bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct behavioral evidence that unique bile acids released by larval sea lamprey (Petromyzon marinus) function as a migratory pheromone
Authors: Bjerselius Rickard , Li Weiming , Teeter John H , Seelye James G , Johnsen Peter B , Maniak Peter J , Grant Gerold C , Polkinghorne Christine N , Sorensen Peter W
Published: April 2011

Four behavioral experiments conducted in both the laboratory and the field provide evidence that adult sea lamprey (Petromyzon marinus) select spawning rivers based on the odor of larvae that they contain and that bile acids released by the larvae are part of this pheromonal odor. First, when tested in a recirculating maze, migratory adult lamprey spent more time in water scented with larvae. However, when fully mature, adults lost their responsiveness to larvae and preferred instead the odor of mature individuals. Second, when tested in a flowing stream, migratory adults swam upstream more actively when the water was scented with larvae. Third, when migratory adults were tested in a laboratory maze containing still water, they exhibited enhanced swimming activity in the presence of a 0.1 nM concentration of the two unique bile acids released by larvae and detected by adult lamprey. Fourth, when adults were exposed to this bile acid mixture within flowing waters, they actively swam into it. Taken together, these data suggest that adult lamprey use a bile acid based larval pheromone to help them locate spawning rivers and that responsiveness to this cue is influenced by current flow, maturity, and time of day. Although the precise identity and function of the larval pheromone remain to be fully elucidated, we believe that this cue will ultimately prove useful as an attractant in sea lamprey control.
Genetic analysis ofveinfunction in theDrosophilaembryonic nervous system
Authors: Lanoue Bradley R , Gordon Michael D , Battye Robin , Jacobs J Roger
Published: April 2011

The Drosophila epidermal growth factor receptor (EGFR) may be activated by two ligands expressed in the embryonic nervous system, Spitz and Vein. Previous studies have established Spitz as an essential activator of EGFR signaling in nervous system development. Here, we report the pattern of expression of vein mRNA in the nervous system and characterize the contribution of vein to cell lineage and axonogenesis. The number of midline glia (MG) precursors is reduced in vein mutants before the onset of embryonic apoptosis. In contrast to spitz, mis-expression of vein does not suppress apoptosis in the MG. These data indicate that early midline EGFR signaling, requiring vein and spitz, establishes MG precursor number, whereas later EGFR signals, requiring spitz, suppress apoptosis in the MG. vein mutants show early irregularities during axon tract establishment, which resolve later to variable defasciculation and thinner intersegmental axon tracts. vein and spitz phenotypes act additively in the regulation of MG cell number, but show synergism in a midline neuronal cell number phenotype and in axon tract architecture. vein appears to act downstream of spitz to briefly amplify local EGFR activation.Key words: Drosophila, vein, midline, axonogenesis, EGF receptor, lineage, neuregulin, spitz, CNS.
Identification of self-incompatibility (S-) locus linked pollen cDNA markers inPetunia inflata
Authors: McCubbin Andrew G , Wang Xi , Kao Teh-hui
Published: April 2011

Solanaceous type self-incompatibility (SI) is controlled by a single polymorphic locus, termed the S-locus. The only gene at the S-locus that has been characterized thus far is the S-RNase gene, which controls pistil function, but not pollen function, in SI interactions between pistil and pollen. One approach to identifying additional genes (including the pollen S-gene, which controls pollen function in SI) at the S-locus and to study the structural organization of the S-locus is chromosome walking from the S-RNase gene. However, the presence of highly repetitive sequences in its flanking regions has made this approach difficult so far. Here, we used RNA differential display to identify pollen cDNAs of Petunia inflata, a self-incompatible solanaceous species, which exhibited restriction fragment length polymorphism (RFLP) for at least one of the three S-haplotypes (S1, S2, and S3) examined. We found that the genes corresponding to 10 groups of pollen cDNAs are genetically tightly linked to the S-RNase gene. These cDNA markers will expedite the mapping and cloning of the chromosomal region of the Solanaceae S-locus by providing multiple starting points.Key words: Petunia inflata, pollen cDNAs, self-incompatibility, S-linked cDNA markers, S-locus.
meiotin-1gene expression in normal anthers and in anthers exhibiting prematurely condensed chromosomes
Authors: Hasenkampf C A , Taylor A A , Siddiqui N U , Riggs C D
Published: April 2011

We have cloned and sequenced the promoter of a meiotin-1 gene, and have determined the precise temporal and spatial pattern of meiotin-1 gene expression. The expression of the meiotin-1 gene is controlled in two increments. The meiotin-1 gene is not expressed in any of the vegetative tissues examined. Early in microsporogenesis, low levels of meiotin-1 RNA can be detected. At the onset of meiosis, there is a dramatic increase in meiotin-1 RNA levels in both tapetal and meiotic cells. However, while meiotin-1 RNA is observed in both the nucleus and cytoplasm of meiotic cells, it is found only in the nucleus of the tapetal cells. We have also examined the expression of the meiotin-1 gene in aberrant meiotic nuclei that prematurely condense their chromosomes; these nuclei have reduced levels of the meiotin-1 protein. The aberrant nuclei have only the basal level of meiotin-1 RNA; they do not exhibit the transcriptional induction seen for normal cells at the onset of meiosis. Implications for the function of meiotin-1 in regulating chromatin condensation, and in coordinating meiotic and tapetal cell activities are discussed.Key words: anther development, chromatin, meiosis, meiotin-1, promoter.
Genetic structure of an introduced pest, grape phylloxera (Daktulosphaira vitifoliaeFitch), in Europe
Authors: Forneck Astrid , Walker M Andrew , Blaich Rolf
Published: April 2011

A model for the genetic structure of grape phylloxera populations in Europe was developed using hierarchical sampling techniques and AFLP-PCR (amplified fragment length polymorphism - polymerase chain reaction) methodology. One-hundred three European and 6 North American phylloxera populations were studied. An additional European sampling set comprising 60 samples was analyzed to study regional subdivision. The populations grouped into two clusters loosely correlated with collection site location. Phylloxera populations collected from northern (above lat 43°) geographic regions were significantly different from southern (below 43°) populations. The northern cluster was more heterogeneous than the southern cluster, possibly reflecting holocyclic versus anholocyclic reproduction. Microgeographic scales of phylloxera genetic structure displayed as much variation within as among host plants. The host plant did not affect the genetic structure of European phylloxera as revealed in two independent experiments.Key words: Daktulosphaira vitifoliae, aphid, genetic structure, AFLP-PCR.
Evolution of an Alu DNA element of type Sx in the lineage of primates and the origin of an associated tetranucleotide microsatellite
Authors: Crouau-Roy Brigitte , Clisson Isabelle
Published: April 2011

A 394-bp DNA fragment, which in human is on chromosome 6 near the MOG (myelin oligodendrocyte glycoprotein) gene and encompasses an Alu element and an associated tetranucleotide microsatellite, was sequenced from a large range of primate species to follow its evolutionary divergence and to understand the origin of the microsatellite. This Alu element is found at the same orthologous position in all primates sequenced, but the tetranucleotide repeat is present only in Catarrhini between the 3'-oligo(dA) of the Alu element and the 3' flanking direct repeat. Little intraspecific variation was found. Sequence identity values for this orthologous primate Alu averaged 90% (82-99%) with transitions comprising between 70% and 100% of the observed nucleotide substitutions. Although the insertion of the Alu element predates the separation of these species, the original sequence of the site of integration can still be identified. This identification of the direct repeats suggests an active role of the oligo(dA) of the Alu element in the origin of the tetranucleotide repeats. The microsatellite probably appeared after the insertion of the Alu element, early in the lineage leading to the common ancestor of the hominoids and the Old World monkeys.Key words: evolution, Alu element, microsatellite, primates.
The chromosomes ofRhynchosciara baschanti(Diptera: Sciaridae): Molecular cytogenetic comparisons with taxa in theamericana-like group
Authors: Stocker Ann Jacob , Gorab Eduardo
Published: April 2011

Polytene chromosome analysis is presented for Rhynchosciara baschanti, a species belonging to the americana-like group of Rhynchosciara. R. baschanti chromosomes show morphological differences in centromeric and telomeric regions compared to two other members within the group, R. americana and R. hollaenderi. In addition, fixed band and autosomal inversion differences were noted. Physical mapping data showed synteny among the taxa under study for DNA puffs and single-copy or histone gene probes, whereas rDNA and poly-(r)A probes showed different diagnostic patterns. The activity of developmentally active genes and the pattern of thymidine incorporation into DNA puff sites of R. baschanti are consistent with those found in the two previously studied species, except for lower levels of expression at some of these sites. These results suggest that differential duplication of specific DNA sequences, in particular repetitive and homopolymeric DNA, has played a role in the chromosomal evolution of these Rhynchosciara species. Inversions and band dimorphisms have also occurred, but the processes leading to their maintenance and fixation appear to have been slow, since these three species are in general chromosomally monomorphic.Key words: Rhynchosciara, polytene chromosomes, chromosomal evolution.
Development of a set of near isogenic and backcross recombinant inbred lines containing most of theLycopersicon hirsutumgenome in aL. esculentumgenetic background: A tool for gene mapping and gene discovery
Authors: Monforte Antonio J , Tanksley Steve D
Published: April 2011

A novel population consisted of a set of 99 near isogenic lines (NILs) and backcross recombinant inbred lines (BCRILs) derived from a cross between the cultivated tomato Lycopersicon esculentum cv. E6206 and L. hirsutum accession LA1777 is presented. Most of the lines contain a single defined introgression from L. hirsutum in the L. esculentum genetic background and together, the lines provide a coverage of more than the 85% of the L. hirsutum genome. These lines represent a new tool to uncover the genetic resources hidden in L. hirsutum as well as to study the genes responsible of its unique biology. Furthermore, the study of the allelic frequency and heterozygosity among BCRILs showed that specific genomic regions were likely subjected to unintentional selection pressures during the stock development. Genes involved in the reproductive behavior and (or) pollen viability are hypothesized to be responsible for these alterations.Key words: germplasm, near isogenic line, tomato, genetic resources.
Isolation, characterization, and expression analysis of starch synthase IIa cDNA from wheat (Triticum aestivumL.)
Authors: Gao Ming , Chibbar Ravindra N
Published: April 2011

We characterized three near-full-length putative homoeologous cDNA (Ss2a-1, Ss2a-2, and Ss2a-3) in wheat endosperm most similar to the maize zSSIIa. Polypeptide sequences deduced from three Ss2a cDNA clones share a 95% overall sequence similarity, and may thus have similar biochemical properties and may make identical contributions to starch biosynthesis in wheat endosperm. The accumulation of RNA transcripts corresponding to three Ss2a genes in developing endosperm varies among three cultivars studied, but usually peaks in young endosperm at about 10 days post anthesis (DPA). The polyclonal antibody for the SSIIa-1 recombinant protein strongly reacted to three previously identified granule-bound starch synthases of 100 to 115 kDa. The polyclonal antibody for the granule-bound starch synthases strongly reacted to the SSIIa-1 recombinant protein. Sequences of the N-terminal and an internal peptide of these three granule-bound starch synthases match well with those of three predicted mature SSIIa polypeptides. These granule-bound starch synthases may therefore be SSIIa polypeptides. The antibodies also recognized a group of three polypeptides with the same gel mobility as the three granule-bound starch synthases, a polypeptide of 90 kDa, and a group of three polypeptides of about 80 to 82 kDa. Thus, the wheat SSIIa may exist in several functional forms in the stroma of amyloplasts.Key words: starch granule, granule-bound proteins, soluble starch synthase, homoeologous isoforms, starch biosynthesis.
Transcript analysis of 203 novel genes fromSaccharomyces cerevisiaeinhap1androx1mutant backgrounds
Authors: Lombardía L J , Cadahía-Rodríguez J L , Freire-Picos M A , González-Siso M I , Rodríguez-Torres A M , Cerdán M E
Published: April 2011

Hap1 and Rox1 are transcriptional regulators that bind regulatory sites in the promoters of oxygen-regulated genes in Saccharomyces cerevisiae. Hap1 is a heme-responsive activator of genes induced in aerobic conditions and Rox1 is a repressor of hypoxic genes in aerobic conditions. We have studied transcriptional regulation of a pool of 203 open reading frames (ORFs) from chromosomes IV, VII, and XIV in wild-type, hap1, and rox1 mutant genetic backgrounds in an attempt to extend the family of oxygen and heme regulated genes. Only three ORFs are significantly repressed by Rox1 but they cannot be considered as typical hypoxic genes because they are not overexpressed during hypoxia.Key words: Saccharomyces cerevisiae, genome analysis, chromosomes IV, VII, and XIV, gene expression, ROX1 and HAP1.
Improving synthetic lethal screens by regulating the yeast centromere sequence
Authors: Barbour Leslie , Zhu Yu , Xiao Wei
Published: April 2011

The synthetic lethal screen is a useful method in identifying novel genes functioning in an alternative pathway to the gene of interest. The current synthetic lethal screen protocol in yeast is based on a colony-sectoring assay that allows direct visualization of mutant colonies among a large population by their inability to afford plasmid loss. This method demands an appropriate level of stability of the plasmid carrying the gene of interest. YRp-based plasmids are extremely unstable and complete plasmid loss occurs within a few generations. Consequently, YCp plasmids are the vector of choice for synthetic lethal screens. However, we found that the high-level stability of YCp plasmids resulted in a large number of false positives that must be further characterized. In this study, we attempt to improve the existing synthetic lethal screen protocol by regulating the plasmid stability and copy number. It was found that by placing a yeast centromere sequence under the control of either inducible or constitutive promoters, plasmid stability can be significantly decreased. Hence, altering the conditions under which yeast cells carrying the plasmid PGAL1-CEN4 were cultivated allowed us to develop a method that eliminated virtually 100% of false positives and drastically reduced the time required to carry out a synthetic lethal screen.Key words: synthetic lethal screen, yeast, centromere, inducible promoter, MRE11.
Ubiquity of the St chloroplast genome in St-containing Triticeae polyploids
Authors: Redinbaugh Margaret G , Jones Thomas A , Zhang Yiting
Published: April 2011

Interspecific hybridization occurs between Tritceae species in the grass family (Poaceae) giving rise to allopolyploid species. To examine bias in cytoplasmic DNA inheritance in these hybridizations, the sequence of the 3' end of the chloroplast ndhF gene was compared among 29 allopolyploid Triticeae species containing the St nuclear genome in combination with the H, I, Ns, P, W, Y, and Xm nuclear genomes. These ndhF sequences were also compared with those from diploid or allotetraploid Triticeae species having the H, I, Ns, P, W, St, and Xm genomes. The cpDNA sequences were highly similar among diploid, allotetraploid, allohexaploid, and allooctoploid Triticeae accessions containing the St nuclear genome, with 0-6-nucleotide (nt) substitutions (0-0.8%) occurring between pairs of species. Neighbor-joining analysis of the sequences showed that the ndhF DNA sequences from species containing the St nuclear genome formed a strongly supported clade. The data indicated a strong preference for cpDNA inheritance from the St nuclear genome-containing parent in hybridizations between Triticeae species. This preference was independent of the presence of the H, I, Ns, P, W, and Xm nuclear genomes, the geographic distribution of the species, and the mode of reproduction. The data suggests that hybridizations having the St-containing parent as the female may be more successful.Key words: interspecies hybridization, cytoplasmic inheritance.
Ty1-copia-like retrotransposons of tomato (Lycopersicon esculentum Mill.)
Authors: Rogers Sean A , Pauls K Peter
Published: April 2011

We have used a PCR and cloning strategy to identify Ty1-copia-like retrotransposons in tomato, Lycopersicon esculentum Mill. Using degenerate oligonucleotide primers corresponding to conserved domains of the Ty1-copia retrotransposon reverse transcriptase (RT), fragments of about 260 bp were obtained by PCR amplification. Sequences of 20 cloned amplification fragments showed similarity to retrotransposon sequences. The copy number for total tomato Ty1-copia-like RT population was estimated to be approximately 2500 and may account for about 1.5% of the tomato genome. Copy numbers for four of the individual RT clones ranged from 20 to 1400 copies. A comparison of the conceptual translations of the RT sequences identified four clusters as well as three sequences which were ungrouped. When compared to RT sequences reported from several other sources, the tomato RT population was found to be widely dispersed with the majority of the RT sequences from Lycopersicon species delineated by the four tomato cluster groups. The gag region of a tomato retrotransposon was cloned from PCRs with primers based on the Tnt1 retrotransposon of tobacco. The tomato clone (pTom1.1) had 81% sequence similarity to the Tnt1 gag region. Several pTom1.1 sequences are present in other solanaceous species as indicated by Southern hybridization.Key words: gag region, retroelements, retrotransposon, reverse transcriptase, tomato.
Automictic parthenogenesis in the parasitoidVenturia canescens(Hymenoptera: Ichneumonidae) revisited
Authors: Beukeboom Leo W , Pijnacker Laas P
Published: April 2011

Both arrhenotokous and thelytokous reproduction are known to occur in the parasitoid wasp Venturia canescens. The cytological mechanism of thelytoky was previously reported to involve the formation of a restitution metaphase after the reduction division, but the exact nature of the subsequent divisions, whether reductional or equational, remained unclear. We reinvestigated the cytological mechanisms in a thelytokous strain collected in France. Our observations confirm previous results, but an equational and not a reduction division was observed after restitution. This type of reproduction can be classified as central fusion automictic parthenogenesis. In two arrhenotokous strains the normal pattern of oogenesis and syngamy of Hymenoptera was observed. In addition, we used PCR amplification to show that thelytoky in V. canescens is not caused by Wolbachia bacteria. The results are discussed in relation to maintenance of heterozygosity and female sex.Key words: automictic parthenogenesis, central fusion, genetic variation, restitution, Venturia canescens, Wolbachia bacteria.
Linkage mapping and nucleotide polymorphisms of the 6-SFT gene of cool-season grasses
Authors: Wei Jun-Zhi , Chatterton N Jerry , Larson Steve R , Wang Richard R.-C
Published: April 2011

Fructan plays an important role as an alternate carbohydrate and may contribute to drought and cold-stress tolerances in various plant species. The gene coding for sucrose:fructan 6-fructosyltransferase (6-SFT; EC 2.4.1.10), an enzyme that catalyzes the formation and extension of β-2,6-linked fructans (levans), is important to fructan synthesis in many cool-season grasses, including cereal species. In this study, we compared a conserved sequence from the 6-SFT gene in barley with comparable sequences in 20 other cool-season grasses. We detected several DNA length polymorphisms, including variations in one simple-sequence repeat (SSR) in a 6-SFT intron of the barley cultivars Steptoe and Morex. Using the 'Steptoe' × 'Morex' doubled-haploid mapping population, the 6-SFT gene was genetically mapped to the distal region in the short arm of barley chromosome 1 (7H), where it is closely linked with trait locus Rpg1. Primers designed from other conserved regions of the barley 6-SFT gene successfully amplified 351- or 354-bp sequences of this gene from diverse cool season grass species. Sequence identities of the PCR products were greater than 80% among the 21 species. Phylogeny, as determined using these DNA sequences, is similar to that obtained from rDNA ITS sequences, and congruent with our current knowledge of genome relationships.Key words: Hordeum vulgare, barley, fructan, phylogeny, fructosyltransferase, intron, genome.
Lineage sorting accounting for the disassociation between chloroplast and mitochondrial lineages in oaks of southern France
Authors: Chiang Tzen-Yuh
Published: April 2011

Dumolin-Lapégue et al. (Mol. Biol. Evol. 15: 1321-1331. 1998) suggested that recurrent inversions of a 4-bp sequence of the mtDNA nad4-1/2 locus due to intramolecular recombination were responsible for the disassociation of chloroplast and mitochondrial genomes of French oaks. Based on their PCR-RFLP (PCR - restriction fragment length polymorphism) data obtained from three noncoding spacers, a minimum spanning network representing the phylogeny of the cpDNA was reconstructed. The mapping of alleles b and c of the mtDNA nad4-1/2 locus on the cpDNA network revealed a nonrandom distribution, which contradicted the expected patterns when repeated, and ongoing inversions had been occurring. The fact that polymorphisms (a mixed c + d type) were mostly restricted to the interior nodes of the network, which represented ancient haplotypes and geographically coincided with probable glacial refugia in southern Europe, agreed with a migrant-pool model. Evidence of a widespread pattern of polymorphism distribution indicated that mtDNA haplotypes were likely to be more ancient than the cpDNA haplotypes. Lineage sorting, due to relative age of cpDNA vs. mtDNA, plus the specific migratory mode, which recruited colonists from a random sample of resource populations during glacial expansion (thereby extending the lineage sorting period, LSP), may have resulted in the disassociation of chloroplast and mitochondrial genomes in oaks.Key words: coalescence, migrant-pool model, minimum spanning network, phylogeny disassociation, relative age.
Structure, expression, and conserved physical linkage of mouse testicular cell adhesion molecule-1 (TCAM-1) gene
Authors: Sakatani S , Takahashi R , Okuda Y , Aizawa A , Otsuka A , Komatsu A , Ono M
Published: April 2011

Isolation and characterization were performed for cDNA encoding mouse testicular cell adhesion molecule-1 (TCAM-1) using 2908 bases coding for a protein having 548 amino acids (60 kDa). Mouse TCAM-1 protein was found to consist of seven domains for signal sequence, five immunoglobulin (Ig) domains, and the transmembrane plus cytoplasmic domain. TCAM-1 gene and the region linking it to growth hormone (GH) gene located downstream from the TCAM-1 gene were then analyzed. The mouse TCAM-1 gene was 11.6 kb in length with 8 exons; the same as for the 12.0 kb rat gene. The distance from the TCAM-1 to GH gene was 12.5 kb in the mouse genome, and 7.6 kb in the rat. By Northern hybridization, 3.1-kb TCAM-1 mRNA was detected in 17-day testis and would appear present in pachytene spermatocytes and round spermatids.Key words: mouse cell adhesion molecule, gene structure, expression.
Genome discrimination by in situ hybridization in Icelandic species of Elymus and Elytrigia (Poaceae: Triticeae)
Authors: Ørgaard Marian , Anamthawat-Jónsson Kesara
Published: April 2011

The genome constitution of Icelandic Elymus caninus, E. alaskanus, and Elytrigia repens was examined by fluorescence in situ hybridization using genomic DNA and selected cloned sequences as probes. Genomic in situ hybridization (GISH) of Hordeum brachyantherum ssp. californicum (diploid, H genome) probe confirmed the presence of an H genome in the two tetraploid Elymus species and identified its presence in the hexaploid Elytrigia repens. The H chromosomes were painted uniformly except for some chromosomes of Elytrigia repens which showed extended unlabelled pericentromeric and subterminal regions. A mixture of genomic DNA from H. marinum ssp. marinum (diploid,Xa genome) and H. murinum ssp. leporinum (tetraploid,Xu genome) did not hybridize to chromosomes of the Elymus species or Elytrigia repens, confirming that these genomes were different from the H genome. The St genomic probe from Pseudoroegneria spicata (diploid) did not discriminate between the genomes of the Elymus species, whereas it produced dispersed and spotty hybridization signals most likely on the two St genomes of Elytrigia repens. Chromosomes of the two genera Elymus and Elytrigia showed different patterns of hybridization with clones pTa71 and pAes41, while clones pTa1 and pSc119.2 hybridized only to Elytrigia chromosomes. Based on FISH with these genomic and cloned probes, the two Elymus species are genomically similar, but they are evidently different from Elytrigia repens. Therefore the genomes of Icelandic Elymus caninus and E. alaskanus remain as StH, whereas the genomes of Elytrigia repens are proposed as XXH.Key words: Elymus, Elytrigia, H genome, St genome, in situ hybridization.
Diversity and genetic structure in populations ofPseudotsuga menziesii(Pinaceae) at chloroplast microsatellite loci
Authors: Viard F , El-Kassaby Y A , Ritland K
Published: April 2011

Genetic variation was compared between uniparentally-inherited (chloroplast simple sequence repeats, cpSSRs) vs. biparentally-inherited (isozyme and random amplified polymorphic DNA, RAPD) genetic markers in Douglas-fir (Pseudotsuga mensiezii) from British Columbia. Three-hundred twenty-three individuals from 11 populations were assayed. In Douglas-fir, the cpSSR primer sites were well-conserved relative to Pinus thunbergii (11 of 17 loci clearly amplified), but only 3 loci were appreciably polymorphic. At these cpSSR loci, we found an unexpectedly low level of polymorphism within populations, and no genetic differentiation among populations. By contrast, the nuclear markers showed variation typical of conifers, with significant among-population differentiation. This difference is likely the outcome of both historical factors and high pollen dispersal.Key words: chloroplast microsatellites, isozymes, RAPDs, gene flow, pollen flow.
Polyploid formation in cotton is not accompanied by rapid genomic changes
Authors: Liu B , Brubaker C L , Mergeai G , Cronn R C , Wendel J F
Published: April 2011

Recent work has demonstrated that allopolyploid speciation in plants may be associated with non-Mendelian genomic changes in the early generations following polyploid synthesis. To address the question of whether rapid genomic changes also occur in allopolyploid cotton (Gossypium) species, amplified fragment length polymorphism (AFLP) analysis was performed to evaluate nine sets of newly synthesized allotetraploid and allohexaploid plants, their parents, and the selfed progeny from colchicine-doubled synthetics. Using both methylation-sensitive and methylation-insensitive enzymes, the extent of fragment additivity in newly combined genomes was ascertained for a total of approximately 22 000 genomic loci. Fragment additivity was observed in nearly all cases, with the few exceptions most likely reflecting parental heterozygosity or experimental error. In addition, genomic Southern analysis on six sets of synthetic allopolyploids probed with five retrotransposons also revealed complete additivity. Because no alterations were observed using methylation-sensitive isoschizomers, epigenetic changes following polyploid synthesis were also minimal. These indications of genomic additivity and epigenetic stasis during allopolyploid formation provide a contrast to recent evidence from several model plant allopolyploids, most notably wheat and Brassica, where rapid and unexplained genomic changes have been reported. In addition, the data contrast with evidence from repetitive DNAs in Gossypium, some of which are subject to non-Mendelian molecular evolutionary phenomena in extant polyploids. These contrasts indicate polyploid speciation in plants is accompanied by a diverse array of molecular evolutionary phenomena, which will vary among both genomic constituents and taxa.Key words: polyploidy, genome evolution, cotton, Gossypium, amplified fragment length polymorphism (AFLP).
Isolation of a chromosomally engineered durum wheat line carrying theAegilops ventricosa Pch1gene for resistance to eyespot
Authors: Huguet-Robert V , Dedryver F , Röder M S , Korzun V , Abélard P , Tanguy A M , Jaudeau B , Jahier J
Published: April 2011

The chromosome 7Dvof Aegilops ventricosa (syn. Triticum ventricosum, 2n = 4x = 28, genome DvDvMvMv) carries the gene Pch1 for resistance to eyespot. This gene has previously been transferred to chromosome 7D of bread wheat, T. aestivum (2n = 6x = 42, genome AABBDD). To (1) enhance the level of resistance of bread wheat by increasing the copy number of Pch1, and (2) create eyespot-resistant triticales, meiotically stable Pch1-carrying durum lines were selected from the backcross progenies of a cross between Ae. ventricosa and T. durum cv. Creso ph1c (2n = 4x = 28, genome AABB). The Pch1 transfer, likely resulting from homoeologous recombination, was located at the distal position on the long arm of chromosome 7A. The 7A microsatellite marker Xgwm 698 was found closely linked in repulsion to the introgression in the resistant recombination lines, and the endopeptidase allele located on chromosome 7A of cv. Creso ph1c was lost.Key words: eyespot, introgression, homoeologous recombination, mapping, wheat.
Development, characterisation, and across-taxa utility of oil palm (Elaeis guineensis Jacq.) microsatellite markers
Authors: Billotte N , Risterucci A M , Barcelos E , Noyer J L , Amblard P , Baurens F C
Published: April 2011

The results of the development of oil palm (Elaeis guineensis Jacq.) microsatellite markers are given step by step, from the screening of libraries enriched in (GA)n, (GT)n, and (CCG)n simple-sequence repeats (SSRs) to the final characterisation of 21 SSR loci. Also published are primer sequences, estimates of allele size range, and expected heterozygosity in E. guineensis and in the closely related species E. oleifera, in which an optimal utility of the SSR markers was observed. Multivariate data analyses showed the ability of SSR markers to efficiently reveal the genetic-diversity structure of the genus Elaeis in accordance with known geographical origins and with measured genetic relationships based on previous molecular studies. High levels of allelic variability indicated that E. guineensis SSRs will be a powerful tool for genetic studies of the genus Elaeis, including variety identification and intra- or inter-specific genetic mapping. PCR amplification tests on a subset of 16 other palm species and allele-sequence data showed that E. guineensis SSRs are putative transferable markers across palm taxa. In addition, phenetic information based on SSR flanking region sequences makes E. guineensis SSR markers a potentially useful molecular resource for any researcher studying the phylogeny of palm taxa.Key words: Palmae, SSR, phenetic analysis, phylogeny.
Spectral karyotyping (SKY) of mouse meiotic chromosomes
Authors: Heng Henry HQ , Liu Guo , Lu Wei , Bremer Steve , Ye Christine J , Hughes Mark , Moens Peter
Published: April 2011

The spectral karyotyping procedure of in situ hybridization with chromosome-specific probes assigns a unique colour code to each of the 21 mouse mitotic chromosomes. We have adapted this procedure to meiotic prophase chromosomes, and the results show that each of the pachytene or metaphase I bivalents can be identified. This technique has the potential to recognize synaptic anomalies and chromosome-specific structural and behavioural characteristics. We confirm these potentials by the recognition of the heterologous synapsis of the X and Y chromosomes and by the variances of synaptonemal complex lengths for each of the colour-coded bivalents in eight prophase nuclei.Key words: SKY, meiosis, synaptonemal complex, multicolour, chromosome painting, spectral karyotyping, protein-SKY co-detection.
Species identification in seven small millet species using polymerase chain reaction - restriction fragment length polymorphism of trnS-psbC gene region
Authors: Parani M , Rajesh K , Lakshmi M , Parducci L , Szmidt A E , Parida A
Published: April 2011

The chloroplast trnS-psbC gene regions from total genomic DNA of 119 accessions from seven small millet species were amplified by polymerase chain reaction (PCR) and digested with eight restriction enzymes individually as well as in combinations of two enzymes to generate restriction fragment length polymorphism (PCRRFLP). PCRRFLP with individual enzymes revealed polymorphism between only some species. However, all the species could be distinguished by using a combination of two enzymes, specifically HaeIII and MspI. PCRRFLP of 11 to 20 accessions with the same enzyme combination showed no intraspecific variation, which established that the differential banding patterns were species specific. In contrast, the same enzyme combination was not useful for differentiating different species of the genera Cajanus, Rhyncosia, Abies, Rhizophora, Ceriops, and Bruguiera, and it also revealed intraspecies variation in three species of Abies. The present study indicated that digestion of trnS-psbC with two four-base recognizing enzymes reveals more variation than with either enzyme alone and that it may be a method of choice for species identification in some genera.Key words: small millets, PCRRFLP, trnS-psbC, chloroplast DNA.
Simple sequence repeat analysis of a clonally propagated species: A tool for managing a grape germplasm collection
Authors: Dangl G Savage , Mendum Mary Lou , Prins Bernard H , Walker M Andrew , Meredith Carole P , Simon Charles J
Published: April 2011

The USDA germplasm repositories help to preserve the genetic variability of important crop species by collecting and maintaining representative cultivars and related germplasm. Simple sequence repeat markers with high allelic diversity were used to type 41 grapevines from 40 accessions. All vines were either seedless table grape cultivars or cultivars with names similar to table grape cultivars. The proportion of shared alleles was selected as the most appropriate statistical measure of genetic distance for this population. In conjunction with morphological traits, known synonyms were confirmed and a previously unknown synonym was discovered. An alleged synonym in the literature was disproved by the DNA data. The data were consistent with known parentage, where such data were available. Two mislabeled vines in the USDA collection were identified. UPGMA grouped the cultivars loosely into three groups: a group of nine mostly Middle Eastern cultivars, a group of 22 accessions mostly from Russia and Afghanistan that were morphologically similar to 'Thompson Seedless', and a third very loose group of 11 accessions consisting mostly of eastern European wine grape cultivars. The limitations and usefulness of this type of analysis are discussed.Key words: Vitis vinifera, grape, germplasm, simple sequence repeats, genetic distance.
Functional analysis of theArabidopsis thalianamismatch repair geneMSH2
Authors: Adé Jules , Haffani Yosr , Belzile François J
Published: April 2011

The Arabidopsis thaliana MSH2 (AtMSH2) gene encodes a protein that belongs to a family of highly conserved proteins (MutS homologues (MSH)) involved in DNA mismatch repair. Sequence analysis strongly suggests that this single copy gene is indeed a homologue of MSH2, a gene known to play a central role in eukaryotic mismatch repair. In this report, we show that the AtMSH2 protein has functional attributes characteristic of previously described mismatch repair proteins. First, over-expression of this protein in Escherichia coli leads to a mutator phenotype similar to that reported previously for known functional homologues. Second, gel retardation assays revealed that the AtMSH2 protein has a 10-fold greater affinity for DNA containing a single pair of mismatched nucleotides versus perfectly matched DNA. These results provide experimental evidence that AtMSH2 is indeed a functional homologue of MutS.Key words: DNA mismatch repair, heteroduplex DNA, mutation rate.
Molecular variation in plant cell populations evolving in vitro in different physiological contexts
Authors: Bogani Patrizia , Simoni Alessandra , Lio' Pietro , Germinario Angela , Buiatti Marcello
Published: April 2011

Previous work has shown the fixation of context-specific random amplified polymorphic DNA (RAPD) patterns in tomato cell cultures grown for 2 years in different hormonal contexts. In this work, RAPD sequences were characterised and RAPD-derived molecular markers used for a further study of variation between and within auto- and auxo-trophic tomato cultures grown in different hormonal equilibria. Results were then compared with those obtained using microsatellite markers located in noncoding regions of differentiation- and hormone-related genes and with those obtained with the external transcribed spacer (ETS) from tomato rDNA. Hybridisation of RAPDs on a tomato genomic DNA bank, or on total DNA after enzymatic digestion, suggested that the markers were repetitive in nature. Sequence analysis, however, showed that the homology between different fragments was due mainly to the presence of homo-AT nucleotide stretches. Moreover, a series of computational methods, such as an information-theory algorithm coupled with ΔG estimates, suggested that the RAPD fragments isolated in our experiments are noncoding. The amplification of SSR-containing RAPD-derived markers, and of other SSRs located in noncoding regions of tomato functional genes, consistently showed polymorphism between auxo- and auto-trophic somaclones (the latter being either habituated or transgenic for Agrobacterium tumefaciens oncogenes) but not within these same clones. Differences were also found between auxotrophic clones and the differentiated tissue. These findings were confirmed by restriction fragment length polymorphism (RFLP) analysis with the REII repetitive element of the ETS from tomato rDNA, which was isolated during this study. The results obtained suggest a possible role for physiological context in the selection of RAPD patterns during the evolution of tomato cells with different endogenous hormonal equilibria. The results are discussed in terms of a possible role for variation in noncoding regions of hormone-related genes in the adaptation to different physiological contexts.Key words: Lycopersicon esculentum, RAPD, SSR, genetic variation, noncoding DNA, hormone control.
Low responsiveness of six-rowed genotypes to androgenesis in barley does not have a pleiotropic basis
Authors: Castillo A M , Cistué L , Romagosa I , Vallés M P
Published: April 2011

A heterozygous mutant for the two- and six-rowed character was isolated in the barley cultivar Igri through application of sodium azide to isolated microspore cultures and posterior regeneration. Six-rowed and two-rowed homozygotic plants were subsequently identified in the self-pollinated M2progenies of the original heterozygous M1. Detailed molecular markers confirmed the isogenic nature of this recovered mutant and the original cultivar Igri. A comparative study of the anther culture response of this six-rowed induced mutant vs. diploid 'Igri' was performed to assess whether the two- or six-rowed gene influences anther culture response in barley through a pleiotropic effect or via linkage disequilibrium. No significant differences for any of the recorded variables throughout the in vitro regeneration process were detected between the 'Igri' six-rowed mutant and any of their two-rowed isogenic lines. This suggests that row-type association with anther culture response in barley cultivars is due to the effect of a tight linkage with other genes directly responsible for androgenic response.Key words: androgenesis, barley, linkage, mutation, pleiotropy, vrs1 locus.
Characterization of waxy proteins andwaxygenes ofTriticum timopheeviiandT. zhukovskyiand implications for evolution of wheat
Authors: Yan Liuling , Bhave Mrinal
Published: April 2011

The granule-bound starch (GBSS I, waxy protein) in Triticum timopheevii (AtAtGG) and T. zhukovskyi (AtAtAzAzGG) and a diagnostic section of the genes encoding GBSS-I from the Wx-TtA and Wx-G loci of T. timopheevii and the Wx-TtA, Wx-G, and Wx-TzA loci of T. zhukovskyi were investigated in this study. The waxy proteins in these two polyploid wheats could not be separated into distinct bands, in contrast to those in the T. turgidum (AABB)  T. aestivum (AABBDD) lineage. Alignment of sequences of the section covering exon4intron4exon5 of the various waxy genes led to the identification of gene-specific sequences in intron 4. The sequences specific to the Wx-TtA and Wx-G genes of T. timopheevii were different from those of the Wx-A1 gene and Wx-B1 genes of T. turgidum and T. aestivum. A surprising observation was that the Wx-TzA of T. zhukovskyi did not match with the Wx-TmA of T. monococcum, a putative donor of the Azgenome, but matched unexpectedly and perfectly with the Wx-B1 gene on chromosome 4A, which is proposed to have translocated from the chromosome 7B of T. aestivum. The possible genetic mechanism explaining these observations is discussed.Key words: waxy proteins, waxy genes, T. timopheevii, T. zhukovskyi, wheat evolution.
Genetic and molecular characterization of a variegatinghsp70-lacZfusion gene in the euchromatic 31B region ofDrosophila melanogaster
Authors: Morcillo Patrick , MacIntyre Ross J
Published: April 2011

A hsp70lacZ fusion gene introduced into Drosophila melanogaster at the euchromatic 31B region by P-element transformation displayed a variegated expression with respect to the lacZ fusion protein in the salivary gland cells under heat-shock conditions. The variegation is also reflected by the chromosome puffing pattern. Subsequent transposition of the 31B P element to other euchromatic positions restored wild-type activity, that is, a nonvariegated phenotype. A lower developmental temperature reduced the amount of expression under heat-shock conditions, similar to genes undergoing position-effect variegation (PEV). However, other modifiers of PEV did not affect the expression pattern of the gene. These results show a novel euchromatic tissue-specific variegation that is not associated with classical heterochromatic PEV.Key words: Drosophila, euchromatic position effect, heat shock construct.
Genetic linkage map ofCoffea canephora: effect of segregation distortion and analysis of recombination rate in male and female meioses
Authors: Lashermes P , Combes M C , Prakash N S , Trouslot P , Lorieux M , Charrier A
Published: April 2011

Two complementary segregating plant populations of Coffea canephora were produced from the same clone. One population (DH) comprised 92 doubled haploids derived from female gametes, while the other population (TC) was a test cross consisting of 44 individuals derived from male gametes. Based on the DH population, a genetic linkage map comprising 160 loci was constructed. Eleven linkage groups that putatively correspond to the 11 gametic chromosomes of C. canephora were identified. The mapped loci included more than 40 specific sequence-tagged site markers, either single-copy RFLP probes or microsatellites, that could serve as standard landmarks in coffee-genome analyses. Furthermore, comparisons for segregation distortion and recombination frequency between the two populations were performed. Although segregation distortions were observed in both populations, the frequency of loci exhibiting a very pronounced degree of distortion was especially high in the DH population. This observation is consistent with the hypothesis of strong zygotic selection among the DH population. The recombination frequencies in both populations were found to be almost indistinguishable. These results offer evidence in favour of the lack of significant sex differences in recombination in C. canephora.Key words: coffee, mapping, sex differences, segregation distortion, recombination frequency.
The genetic identity of alien chromosomes in potato breeding lines revealed by sequential GISH and FISH analyses using chromosome-specific cytogenetic DNA markers
Authors: Dong Fenggao , McGrath J Mitchell , Helgeson John P , Jiang Jiming
Published: April 2011

Genomic in situ hybridization (GISH) is one of the most popular and effective techniques for detecting alien chromatin introgressed into breeding lines; however, GISH analysis alone does not reveal the genetic identity of the alien chromosomes. We previously isolated a set of bacterial artificial chromosomes (BACs) specific to each of the 12 potato chromosomes. These BAC clones can be used as chromosome-specific cytogenetic DNA markers (CSCDMs) for potato chromosome identification. Here we demonstrate that GISH and fluorescence in situ hybridization (FISH), using CSCDMs, can be performed sequentially on the same chromosome preparations. Somatic metaphase chromosomes prepared using an enzymatic digestion and "flame-drying" procedure allows repeated probing up to five times without significant damage to chromosome morphology. The sequential GISH and FISH analyses reveal the genomic origin and genetic identity of the alien chromosomes in a single experiment and also determine whether an alien chromosome has been added to the genetic background of potato or is substituting for a homoeologous potato chromosome. The sequential GISH and FISH procedures should be widely applicable for germplasm characterization, especially in plant species with small-sized chromosomes.Key words: FISH, GISH, chromosome indentification, molecular cytogenetics, potato.