bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of RAPD markers linked to A and B genome sequences in Musa L.
Authors: Pillay M , Nwakanma D C , Tenkouano A
Published: April 2011

Plantains and bananas (Musa spp. sect. eumusa) originated from intra- and interspecific hybridization between two wild diploid species, M. acuminata Colla. and M. balbisiana Colla., which contributed the A and B genomes, respectively. Polyploidy and hybridization have given rise to a number of diploid, triploid, and tetraploid clones with different permutations of the A and B genomes. Thus, dessert and highland bananas are classified mainly as AAA, plantains are AAB, and cooking bananas are ABB. Classification of Musa into genomic groups has been based on morphological characteristics. This study aimed to identify RAPD (random amplified polymorphic DNA) markers for the A and B genomes. Eighty 10-mer Operon primers were used to amplify DNA from M. acuminata subsp. burmannicoides clone 'Calcutta 4' (AA genomes) and M. balbisiana clone 'Honduras' (BB genomes). Three primers (A17, A18, and D10) that produced unique genome-specific fragments in the two species were identified. These primers were tested in a sample of 40 genotypes representing various genome combinations. The RAPD markers were able to elucidate the genome composition of all the genotypes. The results showed that RAPD analysis can provide a quick and reliable system for genome identification in Musa that could facilitate genome characterization and manipulations in breeding lines.Key words: banana and plantain, A and B genomes, genomic groups, RAPD markers.
Isolation and mapping of microsatellite markers specific for the D genome of bread wheat
Authors: Pestsova E , Ganal M W , Röder M S
Published: April 2011

The potential of Aegilops tauschii, the diploid progenitor of the D genome of wheat, as a source of microsatellite markers for hexaploid bread wheat was investigated. By screening lambda phage and plasmid libraries of Ae. tauschii genomic DNA, dinucleotide microsatellites containing GA and GT motifs were isolated and a total of 65 functional microsatellite markers were developed. All primer pairs that were functional in Ae. tauschii amplified well in hexaploid wheat. Fifty-five loci amplified by 48 primer sets were placed onto a genetic framework map of the reference population of the International Triticeae Mapping Initiative (ITMI) 'Opata 85' × 'W7984'. The majority of microsatellite markers could be assigned to the chromosomes of the D genome of wheat. The distribution of the markers along the chromosomes is random. Chromosomal location of 22 loci nonpolymorphic in the reference population was determined using nullitetrasomic lines of Triticum aestivum 'Chinese Spring'. The results of this study demonstrate the value of microsatellite markers isolated from Ae. tauschii for the study of bread wheat. The microsatellite markers developed improve the existing wheat microsatellite map and can be used in a wide range of genetic studies and breeding programs.Key words: Aegilops tauschii, wheat, molecular markers, genetic map, simple sequence repeats.
Repetitive DNA sequences in Crocus vernus Hill (Iridaceae): The genomic organization and distribution of dispersed elements in the genus Crocus and its allies
Authors: Frello S , Heslop-Harrison J S
Published: April 2011

Eight clones of repetitive DNA were isolated from Crocus vernus Hill. The genomic organization of the clones was analyzed by in situ hybridization to C. vernus and Southern hybridization to a range of Crocus and other species. Seven clones were used for in situ hybridization. Sequence analysis showed that all eight clones were nonhomologous, and thus represented eight different sequence-families. In situ hybridization showed that six were dispersed in high copy numbers on all chromosomes of the C. vernus genome, whereas one was localized proximal to the secondary constriction, at the NOR (nucleolar organizer region) and was not further analyzed, as it was considered part of the 18S-25S rDNA repeat. Except for short palindromes, none of the sequences showed notable internal structures. Clone pCvKB4 showed homology to the reverse transcriptase gene of Ty1-copia-like retrotransposons; the others showed no homology to known sequences. When used as probes for Southern hybridization, four showed a ladder of 3-4 bands superimposed by irregular patterns, indicating organization in short tandem arrays. Each clone had a unique distribution among Crocus species (12-16 species analyzed with each clone) and six species of Iridaceae, Liliaceae, and Amaryllidaceae; all seven investigated sequences were Iridaceae specific and four were Crocus specific. The species distribution of these seven clones showed notable discrepancies with the taxonomic subdivision of the genus at the subgenus, section, and series levels. The results suggest that the phylogeny and taxonomic structure of the genus Crocus might need reconsideration. The analysis of repetitive DNA as a major and rapidly evolving part of the genome could contribute to the study of species relationships and evolution.Key words: phylogeny, evolution, in situ hybridization, sequence analysis, dispersed elements.
Copepod development rates in relation to genome size and 18S rDNA copy number
Authors: White M M , McLaren I A
Published: April 2011

It is known that body sizes and temperature-independent developmental durations within two genera of calanoid Copepoda (Crustacea) are positively related to nuclear DNA contents of their somatic nuclei. Evidently because of the constraint of similar cell numbers among the species, (nucleotypic) effects of nucleus size on cell size and on cell-level processes are expressed at the whole-organism level. Here, we show that developmental durations of eight species of five genera are also negatively related to their greatly differing numbers of 18S rRNA genes per unit DNA. We propose that levels of rDNA iteration among copepods have been controlled by natural selection to regulate ribosome concentrations, therefore protein production and development rates, independently of the large variations in genome sizes, which are in turn adapted to regulating cell and therefore body sizes.Key words: Copepoda, rDNA repeats, development rate, iteration, nucleotype.
Genomic structure and sequence of the gilthead seabream (Sparus aurata) growth hormone-encoding gene: Identification of minisatellite polymorphism in intron I
Authors: Almuly R , Cavari B , Ferstman H , Kolodny O , Funkenstein B
Published: April 2011

The growth hormone (GH) gene of the gilthead seabream (Sparus aurata) (saGH) has been cloned, sequenced, and characterized. The saGH gene spans approximately 4.3 kb and consists of six exons and five introns, as found for all cloned teleost GH genes with the exception of carps and catfish. The first and third introns contain long stretches of repetitive tandem repeats. The second intron, which is unusually long compared with that in other teleosts (and other vertebrates) spans 1747 nucleotides (nt) and contains several inverted repeats. Intron-targeted polymerase chain reaction (PCR) analysis identified length polymorphism of the first intron. Sequence analysis of four variants (405, 424, 636, and 720 nt) out of many variants found revealed that the variation in length is due to differences in the number of repeat monomers (17-mer or 15-mer) as well as minor changes in their length. This repeat unit contains the consensus half-site motif of the thyroid hormone response element (TRE) and estrogen response element (ERE). Polymorphism was found also in the third intron. This is the first report of such high polymorphism of the first intron of GH gene in a vertebrate.Key words: growth hormone, gene, intron polymorphism, fish, Sparus aurata.
Intercontinental karyotypic differentiation of Chironomus entis Shobanov, a Holarctic member of the C. plumosus group (Diptera, Chironomidae)
Authors: Kiknadze Iya I , Butler Malcolm G , Golygina Veronica V , Martin Jon , Wülker Wolfgang F , Sublette James E , Sublette Mary F
Published: April 2011

Analysis of banding sequences of polytene chromosomes in Palearctic (Russian) and Nearctic (North American) Chironomus entis shows strong karyotype divergence between populations on the two continents. Four out of seven chromosomal arms in the North American C. entis karyotype are characterized by sequences found only in the Nearctic. In total, 44 banding sequences are now known for this species across the Holarctic, including 22 exclusively Palearctic, 6 Holarctic, and 16 exclusively Nearctic sequences. The degree of cytogenetic differentiation between Palearctic and Nearctic C. entis populations is an order of magnitude greater than differentiation among populations within either continent, but is only one third as great as the cytogenetic distance between the sibling species C. entis and C. plumosus. C. entis is the only sibling species of C. plumosus uncovered during cytological identification of Chironomus species from more than 50 North American lakes, indicating that the plumosus sibling-species group is much smaller in the Nearctic than in the Palearctic, where a dozen sibling species are known. Cytogenetic distance values calculated between Nearctic and Palearctic representatives of both C. entis and its sibling species C. plumosus are similar, but result from different patterns of karyotype divergence. New World C. entis is distinguished from Old World populations by the 16 uniquely Nearctic sequences, four of which occur in the homozygous state. In contrast, North American C. plumosus has fewer uniquely Nearctic sequences, and only one that occurs as a homozygote. However, four chromosomal arms in C. plumosus that are polymorphic in the Palearctic show fixation, or near fixation, of Holarctic sequences in the Nearctic C. plumosus karyotype. Thus, both the fixation of Holarctic sequences, and the occurrence or fixation of distinctly Nearctic sequences, contribute significantly to karyotype divergence. Patterns of karyotype divergence in Palearctic and Nearctic populations of different Holarctic chironomid species are discussed relative to intercontinental cytogenetic differentiation in other dipterans.Key words: karyotype, inversion polymorphism, cytogenetic divergence, Chironomus.
Retrotransposon activation followed by rapid repression in introgressed rice plants
Authors: Liu Bao , Wendel Jonathan F
Published: April 2011

Plant retrotransposons are largely inactive during normal development, but may be activated by stresses. Both copia-like and gypsy-like retrotransposons of rice were activated by introgression of DNA from the wild species Zizania latifolia Griseb. The copy number increase was associated with cytosine methylation changes of the elements. Activity of the elements was ephemeral, as evidenced by nearly identical genomic Southern hybridization patterns among randomly chosen individuals both within and between generations for a given line, and the absence of transcripts based on Northern analysis. DNA hypermethylation, internal sequence deletion, and possibly other mechanisms are likely responsible for the rapid element repression. Implications of the retroelement dynamics on plant genome evolution are discussed.Key words: epigenetics, DNA methylation, genome evolution, retrotransposons, rice, introgression.
In vitro binding of cattlePstI SINE with a 33-kDa nuclear protein
Authors: Mukhopadhyay Sudit S , Sheikh Faruk G , Gupta Prabhakar
Published: April 2011

A PstI family of SINEs (short interspersed elements) has been identified in some of the members of the family Bovidae, for example, cattle, buffalo and goat. In vitro DNA-protein interactions were studied to provide a better understanding of the function of these SINEs in the genome. Use of one such cattle PstI interspersed repeat sequence, as a probe in gel retardation assays, has lead to the identification of a repeat DNA-binding factor PIRBP (PstI interspersed repeat binding protein) from cattle liver nuclear extract. Southwestern analysis with liver nuclear extracts from cattle, goat, and buffalo revealed the presence of a PIRBP-like nuclear factor in all three species belonging to the family Bovidae. Deletion analysis localized the PIRBP binding site to an 80-bp (337-417bp) region within the cattle PstI sequence. UV crosslinking and Southwestern analyses clearly indicated that PIRBP is a singular, small polypeptide of 33-kDa molecular mass. Homology search of the nucleic acids database revealed that the cattle PstI sequence was associated with many different genes of the family Bovidae, either in the 5' flanking region, 5' locus activating region, 3' UTR or in intervening sequences. The binding of the cattle PstI SINE by PIRBP and its association with the regulatory regions of the genes suggests that it plays an important role in the bovine genome.Key words: repetitive DNA, SINE, Bovidae, nuclear protein, DNA-binding protein.
Different classes of retrotransposons in coniferous spruce species
Authors: L'Homme Yvan , Séguin Armand , Tremblay Francine M
Published: April 2011

We have used the conservation of reverse transcriptase and integrase domains among retroelements to PCR-amplify three well-known types of these mobile genetic elements. Reverse transcriptase sequences from Ty1-copia were identified in spruce in this way, as well as integrase sequences from the Ty3-gypsy group. Using these sequences as probes against a Picea glauca genomic bank, individual members from the LTR (long terminal direct repeat) groups were obtained. A partial Ty1-copia-type element named Spcl was isolated along with a Ty3-gypsy-type element named Spdl. Genomic Southern hybridizations revealed the complexity and high copy number of LTR retrotransposons in black and white spruce.Key words: copia, gypsy, Picea, PCR.
Visualization of A- and B-genome chromosomes in wheat (Triticum aestivum L.) × jointed goatgrass (Aegilops cylindrica Host) backcross progenies
Authors: Wang Z N , Hang A , Hansen J , Burton C , Mallory-Smith C A , Zemetra R S
Published: April 2011

Wheat (Triticum aestivum) and jointed goatgrass (Aegilops cylindrica) can cross with each other, and their self-fertile backcross progenies frequently have extra chromosomes and chromosome segments, presumably retained from wheat, raising the possibility that a herbicide resistance gene might transfer from wheat to jointed goatgrass. Genomic in situ hybridization (GISH) was used to clarify the origin of these extra chromosomes. By using T. durum DNA (AABB genome) as a probe and jointed goatgrass DNA (CCDD genome) as blocking DNA, one, two, and three A- or B-genome chromosomes were identified in three BC2S2 individuals where 2n = 29, 30, and 31 chromosomes, respectively. A translocation between wheat and jointed goatgrass chromosomes was also detected in an individual with 30 chromosomes. In pollen mother cells with meiotic configuration of 14 II + 2 I, the two univalents were identified as being retained from the A or B genome of wheat. By using Ae. markgrafii DNA (CC genome) as a probe and wheat DNA (AABBDD genome) as blocking DNA, 14 C-genome chromosomes were visualized in all BC2S2 individuals. The GISH procedure provides a powerful tool to detect the A or B-genome chromatin in a jointed goatgrass background, making it possible to assess the risk of transfer of herbicide resistance genes located on the A or B genome of wheat to jointed goatgrass.Key words: Triticum aestivum L., Aegilops cylindrica Host, GISH, biological risk.
DNA content, karyotypes, and chromosomal location of 18S-5.8S-28S ribosomal loci in some species of bivalve molluscs from the Pacific Canadian coast
Authors: González-Tizón A M , Martínez-Lage A , Rego I , Ausió J , Méndez J
Published: April 2011

The DNA content of 10 species of bivalve molluscs from British Columbia coast was determined by image analysis, and the karyotypes of the horse clam Tressus capax, the bent-nose macoma Macoma nasuta, and the nuttall's mahogany clam Nuttallia nuttallii are described here for the first time. We also have analyzed the location of rDNA loci using a 28S-5.8S-18S probe in four of these species: Mytilus californianus, M. trossulus, Macoma nasuta and N. nuttallii. Results obtained report new data about cytogenetic characteristics of bivalve molluscs.Key words: Mollusca, bivalves, C-value, karyotype, ribosomal loci.
Apomixis inTripsacum: Comparative mapping of a multigene phenomenon
Authors: Blakey C A , Goldman S L , Dewald C L
Published: April 2011

A relationship has been established between the expression of apomixis in natural polyploids of Tripsacum dactyloides and fertility as measured by percent seed set. Thus, fertility may be reliably used as a defining phenotype for apomixis when scoring the progeny from diploid (2n = 2x = 36) × tetraploid (2n = 4x = 72) crosses in Tripsacum. By exploiting the relationship between apomixis and fertility, as defined by seed set, analyses were performed on a set of related second-generation triploid populations segregating for apomixis. These populations were derived from sexual (diploid) × apomictic (tetraploid) crosses. Six out of 25 genome-dispersed restriction fragment length polymorphism (RFLP) markers co-segregate with fertility. Five of these markers were previously reported and include: php20855, tda48, tda53, umc62, and umc83, and are linked to Tripsacum genetic linkage groups F, I, H, L, and A, respectively. Significantly, we report here the syntenic relationships of the maize chromosome intervals to Tripsacum that segregate for numerous meiosis-specific and fertility-associated genes. Utilizing RFLP locus comparative mapping based on conservation of chromosome (genic) regions between related species, it may be concluded that the genes controlling fertility have been preserved in both Tripsacum and maize. A sixth marker, umc166, has also been shown to co-segregate with fertility and is conserved in both grass species. Specifically, umc166 is linked to Tripsacum linkage group D and, by syntenic comparison, to the short arm of maize chromosome 5. Encoded within this marked interval is the gene Ameiotic1 (Am1) whose function is required for the initiation of meiosis in both micro- and megaspore mother cells and whose absence of expression in the female is, in all likelihood, a prerequisite for the expression of apomixis.Key words: Tripsacum, apomixis, diplospory, comparative mapping, Zea.
Chromosomal principle of radiation-induced F1 sterility in Ephestia kuehniella (Lepidoptera: Pyralidae)
Authors: Tothová Alena , Marec Frantiek
Published: April 2011

A dose-response analysis of chromosomal aberrations was performed in male progeny of gamma-irradiated males in the flour moth, Ephestia kuehniella. For comparison, several female progeny from each dose level were examined. Aberrations were detected on microspread preparations of pachytene nuclei in the electron microscope and classified according to pairing configurations of synaptonemal complexes (SCs). Fragmentation and various translocations were the most numerous aberrations, whereas interstitial deletion and inversion were rare. At 100 Gy, relatively simple multiple translocations were found. Multiple translocations showing complicated configurations occurred at 150 and 200 Gy, and their number increased with the dose. In males, the mean number of chromosomal breaks resulting in aberrations linearly increased with the dose from 8.4 to 16.2 per nucleus. In females, this value achieved a maximum of 11.2 breaks/nucleus at 200 Gy. Three factors were suggested to contribute to the reported higher level of F1 sterility in males than females: (i) survival of males with high numbers of breaks, (ii) crossing-over in spermatogenesis but not in the achiasmatic oogenesis, and (iii) a higher impact of induced changes on the fertility of males than females. It was concluded that translocations are most responsible for the production of unbalanced gametes resulting in sterility of F1 moths. However, F1 sterility predicted according to the observed frequency of aberrations was much higher than the actual sterility reported earlier. This suggests a regulation factor which corrects the predicted unbalanced state towards balanced segregation of translocated chromosomes.Key words: Lepidoptera, Ephestia kuehniella, irradiation, inherited sterility, chromosomal aberrations, synaptonemal complexes.
Construction of a framework map inPinus contortasubsp.latifoliausing random amplified polymorphic DNA markers
Authors: Li Changxi , Yeh Francis C
Published: April 2011

We report on the construction of the first random amplified polymorphic DNA (RAPD) framework map in Pinus contorta subsp. latifolia. Genomic DNA of haploid megagametophytes from 90 open-pollinated seeds originating from a single tree were amplified with 840 random decamer oligonucleotide primers by the polymerase chain reaction. Three-hundred twenty-eight RAPD markers with fragment sizes that ranged between 260 and 3080 base pairs were found segregating at 110 random decamer oligonucleotide primers. Of these 328 RAPD markers, 148 were mapped to 16 framework linkage groups and 77 were mapped as accessory markers onto the framework linkage groups, on a support interval of minimal LOD score of 3. The 16 framework maps cover a distance of 2287 cM. The estimate of genome size was 2407 cM with a 95% confidence interval of 23042459 cM.Key words: framework genomic map, RAPD, Pinus contorta subsp. latifolia.
Identification ofBilby, a diverged centromeric Ty1-copiaretrotransposon family from cereal rye (Secale cerealeL.)
Authors: Francki Michael G
Published: April 2011

A diminutive rye chromosome (midget) in wheat was used as a model system to isolate a highly reiterated centromeric sequence from a rye chromosome. Fluorescence in situ hybridization (FISH) shows this sequence localized within all rye centromeres and no signal was detected on wheat chromosomes. DNA sequencing of the repetitive element has revealed the presence of some catalytic domains and signature motifs typical of retrotransposon genes and has been called the Bilby family, representing a diverged family of retrotransposon-like elements. Extensive DNA database searching revealed some sequence similarity to centromeric retrotransposons from wheat, barley, and centromeric repetitive sequences from rice. Very low levels of signal were observed when Bilby was used as a probe against barley, and no signal was detected with rice DNA during Southern hybridization. The abundance of Bilby in rye indicates that this family may have diverged from other distantly related centromeric retrotransposons or incorporated in the centromere but rapidly evolved in rye during speciation. The isolation of a rye retrotransposon also allowed the analysis of centromeric breakpoints in wheat-rye translocation lines. A quantitative analysis shows that the breakpoint in 1DS.1RL and 1DL.1RS and recombinant lines containing proximal rye chromatin have a portion of the rye centromere that may contribute to the normal function of the centromeric region.Key words: centromere, retrotransposon, rye, midget chromosome, cereals.
Imprinting and deviation from Mendelian transmission ratios
Authors: Naumova Anna K , Greenwood Celia MT , Morgan Kenneth
Published: April 2011

Deviations from a Mendelian 1:1 transmission ratio have been observed in human and mouse chromosomes. With few exceptions, the underlying mechanism of the transmission-ratio distortion remains obscure. We tested a hypothesis that grandparental-origin dependent transmission-ratio distortion is related to imprinting and possibly results from the loss of embryos which carry imprinted genes with imprinting marks that have been incorrectly reset. We analyzed transmission of alleles in four regions of the human genome that carry imprinted genes presumably critical for normal embryonic growth and development: 11p15.5 (H19, IGF2, HASH2, etc.), 11p13 (WT1), 7p11-12 (GRB10), and 6q25-q27 (IGF2R), among the offspring of 31 three-generation Centre d'Étude de polymorphism Humain (CEPH) families. Deviations from expected 1:1 ratios were found in the maternal chromosomes for regions 11p15.5, 11p13, and 6q25-27 and in the paternal chromosomes for regions 11p15 and 7p11-p12. The likelihood of the results was assessed empirically to be statistically significant (p = 0.0008), suggesting that the transmission ratios in the imprinted regions significantly deviated from 1:1. We did not find deviations from a 1:1 transmission ratio in imprinted regions that are not crucial for embryo viability (13q14 and 15q11-q13). The analysis of a larger set of 51 families for the 11p15.5 region suggests that there is heterogeneity among the families with regard to the transmission of 11p15.5 alleles. The results of this study are consistent with the hypothesis that grandparental-origin dependent transmission-ratio distortion is related to imprinting and embryo loss.Key words: imprinting, transmission-ratio distortion, grandparental origin, embryo loss.
Analysis of random and specific sequences of nuclear and cytoplasmic DNA in diploid and tetraploid American wild rice species (Oryzaspp.)
Authors: Buso Glaucia Salles Cortopassi , Rangel Paulo Hideo Nakano , Ferreira Márcio Elias
Published: April 2011

A sample of American wild rice and other accessions of the genus Oryza were studied at polymorphic regions of nuclear, mitochondrial, and chloroplastic genomes. First, flow cytometry, genome-specific RAPD markers, and chromosome counting were utilized to verify the original ploidy and classification of 230 accessions studied. Based on these methods, 8% of the accessions were considered to be misclassified either taxonomically or as a result of contamination. Second, a fine resolution analysis was conducted at genomic regions sampled at random by RAPD markers and at specific sites of the chloroplast and mitochondrial DNA by cleaved amplified polymorphic sequence (CAPS) analysis. Phylogenetic trees resulting from phenetic and cladistic analyses of RAPD, cpDNA, and mtDNA polymorphisms were obtained. The results indicated that the American diploid species O. glumaepatula should be considered an individual species, distinct from O. rufipogon, and confirmed that the American tetraploid species (O. alta, O. grandiglumis, and O. latifolia) belong to the O. officinalis complex. The data indicate that these species should still be treated as a group rather than as three distinct species and that their closest relative is a CC-genome species. It was estimated that the diploid and tetraploid American species diverged from O. sativa  O. nivara (AA genome) and CC- and BBCC-genome species, respectively, 20 million years ago.Key words: RAPD, cleaved amplified polymorphic sequences, flow cytometry, Oryza glumaepatula, rice evolution.
Ancient and recent duplications of the rainbow trout Wilms' tumor gene
Authors: Brunelli Joseph P , Robison Barrie D , Thorgaard Gary H
Published: April 2011

The Wilms' tumor suppressor (WT1) gene plays an important role in the development and functioning of the genitourinary system, and mutations in this gene are associated with nephroblastoma formation in humans. Rainbow trout (Oncorhynchus mykiss) is one of the rare animal models that readily form nephroblastomas, yet trout express three distinct WT1 genes, one of which is duplicated and inherited tetrasomically. Sequence analyses suggest an ancient gene duplication in the common ancestor of bony fishes resulted in the formation of two WT1 gene families, that conserve the splicing variations of tetrapod WT1, and a second duplication event occurred in the trout lineage. The WT1 genes of one family map to linkage groups 6 and 27 in the trout genome map. Reverse transcribed polymerase chain reaction (RT-PCR) expression analysis demonstrated little difference in WT1 tissue expression pattern between genes.Key words: tumor suppressor, nephroblastoma, RT-PCR expression, kidney, cancer, cDNA, gene mapping.
Large-scale selection of lines with deletions in chromosome 1B in wheat and applications for fine deletion mapping
Authors: Tsujimoto H , Yamada T , Hasegawa K , Usami N , Kojima T , Endo T R , Ogihara Y , Sasakuma T
Published: April 2011

Terminal deletions of chromosome 1B in common wheat were selected on a large scale. The gametocidal gene of Aegilops cylindrica was used as the inducer of chromosome breakage. First, genes for endosperm storage proteins located on both arms of chromosome 1B were used as the selection markers. However, it was found that the chromosome breakage occurred during female gametogenesis, causing genotypic inconsistency between the embryo and endosperm. Thus, we isolated plants with terminal deletions in chromosome 1B by C-banding. Of 1327 plants examined, 128 showed aberrations in chromosome 1B: 47 in the short arm, 76 in the long arm, and 5 in both arms. The present deletions tended to have the breakpoint at more proximal regions than those produced previously by T.R. Endo and B.S. Gill. Using 33 deletion lines produced in this study and 34 lines previously produced, we mapped 39 RFLP loci and a nucleolar organizer region (NOR) on a specific region of chromosome 1B. The NOR was found to consist of two subregions with different repetitive units, which were termed NOR-B1d and NOR-B1p. Based on this fine deletion map and genotypic inconsistency between embryo and endosperm, the features of the gametocidal gene are discussed.Key words: deletion line, gametocidal gene, Triticum aestivum, deletion map, nucleolar organizer region.
Genomic interspersions determine the size and complexity of transgene loci in transgenic plants produced by microprojectile bombardment
Authors: Svitashev Sergei K , Somers David A
Published: April 2011

The structure of transgene loci in six transgenic allohexaploid oat (Avena sativa L.) lines produced using microprojectile bombardment was characterized using fluorescence in situ hybridization (FISH) on extended DNA fibers (fiber-FISH). The transgene loci in five lines were composed of multiple copies of delivered DNA interspersed with genomic DNA fragments ranging in size from ca. 3 kb to at least several hundred kilobases, and in greater numbers than detected using Southern blot analysis. Although Southern analysis predicted that the transgene locus in one line consisted of long tandem repeats of the delivered DNA, fiber-FISH revealed that the locus actually contained multiple genomic interspersions. These observations indicated that transgene locus size and structure were determined by the number of transgene copies and, possibly to a greater extent, the number and the length of interspersing genomic DNA sequences within the locus. Large genomic interspersions detected in several lines were most likely the products of chromosomal breakage induced either by tissue culture conditions or, more likely, by DNA delivery into the nucleus using microprojectile bombardment. We propose that copies of transgene along with other extrachromosomal DNA fragments are used as patches to repair double-strand breaks (DSBs) in the plant genome resulting in the formation of transgene loci.Key words: genetic transformation, microprojectile bombardment, transgenic oat, FISH, transgene locus structure.
Preliminary interspecific genetic maps of thePopulusgenome constructed from RAPD markers
Authors: Yin Tongming , Huang Minren , Wang Mingxiu , Zhu Li-Huang , Zeng Zhao-Bang , Wu Rongling
Published: April 2011

We have constructed RAPD-based linkage maps for an interspecific cross between two species of the genus Populus (P. adenopoda and P. alba), based on a double pseudo-test-cross strategy. Of a total of 360 polymorphic fragments scored, 290 showed a test-cross configuration, corresponding to DNA polymorphisms heterozygous in one parent and null in the other. In the female parent, P. adenopoda, 82 markers were grouped in 19 different linkage groups (553 cM), whereas in the male parent P. alba, 197 markers established a much more complete framework map with an observed genome length of 2300 cM covering 87% of the total P. alba genome. The larger number of test-cross markers detected for the P. alba parent than for the P. adenopoda parent might be due to a higher level of heterozygosity in the former than in the latter. In this study, we detected only a small percentage (2%) of the intercross dominant markers heterozygous in both parents and segregating 3:1 in the progeny. The further focus in this mapping study should be on the identification of more intercross markers, to align the two parent-specific maps into a consensus map for mapping important genes causing species differentiation during long evolutionary divergences.Key words: interspecific hybrids, linkage map, poplar, pseudo-testcross mapping strategy.
Searching for telomeric sequences in two Allium species
Authors: Cuñado N , Sánchez-Morán E , Barrios J , Santos J L
Published: April 2011

Some Alliaceae species have no tandemly repeated TTTAGGG sequences. Instead, at the very end of their chromosomes, there are highly repetitive satellite and (or) rDNA sequences. These sequences apparently replace the canonical plant telomeric sequences in these species. A method of preparing two-dimensional surface spreads of plant synaptonemal complexes (SCs), combined with fluorescent in situ hybridization, has revealed that telomeric chromatin is tightly condensed at the ends of SCs in plants and animals. Using this method, we have tested the organization and location of those sequences postulated to cap the chromosomes in two species of the genus Allium: A. cepa and A. altaicum. We have also extended this study to other putative telomere candidates, such as LTR (long terminal repeat) and non-LTR retrotransposons. None of the DNA sequences analyzed showed the characteristic telomeric organization at pachytene.Key words: fluorescent in situ hybridization, meiosis, repetitive DNA, Allium, synaptonemal complex.
Ecdysone-regulated chromosome puffing in the salivary glands of the Mediterranean fruit fly, Ceratitis capitata
Authors: Gariou-Papalexiou Angeliki , Mintzas Anastassios C , Zacharopoulou Antigone
Published: April 2011

The effect of ecdysone on the puffing activity of the polytene chromosomes of Ceratitis capitata has been studied in organ cultures of late-larval salivary glands. Culture of glands from 120-h-old larvae (puff stage 1) in the presence of ecdysone resulted in the initiation of the late-larval puffing cycle that is normally observed in 145-h-old larvae (puff stage 4). During a 7-h period in the presence of ecdysone, the puffing patterns of most loci resembled the in vivo patterns observed in the period between puff stages 4 and 10, indicating that the first puffing cycle can be initiated by the hormone and proceed almost to completion, in vitro. Culture of salivary glands in the presence of ecdysone and a protein-synthesis inhibitor, as well as ecdysone withdrawal and readdition experiments, indicated that most of the ecdysone-regulated puffs could be categorized into three classes: (i) the puffs that were suppressed immediately by ecdysone, even in the absence of protein synthesis; (ii) the puffs that were induced directly by ecdysone; and (iii) the puffs that were induced indirectly by ecdysone, that is, they were induced after a lag period of a few hours and required protein synthesis for their induction.Key words: polytene chromosomes, puffing patterns, ecdysone, Ceratitis capitata.
Segregation of microsatellite alleles and residual heterozygosity at single loci in homozygous androgenetic common carp (Cyprinus carpioL.)
Authors: Tanck M WT , Palstra A P , Weerd M van de , Leffering C P , Poel JJ van der , Bovenhuis H , Komen J
Published: April 2011

Thirty-three androgenetic progeny groups of common carp were analysed using 11 microsatellite markers to (i) verify the homozygous status of the 566 androgenetic individuals, (ii) analyse the microsatellite allele segregation, and (iii) study the possible association of microsatellite alleles with phenotypic traits. In total, 92% of the androgenetic individuals proved to be homozygous at all 11 loci. Forty-three of the 47 heterozygous individuals were heterozygous at a single locus only. This heterozygosity was probably due to DNA fragments caused by UV irradiation of the eggs, although the maternal origin of the fragments could not be proved beyond doubt. Screening with 11 microsatellites also revealed two linkage groups, a segregation distortion at two microsatellite loci, and the possible association of some microsatellites with mass, length, stress-related plasma cortisol levels, and basal plasma glucose levels. The success of the linkage and association study could be explained by a low recombination frequency due to high chiasma interference. This would imply a relatively short genetic map for common carp.Key words: doubled haploids, residual heterozygosity, microsatellite allele segregation, linkage analysis, common carp.
Genome size in Arachis duranensis: a critical study
Authors: Temsch Eva M , Greilhuber Johann
Published: April 2011

Arachis duranensis is a diploid wild relative of the tetraploid cultivated peanut Arachis hypogaea. The literature indicates two 2C genomic DNA mean values (genome size) for A. duranensis, 4.92 and 5.64 pg, and intraspecific variation of up to 11% negatively correlated with altitude above sea level of the collection sites has been reported. Our recent investigations of Arachis species have shown that unrecognized technical problems with peanut material may have influenced previous genome-size data and rendered them open to critical comments. In the present study, 20 accessions of A. duranensis were investigated by means of DNA flow cytometry (propidium iodide staining) and several of these also by Feulgen DNA image analysis. Pisum sativum was used as the internal standard (2C = 8.84 pg). 2C values in A. duranensis were about half those described previously and varied between 2.49 and 2.87 pg (flow cytometry). This variation was statistically significant and reproducible. There was a negative correlation of genome size with latitude and altitude above sea level of the collection sites. Such a correlation had been already found in one of the previous studies. However, the incongruences between the absolute DNA content values obtained in the present investigation and those in the literature point to the importance of carrying out methodological studies on best practice in DNA-content determinations in plants.Key words: Arachis duranensis, genome size, flow cytometry, Feulgen densitometry.
Molecular characterization of a Thinopyrum intermedium Group 2 chromosome (2Ai-2) conferring resistance to barley yellow dwarf virus
Authors: Zhang Z Y , Xin Z Y , Larkin P J
Published: April 2011

The wheat  Thinopyrum intermedium addition lines Z1 and Z2 carry 21 pairs of wheat chromosomes and one pair of Th. intermedium chromosomes (2Ai-2) conferring resistance to barley yellow dwarf virus (BYDV). GISH results using the genomic DNA of Pseudoroegneria strigosa (S genome) as the probe indicated that the 2Ai-2 chromosome in Z1 and Z2 is an SJ intercalary translocation. Most of the 2Ai-2 chromosome belongs to the S genome, except for about one third in the middle region of the long arm that belongs to the J genome. The results of detailed RFLP analyses confirmed that the 2Ai-2 chromosome is extensively homoeologous to wheat group 2 chromosomes. Some new RFLP markers specific to the 2Ai-2 chromosome were identified. A RAPD marker, OP-R16340, specific to the 2Ai-2 chromosome, was screened. We converted the RAPD marker into a sequence-characterized amplified region (SCAR) marker (designated SC-R16). The study establishes the basis for selecting translocation lines with small segments of the 2Ai-2 chromosome and localizing the BYDV resistance gene when introgressed into a wheat background.Key words: Thinopyrum intermedium, barley yellow dwarf virus (BYDV), genomic in situ hybridization (GISH), RFLP, SCAR, homoeologous group 2.
Introgression of rye chromatin on chromosome 2D in the Portuguese wheat landrace 'Barbela'
Authors: Ribeiro-Carvalho C , Guedes-Pinto H , Heslop-Harrison J S , Schwarzacher T
Published: April 2011

The old Portuguese wheat landrace aggregate known as 'Barbela' shows good productivity under the low-fertility conditions often associated with acid soils. The use of genomic rye DNA, in combination with 45S rDNA and the repetitive sequences dpTa1 and pSc119.2 as probes, in two sequential in situ hybridization steps enabled the identification of all chromosomes in the 'Barbela' wheat lines and the detection of the introgression of rye-origin chromatin onto wheat chromosome arm 2DL in two of the lines. Amplification of microsatellite loci using published primer pairs showed that the distal segment of wheat chromosome 2DL, which was involved in the rye translocation, was deleted. The identification and characterization of small recombinant chromosome segments in wheatrye lines may allow their use in plant breeding programmes. Their presence in farmer-maintained material demonstrates the importance of maintaining, characterizing, and collecting landrace material before valuable genetic combinations are lost as uniform commercial crops are introduced.Key words: biodiversity, in situ hybridization, microsatellites, plant breeding, recombination, alien chromosomes, marker selection.
Polymorphisms flanking themarinerintegration sites in the rice gall midge (Orseolia oryzaeWood-Mason) genome are biotype-specific
Authors: Behura Susanta K , Nair Suresh , Mohan Madan
Published: April 2011

In an effort to study genome diversity within and between the Indian biotypes of the Asian rice gall midge, Orseolia oryzae, a major insect pest of rice, we made use of mariner transposable element integration site polymorphisms. Using degenerate primers, the design of which is based on mariner sequences, we amplified a ca. 450 bp mariner sequence from the rice gall midge. The mariner sequence showed homology with that of a mariner element isolated from the Hessian fly, Mayetiola destructor, a major dipteran pest of wheat. Southern hybridization, using this mariner fragment as a probe, revealed that the mariner elements are moderately to highly repetitive in the rice gall midge genome. Based on the sequence information of this 450-bp PCR-amplified fragment, outward-directed primers were designed and used in an inverse PCR (iPCR) to amplify the DNA flanking the conserved regions. To study the regions flanking the mariner integration sites, we employed a novel PCR-based approach: a combination of sequence specific amplification polymorphism (SSAP) and amplified fragment length polymorphism (AFLP). The outward-directed mariner-specific primer was used in combination with adapter-specific primers with 13 selective nucleotides at their 3' ends. The amplification products were resolved on an agarose gel, Southern-transferred onto nylon membranes, and probed with the iPCR fragment. Results revealed biotype-specific polymorphisms in the regions flanking the mariner integration sites, suggesting that mariner elements in the rice gall midge may be fixed in a biotype-specific manner. The implications of these results are discussed in the context of biotype differentiation.Key words: DNA fingerprinting, inverse PCR (iPCR), Oryza sativa, rice pest, transposon.
The pericentromeric heterochromatin of the grassZingeria biebersteiniana(2n= 4) is composed of Zbcen1-type tandem repeats that are intermingled with accumulated dispersedly organized sequences
Authors: Saunders Verity A , Houben Andreas
Published: April 2011

DNA reassociation and hydroxyapatite chromatography were used to isolate high-copy DNA of the grass Zingeria biebersteiniana (2n = 4). In situ hybridization demonstrated that the DNA isolated was enriched for pericentromere-specific repetitive sequences. One abundant pericentromere-specific component is the differentially methylated tandem-repeat family Zbcen1. Other sequences isolated, Zb46 and Zb47A, are dispersed and display similarity to parts of the gypsy- and copia-like retrotransposable elements of other grasses. In situ hybridization with the copia-like sequence Zb47A resulted in dispersed labelling along the chromosome arms, with a significant signal accumulation in the pericentromeric region of all chromosomes. It is concluded that the pericentromeric heterochromatin of Z. biebersteiniana is composed of members of the Zbcen1 tandem repeat family and that these tandem arrays are intermingled with accumulated putative copia-like retrotransposon sequences. An observed Rabl interphase orientation suggests that the length of the chromosomes rather than the genome size is the determining factor of the Rabl phenomenon.Key Words: centromere, heterochromatin, tandemly repeated DNA, retrotransposon-like, DNA reassociation.
Genotypic variation in tetraploid wheat affecting homoeologous pairing in hybrids withAegilops peregrina
Authors: Ozkan Hakan , Feldman Moshe
Published: April 2011

The Ph1 gene has long been considered the main factor responsible for the diploid-like meiotic behavior of polyploid wheat. This dominant gene, located on the long arm of chromosome 5B (5BL), suppresses pairing of homoeologous chromosomes in polyploid wheat and in their hybrids with related species. Here we report on the discovery of genotypic variation among tetraploid wheats in the control of homoeologous pairing. Compared with the level of homoeologous pairing in hybrids between Aegilops peregrina and the bread wheat cultivar Chinese Spring (CS), significantly higher levels of homoeologous pairing were obtained in hybrids between Ae. peregrina and CS substitution lines in which chromosome 5B of CS was replaced by either 5B of Triticum turgidum ssp. dicoccoides line 09 (TTD09) or 5G of Triticum timopheevii ssp. timopheevii line 01 (TIM01). Similarly, a higher level of homoeologous pairing was found in the hybrid between Ae. peregrina and a substitution line of CS in which chromosome arm 5BL of line TTD140 substituted for 5BL of CS. It appears that the observed effect on the level of pairing is exerted by chromosome arm 5BL of T. turgidum ssp. dicoccoides, most probably by an allele of Ph1. Searching for variation in the control of homoeologous pairing among lines of wild tetraploid wheat, either T. turgidum ssp. dicoccoides or T. timopheevii ssp. armeniacum, showed that hybrids between Ae. peregrina and lines of these two wild wheats exhibited three different levels of homoeologous pairing: low, low intermediate, and high intermediate. The low-intermediate and high-intermediate genotypes may possess weak alleles of Ph1. The three different T. turgidum ssp. dicoccoides pairing genotypes were collected from different geographical regions in Israel, indicating that this trait may have an adaptive value. The availability of allelic variation at the Ph1 locus may facilitate the mapping, tagging, and eventually the isolation of this important gene.Key words: diploid-like meiotic behavior, genetic control of pairing, Ph1 gene, Triticum turgidum ssp. dicoccoides, wild emmer.
Dinucleotide microsatellites fromEucalyptus sieberi: inheritance, diversity, and improved scoring of single-base differences
Authors: Glaubitz J C , Emebiri L C , Moran G F
Published: April 2011

Eight dinucleotide microsatellites were developed in Eucalyptus sieberi L. Johnson (silvertop ash), a member of the subgenus Eucalyptus. Transfer of six of these to the subgenus Symphyomyrtus and their Mendelian inheritance are demonstrated using a full-sib cross in Eucalyptus nitens. Genetic diversity parameters are presented for the eight loci based on a sample of 100 old-growth E. sieberi trees from a single natural stand. One locus, Es266, had an atypically high fixation index, and significantly deviated from Hardy-Weinberg equilibrium genotypic proportions, indicating the likely presence of null alleles. Two of the loci, Es076 and Es140, had many alleles that differed in size by only a single base pair, possibly because of short poly(A) or poly(T) stretches in their flanking regions. These two loci were by far the most polymorphic, but were difficult to score reliably on a capillary DNA sequencer. Reliability of scoring of these two one-base microsatellite loci was markedly improved by the incorporation of internal reference alleles into each sample analysed.Key words: SSRs, single base pair alleles, null alleles, internal reference alleles.