler S. M. , Graybosch R. A. , Sears R. G.
Published: May 2008

A 2RL.2BS wheat–rye translocation, present in the wheat germplasm line Hamlet, carries a gene for resistance to Hessian fly biotype L, one of the most virulent biotypes presently encountered in wheat production environments. Unlike several other wheat–rye chromosome translocations common in wheat breeding programs, 2RL lacks genes encoding storage proteins or other easily selected markers. Oligonucleotide primers synthesized from published sequences derived from the R173 family of moderately repetitive rye DNA were used in the DNA polymerase chain reaction (PCR) to identify specific markers for 2RL. The same primers, when used with DNA extracted from additional wheat–rye translocation lines of importance to the wheat breeding community, gave distinctive PCR products for each genotype. The single primer pair, PAWS5 and PAWS6, may, therefore, have wide applicability for the identification of wheat–rye chromosomal translocations presently encountered in wheat breeding populations. Key words : 2RL.2BS wheat–rye chromosome translocation, polymerase chain reaction, detection.
Isolation and characterization of new polymorphic simple sequence repeat loci in grape (Vitis viniferaL.)
Authors: Bowers J. E. , Dangl G. S. , Vignani R. , Meredith C. P.
Published: May 2008

Four new simple sequence repeat (SSR) loci (designated VVMD5, VVMD6, VVMD7, and VVMD8) were characterized in grape and analyzed by silver staining in 77 cultivars of Vitis vinifera. Amplification products ranged in size from 141 to 263 base pairs (bp). The number of alleles observed per locus ranged from 5 to 11 and the number of diploid genotypes per locus ranged from 13 to 27. At each locus at least 75% of the cultivars were heterozygous. Alleles differing in length by only 1 bp could be distinguished by silver staining, and size estimates were within 1 or 2 bp, depending on the locus, of those obtained by fluorescence detection at previously reported loci. Allele frequencies were generally similar in wine grapes and table grapes, with some exceptions. Some alleles were found only in one of the two groups of cultivars. All 77 cultivars were distinguished by the four loci with the exception of four wine grapes considered to be somatic variants of the same cultivar, 'Pinot noir', 'Pinot gris', 'Pinot blanc', and 'Meunier'; two table grapes that are known to be synonymous, 'Keshmesh' and 'Thompson Seedless'; and three table grapes, 'Dattier', 'Rhazaki Arhanon', and 'Markandi', the first two of which have been suggested to be synonymous. Although the high polymorphism at grape SSR loci suggests that very few loci would theoretically be needed to separate all cultivars, the economic and legal significance of grape variety identification requires the increased resolution that can be provided by a larger number of loci. The ease with which SSR markers and data can be shared internationally should encourage their broad use, which will in turn increase the power of these markers for both identification and genetic analysis of grape. Key words : grape, Vitis, microsatellite, simple sequence repeat, DNA typing, identification.
Characterization and population diversity of interspersed repeat sequence variants (IRS-morphs)
Authors: Kass David H. , Batzer Mark A. , Deininger Prescott L.
Published: May 2008

Inter-Alu PCR is increasingly useful in human genome mapping studies. One use is the generation of alumorphs, polymorphisms resulting from the presence or absence of inter-Alu PCR products. In this study, we have increased the proportion of the genome that can be analyzed by this technique with the use of long interspersed elements (LINEs). The set of polymorphisms detected by both Alu and LINE primers are referred to as interspersed repetitive sequence variants or IRS-morphs. Since a presence–absence variant may have been the result of a recent Alu or LINE insertion, we analyzed 7 isolated IRS-morphs that were generated, in part, with a primer derived from either a consensus LINE or a young Alu subfamily specific sequence, and observed by Southern blot analysis that these variants resulted from other types of genomic alterations. The use of these primers, however, reduces background from the numerous LINEs and Alu elements in the genome, providing sharp DNA fingerprint profiles. We have demonstrated the potential usefulness of these IRS-morph profiles in human population studies. We compared 12 IRS-morphs from a single amplification reaction from five distinct population groups (Caucasian (northern European descent), Hispanic (Mexican-American), Hindu-Indian, Papua New Guinean, and Greenland Eskimo) and observed that most have variable allelic frequencies among populations. The utilization of additional IRS-morph profiles will perpetuate this technique as a tool for DNA fingerprinting and for the analysis of human populations. Key words : Alu elements, DNA fingerprint, human populations, LINEs, SINEs.
The genome sizes ofHordeumspecies show considerable variation
Authors: Kankanpää Juha , Schulman Alan H. , Mannonen Leena
Published: May 2008

Hordeum, distributed worldwide in temperate zones, is the second largest genus in the tribe Triticeae and includes diploid, tetraploid, and hexaploid species. We determined, by DAPI staining and flow cytometry, the nuclear DNA content for 35 accessions of the genus Hordeum, from a total of 19 species, including specimens of 2 cultivars and 2 landraces of Hordeum vulgare ssp. vulgare as well as samples of 12 Hordeum vulgare ssp. spontaneum populations. Genome sizes ranged from 5.69 to 9.41 pg for the G1nuclei of the diploids, and from 13.13 to 18.36 pg for those of the tetraploids. This constitutes a 1.7-fold variation for the diploids, contrasting with a 4% variation previously reported. For H. vulgare ssp. vulgare (barley), the accessions examined differed by 18%. These variations in genome size cannot be correlated with meiotic pairing groups (I, H, X, Y) or with proposed phylogenetic relationships within the genus. Genome size variation between barley accessions cannot be related to status as cultivated or wild, or to climatic or geological gradients. We suggest these data may indicate rapid but sporadic changes in genome size within the genus. Key words : barley, Hordeum, Triticeae, genome size, flow cytometry.
An improved amplification and sequencing strategy for phylogenetic studies using the mitochondrial large subunit rRNA gene
Authors: Parker Alex , Kornfield Irv
Published: May 2008

Numerous molecular systematic studies have employed variation in the mitochondrial large subunit (16s) rRNA gene to infer patterns of relationship among species and higher taxa. The primers most commonly employed in 16s rRNA amplification and sequencing bracket an approximately 600 bp portion of this gene. However, most of the informative variation occurs within a 200 bp subset of this segment. We describe a novel primer pair designed to amplify this variable region in a wide range of taxa, allowing broader application and considerable streamlining of data acquisition for studies using this gene. Key words : molecular phylogenetics, polymerase chain reaction, mtDNA, large ribosomal subunit, control region.
Transfer of sequence tagged site PCR markers between wheat and barley
Authors: Erpelding J. E. , Blake N. K. , Blake T. K. , Talbert L. E.
Published: May 2008

Transfer of mapping information between related species has facilitated the development of restriction fragment length polymorphism (RFLP) maps in the cereals. Sequence tagged site (STS) primer sets for use in the polymerase chain reaction may be developed from mapped RFLP clones. For this study, we mapped 97 STS primer sets to chromosomes in wheat and barley to determine the potential transferability of the primer sets and the degree of correspondence between RFLP and STS locations. STS products mapped to the same chromosome group in wheat and barley 75% of the time. RFLP location predicted STS location 69% of the time in wheat and 56% of the time in barley. Southern hybridizations showed that most primer sets amplified sequences homologous to the RFLP clone, although additional sequences were often amplified that did not hybridize to the RFLP clone. Nontarget sequences were often amplified when primer sets were transferred across species. In general, results suggest a good probability of success in transferring STSs between wheat and barley, and that RFLP location can be used to predict STS location. However, transferability of STSs cannot be assumed, suggesting a need for recombinational mapping of STS markers in each species as new primer sets are developed. Key words : sequence tagged sites, PCR, wheat, barley.
Characterization of four dispersed repetitive DNA sequences fromZea maysand their use in constructing contiguous DNA fragments using YAC clones
Authors: Edwards Keith J. , Veuskens Jacky , Rawles Heather , Daly Allan , Bennetzen Jeffrey L.
Published: May 2008

We have isolated four repetitive DNA fragments from maize DNA. Only one of these sequences showed homology to sequences within the EMBL database, despite each having an estimated copy number of between 3 × 104and 5 × 104per haploid genome. Hybridization of the four repeats to maize mitotic chromosomes showed that the sequences are evenly dispersed throughout most, but not all, of the maize genome, whereas hybridization to yeast colonies containing random maize DNA fragments inserted into yeast artificial chromosomes (YACs) indicated that there was considerable clustering of the repeats at a local level. We have exploited the distribution of the repeats to produce repetitive sequence fingerprints of individual YAC clones. These fingerprints not only provide information about the occurrence and organization of the repetitive sequences within the maize genome, but they can also be used to determine the organization of overlapping maize YAC clones within a contiguous fragment (contigs). Key words : maize, repetitive DNA, YACs.
On sex determination in the Turkish desert woodlouse Hemilepistus elongatus (Crustacea, Isopoda, Oniscidea): searching for sex chromosomes and for sex-specific differences in simple DNA repeats
Authors: Röder G. , Linsenmair K. E. , Nanda I. , Schmid M.
Published: May 2008

The karyotype of male and female Hemilepistus elongatus was investigated by means of C-banding. The diploid chromosome number in both sexes is 2n = 50. By scrutinizing general morphology and localization of the constitutive heterochromatin, no heteromorphic sex chromosomes were found. All chromosome pairs in males are well paired during diakinesis. Hybridization of genomic DNA with (GACA)4 and (GATA)4 oligonucleotides revealed no sex-specific patterns. Key words : karyotype, C-banding, sex determination, simple DNA-repeats, Isopoda.