bluuebunny/crossref_metadata_2025 huggingface dataset:
Mitochondrial DNA diversity in the pea aphid Acyrthosiphon pisum
Authors: Barrette Richard J. , Crease Teresa J. , Hebert Paul D. N. , Via Sara
Published: April 2011

The pea aphid Acyrthosiphon pisum has been established in North America for at least a century and occurs on a broad range of host plants. Despite its importance as a crop pest, there is little understanding of the genetic structure of its populations or the extent of genetic divergence associated with different host plant utilization. This study examined the extent of mitochondrial DNA (mtDNA) diversity among 35 clones of pea aphids from alfalfa. Polymorphisms were detected at only 2 of 126 restriction sites, suggesting the same impoverished level of genetic diversity found in prior allozyme studies. However, length variation was common and apparently arose as a result of tandem repeats in two regions of the mtDNA molecule. Region 1 occurred in proximity to the control region of the molecule, while region 2 was close to a cluster of tRNA genes flanking the NAD-dehydrogenase subunit 3 gene on the opposite side of the mtDNA molecule. Each of the aphid clones was homoplasmic for a single length variant in region 1, which varied with respect to the number of copies of a 120-bp repeat. By contrast, one-third of the clones were heteroplasmic at region 2, where they possessed a variable number of copies of a 210-bp repeat. Reanalysis of clones after 30 generations of parthenogenetic reproduction established the stability of length variants over this interval, suggesting their value in studies of the genetic structure of aphid populations.Key words: pea aphid, mitochondrial DNA, polymerase chain reaction, length heteroplasmy.
Introgression analysis of an interspecific hybrid population in peanuts (Arachis hypogaeaL.) using RFLP and RAPD markers
Authors: Garcia G. M. , Stalker H. T. , Kochert G.
Published: April 2011

Forty-six introgression lines (F10C9) from a cross between Arachis hypogaea L. (2n = 4x = 40) and A. cardenasii Krapov. &W.C. Gregory (2n = 2x = 20) were analyzed for the introgression of A. cardenasii chromosome segments. Seventy-three RFLP probes and 70 RAPD primers, expressing from one to four A. cardenasii-specific bands, were used to evaluate the set of introgression lines. Thirty-four RFLP probes and 45 RAPD primers identified putative A. cardenasii introgressed chromosome segments in one or more lines. Introgressed segments were detected by RFLP analysis in 10 of the 11 linkage groups; the smallest introgressed fragments were detected by single RFLP markers and the largest were detected by three or four adjacent markers and represented introgressed segments of 30–40 cM. Similar results were obtained with RAPD markers, although markers detecting introgressed fragments could not be placed on the peanut linkage map. Introgression into both A. hypogaea genomes was detected and its implication in breeding for disease resistance is discussed.Key words: peanut, Arachis hypogaea, Arachis cardenasii, RFLPs, RAPDs, introgression, reciprocal recombination, translocation, alien gene transfer, wide cross.
Polytene chromosome relationships of five species of the Anopheles dirus complex in Thailand
Authors: Poopittayasataporn Anan , Baimai Visut
Published: April 2011

Photographic maps and rearrangements of each salivary gland polytene chromosome arm of Anopheles nemophilous (species F) and of An. dirus species A, B, C, and D of the Dirus group from natural populations in Thailand are presented. Structural conformation of heterokaryotypes and comparison of chromosome banding sequences reveal 10 paracentric inversions. The data on fixed inversion of 3Rb and inversion polymorphism of the X chromosome shared by these species were used to construct a phylogeny of the five members of the An. dirus complex, thereby outlining their patterns of speciation through chromosomal rearrangements.Key words: polytene chromosome rearrangements, Anopheles dirus, phylogeny.
Molecular mapping of wheat. Homoeologous group 3
Authors: Nelson James C. , Deynze Allen E. Van , Sorrells Mark E. , Autrique Enrique , Lu Yun Hai , Negre Sylvie , Bernard Michel , Leroy Philippe
Published: April 2011

A prerequisite for molecular level genetic studies and breeding in wheat is a molecular marker map detailing its similarities with those of other grass species in the Gramineae family. We have constructed restriction fragment length polymorphism maps of the A-, B-, and D-genome chromosomes of homoeologous group 3 of hexaploid wheat (Triticum aestivum L. em. Thell) using 114 F7–8lines from a synthetic × bread wheat cross. The map consists of 58 markers spanning 230 cM on chromosome 3A, 62 markers spanning 260 cM on 3B, and 40 markers spanning 171 cM on 3D. Thirteen libraries of genomic or cDNA clones from wheat, barley, and T. tauschii, the wheat D genome donor, are represented, facilitating the alignment and comparison of these maps with maps of other grass species. Twenty-four clones reveal homoeoloci on two of the three genomes and the associated linkages are largely comparable across genomes. A consensus sequence of orthologous loci in grass species genomes is assembled from this map and from existing maps of the chromosome-3 homoeologs in barley (Hordeum spp.), T. tauschii, and rice (Oryza spp.). It illustrates the close homoeology among the four species and the partial homoeology of wheat chromosome 3 with oat (Avena spp.) chromosome C. Two orthologous red grain color genes, R3 and R1, are mapped on chromosome arms 3BL and 3DL.Key words: RFLP, wheat, barley, Triticum tauschii, grain color.
The identification of restriction fragment length polymorphisms linked to seed colour genes inBrassica napus
Authors: Deynze A. E. Van , Landry B. S. , Pauls K. P.
Published: April 2011

Restriction fragment length polymorphisms (RFLPs) linked to genes controlling seed colour were identified in rapeseed (Brassica napus). The efficiency of the RFLP analysis was enhanced by utilizing bulked segregant analysis, DNA clones that had previously been used to construct a RFLP map of B. napus, and a doubled-haploid (DH) population segregating for seed colour. Markers for two of the three seed colour genes segregating in the DH population were identified on the basis of χ2analyses of marker distributions among visually classified black-, brown-, and yellow-seeded DH lines as well as ANOVA and quantitative trait locus analysis of light-reflectance measurements from seeds of the DH lines. The RFLP markers linked to seed colour that were identified in the present study will allow breeding strategies based on genotype selection to be developed for seed colour in rapeseed.Key words: RFLP markers, seed colour genes, rapeseed.
Identification of RAPD markers linked to a gene governing cadmium uptake in durum wheat
Authors: Penner Greg A. , Bezte Leslie J. , Leisle Dave , Clarke John
Published: April 2011

Temperature sweep gel electrophoresis in combination with random amplified polymorphic DNA analysis was employed to detect two markers for a single gene governing low cadmium uptake in western Canadian durum wheat (Triticum turgidum L. var. durum). Analysis of progeny derived from a cross of the high cadmium accumulating cultivar Kyle by the low cadmium accumulating cultivar Nile resulted in linkage estimates of 4.6 (OPC-20) and 21.2 (UBC-180) cM. The closest marker (OPC-20) was shown to be useful for making low cadmium uptake selections from two other sources of low cadmium, 'Biodur' and 'Hercules'. The marker was further used to determine the genetic basis of resistance in 20 introduced durum wheat lines. Within this diverse range of germplasm the marker was correlated with cadmium contents as expected in all but two cases. Plant breeding selection for low cadmium genotypes is hindered by the high cost of chemical determination of cadmium content. Marker assisted selection for a low cadmium uptake gene offers an effective alternative.Key words: cadmium, durum wheat, RAPD markers, marker assisted selection, temperature sweep gel electrophoresis.
Ribosomal cistrons in Bothrops neuwiedi (Serpentes) subspecies from Brazil
Authors: Trajtengertz Isa , Beçak M. L. , Ruiz Itamar R. G.
Published: April 2011

The ribosomal cistrons of six subspecies of Bothrops neuwiedi (Serpentes) were studied at both the cytogenetic and molecular levels. These subspecies populations occur in several Brazilian regions. The analysis of the nucleolar organizing region banding patterns showed variability in the chromosomal localization of rDNA cistrons. The rDNA clusters were found in two microchromosomes, in chromosome pair Number 6, or even in the one homologue of chromosome 6, and one microchromosome, according to the specimen examined but independent of the population from which it was selected. The organization of the rDNA repeat was studied by Southern blot hybridization using Xenopus laevis ribosomal DNA probes. The size of the repeat is 10.4 kilobases (kb), and the intergenic spacer (IGS), 2.6 kb long, is relatively small compared with the size of other vertebrate IGSs. Restriction mapping using the restriction enzymes EcoRI, BamHI, HindIII, and PvuII showed a highly conserved organization of the ribosomal repeats in the total genomic DNA of the subspecies studied.Key words: ribosomal cistrons, Bothrops neuwiedi, Serpentes.
Analysis of the genetic composition of anther-derived potato by randomly amplified polymorphic DNA and simple sequence repeats
Authors: Veilleux Richard E. , Shen L. Yin , Paz Margarita M.
Published: April 2011

Randomly amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) analyses were used to characterize the genetic composition of anther-derived plants of a diploid potato clone, CP2 (Solanum chacoense 80-1 × S. phureja 1-3). The ploidy of anther-derived plants was first determined by flow cytometry. A total of 44 decamer primers was screened for RAPD polymorphism. The loci that segregated were selected and scored. The monoploids had less than half as many loci carrying RAPD markers compared with the anther donor. Among 14 anther-derived diploids, 5 were identified as homozygous by marker frequency similar to monoploids and 9 as heterozygous. Five of seven SSRs obtained from published potato sequences were polymorphic in CP2. CP2 was found to be heterozygous with two alleles at four SSR loci (TC/TA, AAG, AGA, CTT) and three alleles at a ACTC locus. Primer pairs flanking each of the five polymorphic SSRs revealed that monoploids had only the allele contributed by S. chacoense 80-1. Homozygous diploids had only one band per SSR locus, whereas heterozygous diploids displayed more than one allele for at least one SSR locus. Results of the SSR analysis supported the findings based on RAPD markers; the same five diploid clones were characterized as homozygous by both SSR and RAPD markers.Key words: androgenesis, anther culture, microsatellites, RAPDs, Solanum phureja, Solanum chacoense, SSRs, short tandem repeats.
Identification, transmission, and cytological behavior ofSolanum lycopersicoidesDun. monosomic alien addition lines in tomato (Lycopersicon esculentumMill.)
Authors: Chetelat Roger T , Rick Charles M , Cisneros Pedro , Alpert Kevin B , DeVerna Joseph W
Published: April 2011

The wild nightshade Solanum lycopersicoides possesses a number of disease- and arthropod-resistance and environmental stress tolerance traits of potential value for the cultivated tomato, Lycopersicon esculentum. F1hybrids are readily obtained by sexual crosses, but backcrosses to tomato are hindered by sterility and incompatibility barriers. In the present studies, intergeneric sesquidiploid hybrids (2 genomes of L. esculentum and 1 of S. lycopersicoides) were pollinated with Lycopersicon pennellii derived bridging lines, yielding diploid, aneuploid (up to 2n + 6), and polyploid (3x, 4x) progeny. After diploids (58% of total progeny), the group most frequently obtained was 2n + 1 (31%), which included all 12 possible monosomic alien addition lines (MAALs) containing a single extra chromosome from S. lycopersicoides in a tomato background. MAAL groups were identified with a combination of allozyme, RFLP, and monogenic visual markers. Transmission rates of the extra chromosomes in MAALs varied from 0%, for chromosome 6, to 24%, for chromosome 10. At diakinesis and metaphase I of meiosis, the alien chromosome was usually unpaired (in an average of 90% of PMCs), but association of homoeologous chromosomes was observed in each of the 12 MAAL groups (in an average of 5.7% of PMCs). The MAALs showed a striking morphological resemblance to the corresponding tomato primary trisomic. In addition, each MAAL expressed S. lycopersicoides specific leaf, flower, and (or) fruit characters. This set of MAALs, the first of its kind in Lycopersicon, is expected to be useful for a variety of gene-mapping and introgression studies.
Phylogenetic relationship ofDiospyros kaki(persimmon) toDiospyrosspp. (Ebenaceae) of Thailand and four temperate zoneDiospyrosspp. from an analysis of RFLP variation in amplified cpDNA
Authors: Yonemori Keizo , Kanzaki Shinya , Parfitt Dan E , Utsunomiya Naoki , Subhadrabandhu Suranant , Sugiura Akira
Published: April 2011

The relationships among 17 Diospyros species from Thailand, with particular emphasis on the relationship of these species to temperate Diospyros species, including Diospyros kaki, were studied, using 81 cpDNA restriction site mutations detected in the 3.2- and 2.1-kb regions of amplified cpDNA and six different length mutations detected in the 2.1-kb region of amplified cpDNA. Parsimony and neighbor-joining analyses were conducted to identify relationships among species. Three temperate zone species, D. kaki, Diospyros lotus, and Diospyros virginiana, were monophyletic with one subtropical species, Diospyros ehretioides, suggesting a close evolutionary relationship among them. An immediate common progenitor for D. kaki and D. virginiana is suggested from cpDNA homology and the polyploidized karyotypes of both species. Our results did not support Ng's hypothesis that Diospyros glandulosa (synonym Diospyros roxburghii) is the progenitor of D. kaki. Two species, Diospyros rhodocalyx and Diospyros confertiflora, were so distant from the remaining species that additional study is needed to determine whether they should be placed in the same genus.Key words: cpDNA, Diospyros, PCR, phylogeny, persimmon, RFLP, taxonomy.
Nucleotide sequence and chromosomal mapping of the 5S rDNA repeat of the crustacean Proasellus coxalis
Authors: Pelliccia F , Barzotti R , Volpi E V , Bucciarelli E , Rocchi A
Published: April 2011

In this investigation we analysed the 5S rRNA genes of the isopod crustacean Proasellus coxalis. 5S rDNA hybridization of digested genomic DNA and amplification by PCR demonstrate that these genes are organized in tandem repeats of 589 bp, 120 of which represent the coding sequence and 469 the spacer sequence. Proasellus coxalis is the first crustacean species in which 5S rRNA genes have been found tandemly arranged without being linked to other repeated genes. The PCR product has been used as a probe in FISH to locate the 5S rRNA genes on two chromosome pairs of the P. coxalis karyotype. Comparison of the 5S rDNA sequence of this species with previously published sequences of six other crustacean species shows the existence of a good correlation between phylogenetic relationships and sequence identity.
Rapid genomic changes in newly synthesized amphiploids of Triticum and Aegilops. I. Changes in low-copy noncoding DNA sequences
Authors: Liu B , Vega J M , Segal G , Abbo S , Rodova M , Feldman M
Published: April 2011

We recently reported that allopolyploid formation in wheat was accompanied by rapid nonrandom elimination of specific low-copy, noncoding DNA sequences. These sequences occur in all diploid progenitors but are chromosome- or genome-specific at the polyploid level. To further investigate this phenomenon, we studied nine of these sequences, six chromosome-specific sequences and three genome-specific sequences, all isolated from common wheat. The various sequences were hybridized to DNA derived from nine newly synthesized amphiploids at different ploidy levels and to DNA from their parental lines. Although sequences homologous to the probes occur in all parental lines, a nonrandom loss of hybridization fragments was found at a high frequency in all amphiploids studied. In addition, a "loss/gain" of a hybridization fragment(s) was noticed in some of the amphiploids at lower frequency. Neither the type nor the frequency of changes was affected by intergenomic recombination or DNA methylation. It is suggested that rapid genomic changes culminated in a "programmed" pattern of elimination and (or) modification of specific low-copy DNA sequences following allopolyploidization. These events augmented the differentiation of homoeologous chromosomes, thus providing the physical basis for the diploid-like cytological behavior of polyploid wheat.Key words: wheat, allopolyploidy, genome evolution, chromosome- or genome-specific sequences, sequence elimination, homoeologous chromosome differentiation.
Genetic mapping of Russian wheat aphid resistance genesDn2andDn4in wheat
Authors: Ma Z -Q , Saidi A , Quick J S , Lapitan NLV
Published: April 2011

To obtain markers for marker-assisted breeding of Russian wheat aphid resistance in wheat (Triticum aestivum L.), resistance genes Dn2 and Dn4 were mapped with restriction fragment length polymorphism (RFLP) markers, using populations derived from PI 62660 x 'Carson' and PI 372129 x 'Yuma'. PI 262660 and PI 372129 are the donor parents of Dn2 and Dn4, respectively. A locus detected by marker KsuA1 was linked to Dn2 at a distance of 9.8 cM on the long arm of chromosome 7D, and a locus detected by marker ABC156 was 11.6 cM away from Dn4 on the short arm of chromosome 1D.Key words: Russian wheat aphid, RFLP markers, Triticum aestivum.
Identification of coupling and repulsion phase RAPD markers for powdery mildew resistance gene er-1 in pea
Authors: Tiwari K R , Penner G A , Warkentin T D
Published: April 2011

Powdery mildew is a serious disease of pea caused by the obligate parasite Erysiphe pisi Syd. Random amplified polymorphic DNA (RAPD) analysis has emerged as a cost-effective and efficient marker system. The objective of this study was to identify RAPD markers for powdery mildew resistance gene er-1. The resistant cultivar Highlight (carrying er-1) and the susceptible cultivar Radley were crossed, and F3 plants were screened with Operon (OP) and University of British Columbia (UBC) primers, using bulked segregant analysis. A total of 416 primers were screened, of which amplicons of three Operon primers, OPO-18, OPE-16, and OPL-6, were found to be linked to er-1. OPO-181200 was linked in coupling (trans to er-1) and no recombinants were found. OPE-161600 (4 ± 2 cM) and OPL-61900 (2 ± 2 cM) were linked in repulsion (cis to er-1). The fragments OPO-181200 and OPE-161600 were sequenced and specific primers designed. The specific primer pair Sc-OPO-181200 will be useful in identifying homozygous resistant individuals in F2 and subsequent segregating generations. Sc-OPE-161600 will have greatest utility in selecting heterozygous BC\dn6 nF1 individuals in backcross breeding programs.Key words: bulked segregant analysis,Erysiphe pisi, pea, RAPD.
Orthologous DNA sequence variation among 5S ribosomal RNA gene spacer sequences on homoeologous chromosomes 1B, 1D, and 1R of wheat and rye
Authors: Campenhout S Van , Aert R , Volckaert G
Published: April 2011

5S ribosomal gene spacer sequences from the short-spacer arrays of wheat and rye were isolated by PCR. The 29 new DNA sequences displayed noticeable heterogeneity at scattered positions. Nevertheless, based on shared DNA sequence polymorphisms, sequence alignment clearly classified the sequences into three groups. Group-specific primer sets were designed to allow chromosomal assignment by PCR on nullitetrasomic wheat stocks, as well as on wheat-rye translocation and addition lines. The three groups were assigned to orthologous loci 5S-Rrna-B1, 5S-Rrna-D1, and 5S-Rrna-R1 on homoeologous chromosomes 1B, 1D, and 1R, respectively. Hence, group-specific DNA sequence variation could be related to fixed orthologous DNA sequence variation between 5S rRNA multigene families on the homoeologous group 1 chromosomes. In addition, members of the three groups showed fixed orthologous length polymorphism. Four sequenced 5S-Rrna-B1 units, however, had a duplication in the gene encoding region and are probably representatives of a nontranscribed subfamily of 5S rDNA repeating units. The observed chromosome-specific polymorphisms among sequences belonging to a multigene family with thousands of copies suggests that this type of polymorphism may exist in many genes and gene families in polyploid wheats. The implication of this finding in relation to the construction of molecular tools for wheat-genome analysis and manipulation is discussed.Key words: 5S ribosomal RNA loci, nontranscribed spacer, chromosome location, PCR markers, wheat-rye translocation.
Mitotic analysis of the North American white sturgeon, Acipenser transmontanus Richardson (Pisces, Acipenseridae), a fish with a very high chromosome number
Authors: Eenennaam A L , Murray J D , Medrano J F
Published: April 2011

The average chromosome number of the North American white sturgeon, Acipenser transmontanus Richardson, was found to be 271 ± 2.5 (ranging from 265 to 276). This number is significantly higher than previous estimates for this species. A representative karyotype was found to consist of 132 meta- and submeta-centric chromosomes, 44 acrocentric chromosomes, and 98 microchromosomes. An improved C-banding technique revealed variation (2-7) between animals in the number of entirely heterochromatic metacentric chromosomes. These heterochromatic chromosomes may represent supernumerary chromosomes. There was no cytogenetic evidence of a heteromorphic sex chromosome pair or any sex-related chromosomal polymorphism in either sex of this species.Key words: C-banding, fish, karyotype, supernumerary chromosomes, white sturgeon.
Bar- and thorn-like abnormalities in synaptonemal complexes of a mutant rye,Secale cereale
Authors: Bogdanov Yu F , Fedotova Yu S , Sosnikhina S P , Smirnov V G , Dadashev S Ya , Mikhailova E I , de Jong J H
Published: April 2011

A novel type of aberration in synaptonemal complex (SC) assembly was found in electron micrographs of surface spread midprophase I nuclei from pollen mother cell preparations of rye. The plants with the mutant phenotype were selected from the fifth- to seventh-generation progenies of an inbred line (Ms6) characterised by partially reduced fertility and known to segregate for the desynaptic mutation sy6. The SC abnormality designated mei6 was at first detected in three sibling plants of the fifth generation of the inbred line. The most striking features were (i) the thorn-like protrusions of the lateral elements (LEs), which were often folded over towards the opposite LE, and (ii) peculiar bars inside the central region of the SC, which were either obliquely or perpendicularly positioned between the LEs. The bars and thorns often coincide with discontinuities in the adjacent LEs, giving rise, in a few cases, to minor branched structures. We analysed 424 surface spread pachytene nuclei obtained from 26 plants selected from the three inbred generations. Bars represented 92% of all abnormalities: their number per cell increased significantly with the progress of meiotic prophase, varying from an average of 1.96 ± 0.39 at midzygotene to 5.16 ± 0.52 at late pachytene and 5.14 ± 0.91 at early diplotene. Our observations suggest that bars are caused by modification and (or) erroneous self-assembly of meiosis-specific proteins intercalating with LE proteins at or near the sites of crossover events. It is also probable that the gene(s) involved is inherited independently from the gene for desynapsis.Key words: Secale cereale, synaptic mutant, meiosis, synaptonemal complex.
Determination of basic chromosome numbers in the genusSaccharumby physical mapping of ribosomal RNA genes
Authors: D'Hont Angélique , Ison David , Alix Karine , Roux Catherine , Glaszmann Jean Christophe
Published: April 2011

18S-5.6S-25S and 5S ribosomal DNA (rDNA) sites were located by in situ hybridization to the three main species of the Saccharum genus. For each species and each rDNA family, the position and number of sites in the various cytotypes suggested the presence of one locus and basic chromosome numbers of 10 for Saccharum officinarum and Saccharum robustum and\i 8 forSaccharum spontaneum. The implications of these results for the genetic maps of modern cultivars derived from crosses between the species S. officinarum and S. spontaneum are discussed.Key words: sugarcane, Saccharum, 18S-5.6S-25S rRNA, 5S rRNA, basic chromosome number, in situ hybridization.
Characterization of the tomato (Lycopersicon esculentum) genome using in vitro and in situ DNA reassociation
Authors: Peterson Daniel G , Pearson William R , Stack Stephen M
Published: April 2011

A detailed in vitro study of the kinetics of DNA renaturation, i.e., a C0t analysis, can be used to determine the size of a genome, the relative proportions of single-copy and repetitive sequences, and the complexity of genome components. Despite the dual importance of tomato (Lycopersicon esculentum) as a model for basic plant research and as a crop plant, to the best of our knowledge a C0t analysis has never been published for this species. This is probably due to difficulties associated with isolating sufficient quantities of polyphenol-free nuclear DNA from tomato. Recently we developed a technique for isolating milligram quantities of purified DNA from tomato nuclei, and we used DNA isolated in this manner to prepare a C0t curve for the tomato genome. Analysis of the C0t data indicates that the tomato genome (1C) consists of approximately 0.86 pg of DNA. In agreement with earlier molecular studies, the C0t analysis suggests that most (~73%) of the tomato genome is composed of single-copy sequences. Since 77% of the DNA in tomato chromosomes is found in constitutive heterochromatin, many of the single-copy sequences must reside in heterochromatin, an unexpected arrangement, considering that the constitutive heterochromatin of most species is predominantly repetitive DNA. To determine the distribution of repetitive and single-copy DNA along tomato pachytene chromosomes, we used hydroxyapatite-purified C0t fractions as probes for fluorescence in situ hybridization (FISH). Our FISH results indicate that highly repetitive DNA hybridizes almost exclusively with heterochromatin. While single-copy DNA comprises most of the DNA in euchromatin, heterochromatin contains the majority of single-copy DNA sequences, an observation consistent with our C0t data and previous cytological studies.Key words: tomato, Lycopersicon esculentum, genome size, heterochromatin, euchromatin, DNA reassociation, fluorescence in situ hybridization, FISH, C0t.
Suppressors of position-effect variegation inDrosophila melanogasteraffect expression of the heterochromatic genelightin the absence of a chromosome rearrangement
Authors: Clegg N J , Honda B M , Whitehead I P , Grigliatti T A , Wakimoto B , Brock H W , Lloyd V K , Sinclair DAR
Published: April 2011

Suppressors of position-effect variegation (Su(var)s) in Drosophila melanogaster are usually studied in the presence of chromosomal rearrangements, which exhibit variegated expression of euchromatic genes moved near to, or heterochromatic genes moved away from, centromeric heterochromatin. However, the effects of Su(var) mutations on heterochromatic gene expression in the absence of a variegating re-arrangement have not yet been defined. Here we present a number of results which suggest that Su(var) gene products can interact to affect the expression of the light gene in its normal heterochromatic location. We initially observed that eye pigment was reduced in several Su(var) double mutants; the phenotype resembled that of light mutations and was more severe when only one copy of the light gene was present. This reduced pigmentation could be alleviated by a duplication for the light gene or by a reduction in the amount of cellular heterochromatin. In addition, the viability of most Su(var) double mutant combinations tested was greatly reduced in a genetic background of reduced light gene dosage, when extra heterochromatin is present. We conclude that Su(var) gene products can affect expression of the heterochromatic light gene in the absence of any chromosomal rearrangements. However, it is noteworthy that mutations in any single Su(var) gene have little effect on light expression; we observe instead that different pairings of Su(var) mutations are required to show an effect on light expression. Interestingly, we have obtained evidence that at least two of the second chromosome Su(var) mutations are gain-of-function lesions, which also suggests that there may be different modes of interaction among these genes. It may therefore be possible to use this more sensitive assay of Su(var) effects on heterochromatic genes to infer functional relationships among the products of the 50 or more known Su(var) loci.Key words: heterochromatin, chromatin, gene interactions.
Characterization of microsatellite loci fromElymus alaskanusand length polymorphism in severalElymusspecies (Triticeae: Poaceae)
Authors: Sun Gen-Lou , Salomon Björn , Bothmer Roland von
Published: April 2011

A size-selected genomic library from Elymus alaskanus was screened for the presence of (GA)n, (GT)n, (CAC)n, and (TCT)nmicrosatellite sequences. A total of 28 positive clones were found for the two dinucleotide repeats, whereas no positive clones were found for the trinucleotide repeats. Positive clones were sequenced to validate the presence of microsatellites and to generate polymerase chain reaction (PCR) primers, based on the sequences flanking the microsatellite. Primer pairs were designed and evaluated for 18 selected microsatellites. The resulting loci were analysed by PCR for their usefulness as molecular markers in an array of 18 accessions representing E. alaskanus and 10 other Elymus species. PCR amplification revealed alleles for the 18 loci, which varied in having 1-10 alleles in these accessions. In the 18 accessions tested, 7 of the 18 loci were polymorphic, with gene diversity values ranging from 0.54 to 0.80 among all species. Within E. alaskanus, gene diversity values ranged from 0.20 to 0.72, with a mean of 0.48. Polymorphism was also detected within accessions. No clear relationship between total repeat length and the degree of polymorphism was observed in this study. Primer pairs designed to amplify microsatellites in E. alaskanus can be used to generate polymorphism products in other species within the genus. Hence, microsatellites are useful markers for studying both inter- and intra-specific genetic variability within Elymus.Key words: Elymus alaskanus, Triticeae, microsatellites, simple sequence repeats, SSRs, polymorphism.
The genomes of Glycine canescens F.J. Herm., and G. tomentella Hayata of Western Australia and their phylogenetic relationships in the genus Glycine Willd.
Authors: Singh Ram J , Kollipara Krishna P , Hymowitz Theodore
Published: April 2011

A multidisciplinary approach is an extremely powerful tool for determining genomic diversity and establishing genomic relationships within and among species. This study used cytogenetics and a molecular method (ITS of the rDNA) to uncover genomic diversity in Glycine canescens and Glycine tomentella and to establish their phylogenetic relationships with the other diploid species of the genus Glycine. Cytogenetics revealed that G. canescens accessions (PIs 583944, 583946, 583953, and 591575) from Western Australia were genomically similar. However, they were differentiated by a paracentric inversion from the standard G. canescens (PI 440932) collected from South Australia. By contrast, G. tomentella (2n = 40) accessions from Western Australia were highly diverse genomically. Cytogenetics and ITS investigations separated the diploid G. tomentella accessions in Australia into four distinct groups. The genome symbols DD (isozyme group D3; PI 505222), D1D1 (isozyme group D5; PI 505301), D2D2 (isozyme group D5; PI 505203), and D3D3 (isozyme group D4; PI 441000) are being assigned to these four groups. The D1 and D2 genome group accessions are distributed in Western Australia. The D3-genome group of G. tomentella accessions are morphologically similar neither to A-genome species nor to the D-, D1-, or D2-genome groups. However, the D3-genome group was phylogenetically grouped with the A-genome species, while the D-, D1-, and D2-genome groups showed a close relationship with E-, H-, and I-genome species. This study demonstrates that diploid G. tomentella of Western Australia is a complex species, and from an evolutionary viewpoint, it is actively radiating out into several genomic variants.Key words: Glycine spp., soybean, genome, cytogenetics, ITS region.
α-Tubulin and F-actin distribution during microsporogenesis in a 2n pollen producer of Solanum
Authors: Genualdo G , Errico A , Tiezzi A , Conicella C
Published: April 2011

Spatial and temporal changes in configurations of microtubules (MTs) and microfilaments (MFs) were determined during microsporogenesis, using -tubulin immunolocalization and rhodamine-phalloidin staining of F-actin, in a 2n pollen producer of Solanum, to assess the anomalies in meiotic spindles and cytokinesis and their relationships to 2n pollen formation. InSolanum, MTs and MFs generally showed patterns of localization similar to those described in other dicotyledons with simultaneous cytokinesis. However, deviations in spatial configurations of both MTs and MFs that are related to 2n pollen were observed in meiosis II and in cytokinesis. MTs and MFs localized in spindles in parallel orientation at meiosis II. In contrast, in the majority of normal meiocytes, the two spindles were seen to be perpendicular to each other. The parallel spindles altered the position of the postmeiotic nuclei, causing a uniplanar instead of a tetrahedral arrangement. Subsequently, the formation of regular radial MT systems was suppressed and only two MT arrays, which lay parallel on one plane, formed between the nuclei at the end of meiosis. A single cell plate formed across the two MT arrays, giving rise to a dyad containing 2n microspores.Key words: cytokinesis, microfilaments, microtubules, spindle, unreduced pollen.
Simple methods for isolating homoeologous loci from allopolyploid genomes
Authors: Cronn Richard , Wendel Jonathan F
Published: April 2011

During allopolyploid formation, divergent sets of chromosomes are combined in a common nucleus. Accordingly, loci that are single-copy in progenitor diploid genomes become duplicated, homoeologous loci in allopolyploids. Although homoeologous loci have been identified using classical genetic and linkage mapping approaches, there are few examples of the isolation and molecular characterization of homoeologous loci from allopolyploids. Here we describe two methods for the isolation of orthologous duplicated loci and demonstrate the feasibility of the techniques using allotetraploid cotton. The methods utilize restriction-digested, size-fractionated genomic DNA as a template for either plasmid cloning or PCR amplification. This fractionation procedure, when combined with Southern hybridization and mapping information, can separate homoeologues from each other and from more divergent cross-hybridizing sequences (paralogues). Each homoeologue can be then be isolated from a pool of size-fractionated genomic DNA that is enriched for target loci. While these methods were specifically designed for isolating homoeologous loci from allotetraploids, they should be applicable to a broad spectrum of diploid and polyploid plants and be useful for studying both ancient and recent gene duplications. In addition, the procedures enrich for orthologous sequences, which can be used for phylogenetic analysis. Thus, a general approach is detailed for the isolation of nuclear genes for phylogeny reconstruction.Key words: polyploidy, homoeology, orthology, Gossypium.
Molecular evidence against phylogenetically distinct host races of the pea aphid (Acyrthosiphon pisum)
Authors: Boulding Elizabeth Grace
Published: April 2011

Pea aphid (Acyrthosiphon pisum) clones have been shown to be adapted to particular host plant species but it is unknown whether there are host races. A 1101 base pair region of the mitochondrial cytochrome oxidase I gene (COI) was sequenced for 21 pea aphid clones that had been collected from different host plants in Canada and the U.S.A. Only five closely related mitochondrial haplotypes were found. A maximum likelihood phylogeny was estimated for these five haplotypes and four related aphid species: Acyrthosiphon macrosiphum, A. kondoi, Fimbriaphis fimbriata, and Macrosiphum creelii. Pea aphids from the same host plant species were no more likely to have the same mitochondrial haplotype than aphids from different host plant species. In addition, aphids from the same geographical regions were no more likely to have the same mitochondrial haplotype than aphids from different geographic regions. I therefore reject the hypothesis that there are monophyletic host races of the pea aphid.Key words: cytochrome oxidase I, exotic species, host plant, mtDNA sequence, phylogeny.
Visualization of Oryza eichingeri chromosomes in intergenomic hybrid plants from O. sativa × O. eichingeri via fluorescent in situ hybridization
Authors: Yan Huihuang , Min Shaokai , Zhu Lihuang
Published: April 2011

Digoxigenin-labeled total genomic DNA from Oryza eichingeri was hybridized in situ to somatic chromosome preparations of F1, F2, backcross progenies, and a pollen-derived tetraploid plant (E24) from O. sativa (2n = 24, genome AA) × O. eichingeri (2n = 24, genome CC), which allowed a definitive discrimination between A- and C-genome chromosomes. Twelve chromosomes in F1, F2, BC1, and twenty-four chromosomes in plant E24 were clearly revealed to be of O. eichingeri origin, thus confirming that both BC1 and F2 were allotriploids (2n = 36, AAC) while plant E24 was an amphiploid (2n = 48, AACC). In addition, the presence of O. eichingeri chromosomes in four alien addition lines was characterized. The results suggest that FISH/GISH may be a powerful tool for monitoring the O. sativa-alien chromosome in the progenies of rice interspecific hybridization.Key words: fluorescent in situ hybridization, Oryza sativa, Oryza eichingeri, amphiploid, alien addition lines.
Evolution of the chloroplast genome and polymorphic ITS regions in Allium subg. Melanocrommyum
Authors: Mes Ted HM , Fritsch Reinhard M , Pollner Sven , Bachmann Konrad
Published: April 2011

Relationships based on PCR-RFLPs of non-coding regions of cpDNA indicate that some of the largest subgenera of the genus Allium and five of the largest sections of the Central Asian subg. Melanocrommyum are artificial. Internested synapomorphic mutations without homoplasy were found only in the chloroplast genomes of plants of subg. Melanocrommyum that occur in the border region of Tajikistan, Uzbekistan, Afghanistan, and Kyrgyzstan. Eighteen of 49 plants surveyed were polymorphic for their ITS regions. Even plants that had identical chloroplast genomes were polymorphic for nuclear ribosomal regions. These individuals had markedly different frequencies of ITS variants that were detected with various restriction enzymes. The geographic partitioning of chloroplast haplotypes and the fact that the ITS variants could not be ordered hierarchically can readily be envisioned to result from gene flow. Processes such as concerted evolution and parallel morphological evolution may also be partly responsible for the disconcordance of mutations in the chloroplast and nuclear genome. However, the chimeric nature of the nuclear ribosomal regions indicates that concerted evolution is not the dominating process in Allium subg. Melanocrommyum.Key words: polymorphic, phylogeny, restriction analysis.
Identification of AFLP markers closely linked to the powdery mildew resistance genes Pm1c and Pm4a in common wheat (Triticum aestivum L.)
Authors: Hartl Lorenz , Mohler Volker , Zeller Friedrich J , Hsam Sai LK , Schweizer Günther
Published: April 2011

A total of 7654 DNA fragments were screened for linkage to wheat powdery mildew resistance gene Pm1c employing fluorescently based AFLP analysis and phenotypic pools from F3 families. F3 and derived F4 families were used for segregation analysis. Pool screening revealed several cosegregating and tightly linked (0.9 cM) AFLP markers for the Pm1c resistance gene. The previously reported RFLP locus Xwhs178 was integrated into the AFLP map in the vicinity of Pm1c. One AFLP marker, 18M2, was determined to be highly specific for the Pm1c gene in diverse genetic backgrounds. As Pm1c allele confers an effective resistance to powdery mildew, the marker 18M2 provides a valuable tool for enhancing marker assisted selection and pyramiding of powdery mildew resistance genes in wheat.Key words: Triticum aestivum, powdery mildew, disease resistance, AFLP, bulked segregant analysis
Recombination nodule mapping and chiasma distribution in spermatocytes of the pigeon, Columba livia
Authors: Pigozzi M I , Solari A J
Published: April 2011

Pigeon spermatocytes were processed with a drying-down technique and their synaptonemal complex (SC) complements were analyzed by electron microscopy. The synaptonemal complex karyotype of the macrobivalents shows an excellent correspondence with the mitotic karyotype. The number and distribution of recombination nodules (RNs) were scored in complete nuclei stained with phosphotungstic acid. The average number of RNs per nucleus is 64.7. The number of nodules per bivalent shows a clear linear relationship with SC length in the 10 longest synaptonemal complexes, while the microbivalents usually bear a single RN. The location of RNs has a non-random distribution along the largest synaptonemal complexes, with lower frequencies near kinetochores and higher frequencies toward the telomeres. The ZZ bivalent is the fourth in size and shows free recombination, having on average 3.8 RNs. The mean number of nodules per cell and the mean number of nodules in the largest bivalents show very good agreement with the corresponding number of chiasmata scored in metaphase-I spermatocytes. It is concluded that the recombination nodules provide a good check for reciprocal exchanges in this and other species of birds. Additionally, a new morphology for the recombination nodules is presented, consisting of groups of electron-dense particles measuring 43 nm in diameter.Key words: meiosis, chiasmata, recombination nodules, pigeon spermatogenesis.
Heritable variation in the ability to produce haploid embryos via pollination with maize and embryo rescue in durum wheat
Authors: David J L , Dusautoir J C , Raynaud C , Roumet P
Published: April 2011

Pollination with maize is commonly used to produce fertile doubled haploid plants in durum wheat. However, the genetic basis for the ability of parental lines to produce haploid seedlings is not well documented. A maximum likelihood procedure was used to analyse the response of 15 F1, from a half diallel design involving six inbred lines, and to document rigorously the existence of heritable variation for haploid embryo production. Cross-effects and "general combining abilities" (GCA) were computed to estimate the ability to produce swollen ovaries and viable embryos. On average, the ovary swelling production was 56% and 11% of emasculated flowers produced a viable embryo. For both variables, cross-effect was significant. Based on GCA estimations, the 6 parental lines could be distributed in 3 different groups. The GCA values explained respectively 69% and 79% of the cross-effect for each variable. On the whole, ovary swelling was a poor predictor of embryo formation. No significant correlation was found between the per se values of the 6 parental lines and their GCA.Key words: Triticum durum, haploid, general combining ability.
Generation and chromosome mapping of expressed sequence tags (ESTs) from a human infant thymus
Authors: Hwang Mee-Yul , Kang Yoon-Joong , Kim Young-Ho , Scherer Steve W , Tsui Lap-Chee , Sohn Uik
Published: April 2011

In an effort to identify novel genes that are expressed differentially in an infant thymus, we constructed an oligo-d(T) primed cDNA library from a human infant thymus followed by single-run partial sequencing to generate expressed sequence tags (ESTs). Characterization of more than 1400 sequences enabled us to convert human thymus transcripts into 1223 useful ESTs. These ESTs consisted of 613 (50.1%) showing homology to known human genes, 51 (4.2%) matching to genes from other species, 289 (23.6%) matching ESTs of unknown functions, and 182 (14.9%) being novel transcripts. The expression profile of an infant thymus features a high number of genes related to cell division-DNA synthesis and gene-protein expression, indicating the active growth stage of an infant thymus. To identify the chromosomal localization of 43 thymus ESTs, PCR-based mapping was performed using a human-rodent somatic cell hybrid or radiation hybrid mapping panel. The results indicated that several novel genes were determined to be located in the vicinity of previously mapped disease loci; histidinemia loci, plasminogen Tochigi disease loci, Ehlers-Danlos syndrome, hypertriglyceridemia, thyroid resistance locus, ocular albinism, galactosemia, porphyria variegata, Charcot-Marie-tooth disease, FEOM (fibrosis of extraocular muscles), Prader-Willi syndrome.Key words: cDNA, expression profile, radiation hybrid mapping, disease locus.
Genome structure and evolution in the allohexaploid weed Avena fatua L. (Poaceae)
Authors: Yang Q , Hanson L , Bennett M D , Leitch I J
Published: April 2011

Allohexaploid wild oat, Avena fatua L. (Poaceae; 2n = 6x = 42), is one of the world's worst weeds, yet unlike some of the other Avena hexaploids, its genomic structure has been relatively little researched. Consequently, in situ hybridisation was carried out on one accession of A. fatua using an 18S-25S ribosomal DNA (rDNA) sequence and genomic DNA fromA. strigosa (AA-genome diploid) and A. clauda (CC-genome diploid) as probes. Comparing these results with those for other hexaploids studied previously: (i) confirmed that the genomic composition of A. fatua was similar to the other hexaploid Avena taxa (i.e., AACCDD), (ii) identified major sites of rDNA on three pairs of A/D-genome chromosomes, in common with other Avena hexaploids, and (iii) revealed eight chromosome pairs carrying intergenomic translocations between the A/D- and C-genomes in the accession studied. Based on karyotype structure, the identity of some of these recombinant chromosomes was proposed, and this showed that some of these could be divided into two types, (i) those common to all hexaploid Avena species analysed (3 translocations) and (ii) one translocation in this A. fatua accession not previously observed in reports on other hexaploid Avena species. If this translocation is found to be unique to A. fatua, then this information, combined with more traditional morphological data, will add support to the view that A. fatua is genetically distinct from other hexaploid Avena species and thus should retain its full specific status.Key words: wild oats, Avena, genomic in situ hybridisation (GISH), intergenomic translocations, ribosomal DNA.