bluuebunny/crossref_metadata_2025 huggingface dataset:
RFLP analysis of the progeny from Oryza alta Swallen × Oryza sativa L.
Authors: Mao Long , Zhu Lihuang , Zhou Qin , Wang Xianping , Hu Han
Published: May 2008

RFLP analyses were carried out in the progeny from a cross of two phylogenetically distant rice species, wild rice Oryza alta Swallen (CCDD, 2n = 48) and cultivated rice O. sativa L. (AA, 2n = 24). The sterile plants gave heterozygous RFLP patterns at most of the loci detected. They looked more like their wild rice parent, with 36 chromosomes in their root-tip cells and pollen mother cells. In two partially fertile plants, however, most of the markers that were used showed RFLP patterns similar to the cultivated parent, O. sativa. By cytological study, it was found that nearly one-third of the chromosomes had been eliminated in the partially fertile plants. Their seeds have short awns, which is a characteristic of their wild parent, O. alta. An introgression occurred in one of the partially fertile plants, which led to the discussion about a nonconventional mechanism in wide hybridization for transference of wild rice chromosome segments to cultivated rice chromosomes.Key words: RFLP, Oryza alta, rice, Oryza sativa, wide hybridization.
Variation of nitrate reductase genes in selected grass species
Authors: Zhou Jizhong , Kilian Andrzej , Warner Robert L. , Kleinhofs Andris
Published: May 2008

In order to study the variation of nitrate reductase (NR) genes among grass species, gene number, intron size and number, and the heme-hinge fragment sequence of 25 grass species were compared. Genomic DNA cut with six restriction enzymes and hybridized with the barley NAD(P)H and NADH NR gene probes revealed a single NAD(P)H NR gene copy and two or more NADH NR gene copies per haploid genome in most of the species examined. Major exceptions were Hordeum vulgare, H. vulgare ssp. spontaneum, and Avena strigosa, which appeared to have a single NADH NR gene copy. The NADH NR gene intron number and lengths were examined by polymerase chain reaction amplification. Introns I and III appeared to be absent in at least one of the NADH NR genes in the grass species, while intron II varied from 0.8 to 2.4 kilobases in length. The NADH NR gene heme-hinge regions were amplified and sequenced. The estimated average overall nucleotide substitution rate in the sequenced region was 7.8 × 10−10substitutions/site per year. The synonymous substitution rate was 2.11 × 10−9substitutions/synonymous site per year and the nonsynonymous substitution rate was 4.10 × 10−10substitutions/nonsynonymous site per year. Phylogenetic analyses showed that all of the wild Hordeum species examined clustered in a group separate from H. vulgare and H. vulgare ssp. spontaneum.Key words: nitrate reductase gene, gene copy number, intron, molecular phylogeny, grasses.
Analysis of genetic diversity in a sweetpotato (Ipomoea batatas) germplasm collection using DNA amplification fingerprinting
Authors: He Guohao , Prakash C. S. , Jarret R. L.
Published: May 2008

A DNA amplification fingerprinting (DAF) approach was employed to develop individual-specific profiles and analyze genetic relationships among 73 plant introductions of sweetpotato (Ipomoea batatas (L.) Lam.) including unadapted lines from around the world and a few selected U.S.A. cultivars. Reliable and informative fingerprint profiles were obtained employing single octamer primers and Stoffel fragment Taq polymerase in the polymerase chain reaction, polyacrylamide-based vinyl polymer for electrophoresis, and silver staining to visualize the DNA. Using seven highly informative octamer primers, individual-specific DAF profiles were obtained for all accessions tested. The degree of polymorphism in the sweetpotato collection was very large, indicating a high level of genetic variability. Several accessions clustered together based on their geographic source. Most U.S.A. cultivars formed a separate cluster in the phenogram, while accessions from Papua New Guinea exhibited the highest genetic diversity. The wild species I. triloba and tetraploid I. batatas formed a group distinct from the cultivated sweetpotato. DAF appears to be useful in sweetpotato germplasm characterization and may be employed to identify duplicate accessions or for creation of core subsets. DAF data may also be useful for facilitating the selection of parents for a breeding program to ensure a broad genetic base.Key words: DNA fingerprinting, DNA markers, germplasm, genetic diversity, RAPD markers.
Detection of maize DNA sequences amplified in wheat
Authors: Zhang Juan , Friebe Bernd , Gill Bikram S.
Published: May 2008

Genomic in situ hybridization to somatic metaphase chromosomes of hexaploid wheat cv. Chinese Spring using biotinylated maize genomic DNA as a probe revealed the existence of amplified maize DNA sequences in five pairs of chromosomes. The in situ hybridization sites were located on chromosomes 1A, 7A, 2B, 3B, and 7B. One pair of in situ hybridization sites was also observed in hexaploid oat. The locations and sizes of in situ hybridization sites varied among progenitor species.Key words: Triticum aestivum, Zea mays, shared DNA sequences, genomic in situ hybridization.
Mapping the anther culture response genes in maize (ZeamaysL.)
Authors: Beaumont V. H. , Rocheford T. R. , Widholm J. M.
Published: May 2008

In order to map the genes conditioning the induction of embryos during our anther culture process, we evaluated F2plants from three different crosses for their anther culture ability and also performed RFLP analysis on these plants. The results showed that six chromosomal regions appear to be associated with the ability to induce embryo-like structures from maize microspores. These regions are located on chromosomes 1 (two regions), 3, 5, 7, and 8. Some of these chromosomes are identical to those found in previous studies and we have localized the regions more precisely. Notably, all chromosome regions identified, except one, are near viviparous mutant loci. Since the viviparous mutations are known to involve the plant hormone abscisic acid (ABA), these results suggest that ABA or its antagonist, gibberellic acid (GA3), might somehow be related to anther culture ability. We also propose some combinations of probes to screen for anther culture ability in the three genotypes studied.Key words: restriction fragment length polymorphism, anther culture, gene mapping, Zea mays L.
Detection of intergenomic translocations with centromeric and noncentromeric breakpoints in Triticum araraticum: mechanism of origin and adaptive significance
Authors: Badaeva Ekatherina D. , Jiang Jiming , Gill Bikram S.
Published: May 2008

Triticum araraticum Jakubz. (2n = 4x = 28, AtAtGG), a wild progenitor of the polyploid cultivated wheat T. timopheevii, shows extensive chromosome translocation polymorphism in natural populations from the Middle East and Transcaucasia. From an extensive survey, eight intergenomic translocation types were observed and their breakpoints analyzed by genomic in situ hybridization. The previously reported species-specific 6At–1G–4G cyclic translocation was found in all accessions studied. In four translocation types, the breakpoints were in interstitial regions of chromosomes and the other four arose via centric–breakage–fusion. A model is presented on the mechanism of origin and the adaptive significance of translocations with centromeric and noncentromeric breakpoints.Key words: intraspecific diversity, intergenomic translocations, Triticum araraticum.
RFLP maps of rye chromosomes 6R and 7R including terminal C-bands
Authors: Wanous M. K. , Goicoechea P. G. , Gustafson J. P.
Published: May 2008

A F2mapping population was created from a cross between 'UC-90' and E-line ryes (Secale cereale L.), two lines that showed polymorphism for eight C-band loci. Clones from rye, as well as other grasses, were used as probes. RFLP maps of rye chromosomes 6R and 7R were generated that include the 6RS and 6RL terminal C-bands and the 7RS terminal C-band. The 6R map spans 230 cM and includes 9 loci. The 7R map covers 225 cM and includes 21 loci. Segregation distortion was detected for several chromosomal regions. Heterochromatic C-bands did not appear to be responsible for the distortion.Key words: Secale cereale, RFLP, genetic mapping, C-band.
Transfer and mapping of the shoot-differentiation locus Shd1 in barley chromosome 2
Authors: Komatsuda T. , Taguchi-Shiobara F. , Oka S. , Takaiwa F. , Annaka T. , Jacobsen H.-J.
Published: May 2008

The locus Shd1, which we previously mapped to the long arm of chromosome 2 of Hordeum vulgare L., controls the differentiation of shoots from immature barley embryo callus. The locus has major effects and its action explains more than 65% of the total genetic variance in the shoot-differentiation rate. The allele of cultivar Kanto Nakate Gold designated Shd1K has a significant positive effect on the shoot-differentiation rate, whereas Shd1A of cultivar Azumamugi does not promote shoot differentiation. To identify gene products and characterize the function of Shd1, a set of near-isogenic lines is essential. In this study we produced BC5F1 plants by repeated backcrossing of 'Azumamugi' to F1 plants ('Azumamugi' × 'Kanto Nakate Gold'). The BC5F1 plants were examined for their RFLP genotype and for the shoot-differentiation ability of immature embryo-derived callus. The results indicated that the Shd1 locus was located in a chromosomal region between MWG2081 and MWG503 that flanks the MWG801, cMWG699, v (ear type), and MWG865 loci. Shd1K from 'Kanto Nakate Gold' functions effectively in the genetic background of 'Azumamugi', an indication that backcross breeding is possible for production of near-isogenic lines that would be very suitable for tissue culture.Key words: Hordeum vulgare L., shoot-differentiation ability, immature embryo callus, backcross breeding, RFLPs.
Metaphase karyotypes of fruit flies of Thailand. I. Five sibling species of theBactrocera dorsaliscomplex
Authors: Baimai V. , Trinachartvanit W. , Grote P. J. , Kijchalao U. , Tigvattananont S. , Poramarcom R.
Published: May 2008

Natural populations of fruit flies of the Bactrocera dorsalis complex exhibit chromosomal variation based on differences in the amount and distribution of constitutive heterochromatin in the centromeric regions of the autosomes and the sex chromosomes. The chromosomal variation, coupled with differences in external morphology and host plant specific preferences, strongly suggest the existence of 5 closely related species within the B. dorsalis complex that have provisionally been designated B. dorsalis species B, C, D, and E in contrast with B. dorsalis s.s. (species A). Analysis of heterochromatin in autosomes and sex chromosomes has revealed 4 distinct groups of mitotic karyotypes. Bactrocera dorsalis is the only representative of Group I, which is characterized by the typical metacentric X chromosome and major blocks of centromeric heterochromatin in autosomes 5 and 6. Group 2 consists of species B and C, which show prominent landmarks of pericentric heterochromatin in all autosomes and in the X chromosome. Group 3 comprises species D, which is characterized by conspicuous blocks of pericentric heterochromatin in all autosomes but the long arm of the subtelocentric X chromosome is euchromatic and lacks a major portion of centromeric heterochromatin. Species E belongs to Group 4, which differs from Group 3 in having major blocks of heterochromatin at the distal portion of the X chromosome in addition to the prominent landmarks of pericentric heterochromatin in all autosomes. Chromosomal evolution among closely related species within the B. dorsalis complex clearly involves the presence or absence of constitutive heterochromatin in the centromeric regions of autosomes as well as in the X chromosome.Key words: Bactrocera dorsalis complex, metaphase karyotype, heterochromatin, chromosomal evolution.
Expression of the cold-induced wheat gene Wcs120 and its homologs in related species and interspecific combinations
Authors: Limin A. E. , Fowler D. B. , Houde M. , Chauvin L. P. , Sarhan F.
Published: May 2008

Low-temperature response was measured at the whole plant and at the molecular level in wheat–rye amphiploids and in other interspecific combinations. Cold tolerance of interspecifics whose parents diverged widely in hardiness levels resembled the less hardy higher ploidy level wheat parent. Expression of the low-temperature induced Wcs120 gene of wheat (Triticum aestivum L. em. Thell.) has been associated with freezing tolerance and was used here to study mRNA and protein accumulation in interspecific and parental lines during cold acclimation. Northern and Western analyses showed that homologous mRNAs and proteins were present in all the related species used in the experiments. Cold-tolerant rye (Secale cereale L.) produced a strong mRNA signal that was sustained throughout the entire 49-day cold-acclimation period. The wheats produced a mRNA signal that had diminished after 49 days of low-temperature exposure. The wheat–rye triticales did not exhibit the independent accumulation kinetics of the cold-tolerant rye parent but, rather, more closely resembled the wheat parent in that the mRNA signal was greatly diminished after 49 days of low-temperature exposure. The influence of the rye genome was manifest in slightly greater mRNA and protein accumulation in earlier stages of acclimation. Protein accumulations in the triticales were also maintained to a somewhat greater extent than found in the wheats at the end of the 49-day acclimation period. Protein accumulations in the wheat-crested wheatgrass (Agropyron cristatum L. Gaertner) interspecific resembled that of the wheat parent. The influence of the higher ploidy level wheats of the expression of homologous gene families from wheat-related hardy diploids in interspecific combinations may in part explain the poor cold tolerance observed.Key words: cold tolerance, transcription, protein accumulation, alien gene expression, Triticeae.
Characterization of loci containing microsatellite sequences among Canadian wheat cultivars
Authors: Lee S. J. , Penner G. A. , Devos K. M.
Published: May 2008

Two microsatellite sequences, one within a γ-gliadin locus and another within a low molecular weight glutenin locus, were characterized on a set of 16 wheat lines. The wheat lines analyzed were primarily Canadian cultivars or breeding lines. A high level of variation was detected, especially between the Canadian Prairie Spring and the Canadian Western Red Spring Wheat classes. Markers based on microsatellite sequence sites appear to be more informative on closely related germplasm than either RFLP- or RAPD-based markers. The applicability of these markers across a wide spectrum of classes and cultivars provides a starting point for developing a point of delivery wheat class identification system.Key words: microsatellite, DNA markers, DNA fingerprints, wheat.
Genetic differences in recombination frequency in the pig (Sus scrofa)
Authors: Ollivierz L.
Published: May 2008

A comparison has been performed on 3 recently published linkage maps of the pig, hereafter designated as the American (A), European (E), and Swedish (S) maps. The cumulated distances between common markers in these 3 maps were in the ratio 1.00 (A): 0.88 (E): 0.77 (S), in keeping with the ratio of the percentages of domestic genome in the reference families used to build the corresponding maps, i.e., 1.00 (A): 0.81 (E): 0.50 (S). From further recombination frequencies reported in wild boars (in the S report), the wild pig genome length (in centimorgans) is expected to represent 66% of the domestic pig genome length. These observations tend to confirm a general result of Burt and Bell (Nature (London), 326: 803–805 (1987)), showing higher chiasma frequencies in domestic mammalian species compared with wild species. Consequences for mapping studies are discussed.Key words: recombination, pig, microsatellites, chiasmata.
Zebrafish chromosome banding
Authors: Pijnacker L. P. , Ferwerda M. A.
Published: May 2008

Banding techniques were carried out on metaphase chromosomes of zebrafish (Danio rerio) embryos. The karyotypes with the longest chromosomes consist of 12 metacentrics, 26 submetacentrics, and 12 subtelocentrics (2n = 50). All centromeres are C-band positive. Eight chromosomes have a pericentric C-band in each arm and 22 chromosomes have one in the longest arm. Two chromosomes have a slightly heterochromatic long arm and five chromosomes have an Ag-NOR at the terminal end of the long arm. Other banding patterns and sex chromosomes could not be revealed.Key words: zebrafish, karyotype, chromosome banding.
Inferring the genetic basis of inbreeding depression in plants
Authors: Ritland Kermit
Published: May 2008

Recent progress in the genetic analysis of inbreeding depression in plants is reviewed. While the debate over the importance of genes of dominance versus overdominance effect continues, the scope of inferences has widened and now includes such facets as the interactions between genes, the relative abundance of major versus minor genes, life cycle stage expression, and mutation rates. The types of inferences are classified into the genomic, where many genes are characterized as an average, and the genic, where individual genes are characterized. Genomic inferences can be based upon natural levels of inbreeding depression, purging experiments, the comparison of individuals of differing F (e.g., prior inbreeding), and various crossing designs. Genic inferences mainly involve mapping and characterizing loci with genetic markers, involving either a single cross or, ideally, several crosses. Alternative statistical models for analyzing polymorphic loci causing inbreeding depression should be a fruitful problem for geneticists to pursue. Key words : inbreeding depression, genetic load, self-fertilization, QTL mapping.
Genomic variation and relationships in aerial yam (Dioscorea bulbifera L.) detected by random amplified polymorphic DNA
Authors: Ramser Juliane , Weising Kurt , Kahl Günter , López-Peralta Cristina , Wetzel Rainer
Published: May 2008

Random amplified polymorphic DNA (RAPD) markers were used to assess intraspecific variability and relationships in aerial yam (Dioscorea bulbifera L.). A total of 23 accessions from different geographic locations in Africa, Asia, and Polynesia were analyzed by 10 arbitrarily chosen GC-rich decamer primers. Using cesium chloride purified genomic template DNA, highly reproducible polymorphic fingerprints were generated by all 10 primers, resulting in a total of 375 informative characters. Only eight bands were monomorphic among all investigated accessions. A binary character matrix was generated by scoring for presence/absence of a band at a particular position, transformed into a matrix of pairwise distances using either the Jaccard or a simple matching coefficient, and analyzed by neighbour joining, UPGMA (unweighted pair group method with arithmetic averaging) cluster analysis, or split decomposition. All methods of data evaluation resulted in similar groupings that reflected the geographical origin of the samples. The African accessions formed a distinct isolated group, whereas Asian and Polynesian accessions proved to be more heterogeneous. With two exceptions (var. suavior and var. sativa), the RAPD data supported previous varietal classification based on morphological characters. Stepwise reduction of the number of evaluated characters did not affect branching patterns of the trees above a minimum threshold of 150. Key words : Dioscorea bulbifera, random amplified polymorphic DNA (RAPD), genetic variation, genetic relatedness.
Development of a sequence characterized amplified region (SCAR) based indirect selection method for a dominant blast-resistance gene in rice
Authors: Naqvi Naweed I. , Chattoo Bharat B.
Published: May 2008

Two randomly amplified polymorphic DNA (RAPD) markers, OPF62700and OPH182400, tightly linked to Pi-10, a dominant blast-resistance gene conferring complete resistance to isolate 106 (international race IB46) of the blast fungus were identified. To derive sequence characterized amplified regions (SCARs) from OPF62700and OPH182400, these amplified RAPD products were cloned and sequenced. Nucleotide sequence information, obtained for each end of the two linked RAPD markers, was used to design 24-mer oligonucleotide primers for PCR amplification of the respective SCARs. Polymorphisms appearing as differences in the length of the SCAR's alternate alleles were considered for the indirect selection of Pi-10. Such polymorphisms converted the linked dominant RAPD loci into codominant SCAR markers and also facilitated the indirect scoring of the blast-resistant and blast-susceptible genotypes. The development of length variant codominant SCAR markers linked to a major gene for blast resistance in rice is described. The codominant SCARs will facilitate marker-assisted selection of the Pi-10 locus in rice breeding programs and will also be useful as genetic markers for high resolution mapping of the Pi-10 region. Key words : SCAR, Pyricularia grisea, Oryza sativa L., blast resistance, indirect selection.
Quantitative trait loci influencing chemical and sensory characteristics of eating quality in sweet corn
Authors: Azanza F. , Tadmor Y. , Klein B. P. , Rocheford T. R. , Juvik J. A.
Published: May 2008

This study was conducted to ascertain the chromosomal location and magnitude of effect of quantitative trait loci (QTL) associated with the chemical and sensory properties of sweet corn (Zea mays L.) eating quality. Eighty-eight RFLPs, 3 cloned genes (sh1, sh2, and dhn1), and 2 morphological markers (a2 and se1) distributed throughout the sweet corn genome were scored in 214 F2:3families derived from a cross between the inbreds W6786su1Se1 and IL731Asu1se1. Kernel properties associated with eating quality (kernel tenderness and starch, phytoglycogen, sucrose, and dimethyl sulfide concentrations) were quantified on F2:3sib-pollinated ears harvested at 20 days after pollination. Sensory evaluation was conducted on a subset of 103 F2:3families to determine intensity of attributes associated with sweet corn eating quality (corn aroma, grassy aroma, sweetness, starchiness, grassy flavor, crispness, tenderness, and juiciness) and overall liking. Single factor analysis of variance revealed significant QTL for all these traits, which accounted for from 3 to 42% of the total phenotypic variation. A proportion of the RFLP markers associated with human sensory response were also found to be associated with kernel characteristics. To our knowledge this is the first report of the identification of QTL associated with human flavor preferences in any food crop. Key words : sweet corn, RFLP, quantitative trait loci, eating quality, sensory evaluation.
Characterization of an Agropyron elongatum chromosome conferring resistance to cephalosporium stripe in common wheat
Authors: Cai Xiwen , Jones Stephen S. , Murray Timothy D.
Published: May 2008

Related wheat (Triticum aestivum L.) breeding lines, PI 561033, REA 9232, REA 9257, and CI 13113 were analyzed cytogenetically to characterize the association of resistance to cephalosporium stripe (caused by Cephalosporium gramineum Nis. & Ika.) with Agropyron elongatum chromatin. One pair of A. elongatum chromosomes was detected in PI 561033, REA 9232, and CI 13113 by genomic in situ hybridization. The sib line of PI 561033 and REA 9232, REA 9257, which is not resistant to this disease, lacked this pair of A. elongatum chromosomes. PI 561033 was characterized as a disomic T. aestivum – A. elongatum 6Ae#2(6A) chromosome substitution line using test crosses and C-banding. In situ hybridization and test crosses showed that the donor parent, CI 13113, also had chromosome 6A substituted by A. elongatum chromosome 6Ae#2. The C-banding pattern of 6Ae#2 showed two subterminal bands on the long arm and one small band proximal to the centromere on the short arm. Based on chromosome pairing and compensation, chromosome 6Ae#2 shows a close homoeologous relationship with wheat chromosome 6A. Key words : Cephalosporium gramineum, Agropyron elongatum, in situ hybridization, C-banding, chromosome substitution.
Construction of a genetic linkage map in the wild plantMimulususing RAPD and isozyme markers
Authors: Lin Jing-Zhong , Ritland Kermit
Published: May 2008

As a first step to mapping quantitative trait loci for mating system differences, a genetic linkage map was generated from an interspecific backcross between Mimulus guttatus and Mimulus platycalyx. The linkage map consists of 99 RAPD and two isozyme markers. Eighty-one of these markers were mapped to 15 linkage groups, spanning 1437 contiguous centiMorgans, and covering 58% of the estimated genome. The genome length of Mimulus is estimated at 2474 ± 35 cM; bootstrapping indicates that only ca. 40 markers are needed to give an accurate estimate of genome length. Further statistical analyses indicate that many RAPD markers cannot be ordered with certainty and that uncertain linkage groups tend to map nonlinearly even under commonly used mapping functions. Strategies for speeding up the mapping process for a wild species and possible applications of a partial linkage map in evolutionary studies are discussed. Key words : linkage map, mating system, Mimulus, RAPD.
Genomic relationships betweenDasypyrum villosum(L.) Candargy andD.hordeaceum(Cosson et Durieu) Candargy
Authors: Blanco A. , Simeone R. , Resta P. , Pace C. De , Delre V. , Caccia R. , Mugnozza G. T. Scarascia , Frediani M. , Cremonini R. , Cionini P. G.
Published: May 2008

The origin and genomic constitution of the tetraploid perennial species Dasypyrum hordeaceum (2n = 4x = 28) and its phylogenetic relationships with the annual diploid Dasypyrum villosum (2n = 2x = 14) have been investigated by comparing the two genomes using different methods. There is no apparent homology between the conventional or Giemsa C-banded karyotypes of the two Dasypyrum species, nor can the karyotype of D. hordeaceum be split up into two similar sets. Polymorphism within several chromosome pairs was observed in both karyotypes. Cytophotometric determinations of the Feulgen–DNA absorptions showed that the genome size of D. hordeaceum was twice as large as that of D. villosum. Both the cross D. villosum × D. hordeaceum (crossability rate 12.1%) and the reciprocal cross (crossability rate 50.7%) produced plump seeds. Only those from the former cross germinated, producing sterile plants with a phenotype that was intermediate between those of the parents. In these hybrids (2n = 21), an average of 13.77 chromosomes per cell paired at meiotic metaphase I. Trivalents were only rarely observed. Through dot-blot hybridizations, a highly repeated DNA sequence of D. villosum was found not to be represented in the genome of D. hordeaceum. By contrast, very similar restriction patterns were observed when a low-repeated DNA sequence or different single-copy sequences of D. villosum or two sequences in the plastidial DNA of rice were hybridized to Southern blots of the genomic DNAs of the two Dasypyrum species digested with different restriction endonucleases. By analyzing glutamic-oxaloacetic-transaminase, superoxide dismutase, alcohol dehydrogenase, and esterase isozyme systems, it was shown that both Dasypyrum species shared the same phenotypes, which differed from those found in hexaploid wheat. In situ hybridizations using DNA sequences encoding gliadins showed that these genes were located close to the centromere of three pairs of D. villosum chromosomes and that they had the same locations in six pairs of D. hordeaceum chromosomes. We conclude that the autoploid origin of D. hordeaceum from D. villosum, which cannot be defended on the basis of chromosomal traits, is suggested by the other findings obtained by comparing the two genomes. Key words : Dasypyrum hordeaceum, Dasypyrum villosum, phylogenetic relationships.
Simple sequence repeat primers used in polymerase chain reaction amplifications to study genetic diversity in barley
Authors: Hoz M. P. Sánchez de la , Dávila J. A. , Loarce Y. , Ferrer E.
Published: May 2008

In combination with oligonucleotides of arbitrary sequence, 5′ anchored oligonucleotides based on simple sequence repeats were used in polymerase chain reaction amplifications to produce barley DNA fingerprints. The aim of this work was (i) to develop a simple nonradioactive experimental procedure to reveal polymorphism in regions containing SSRs, (ii) to determine the genetic nature of polymorphisms, and (iii) to investigate the efficacy of polymorphisms contained in such fingerprints in disclosing genetic relationships between 14 European barley cultivars with known pedigrees. Different 10-mer oligonucleotides containing a dinucleotide motif were used as single primers and also in pairs with 10-mer oligonucleotides of arbitrary sequence. Further, the arbitrary oligonucleotides were used as single primers to produce RAPDs. Thirteen combinations of primers containing either GT(CA)4or GC(CA)4were selected on the basis of number and intensity of scorable bands in silver-stained 7% polyacrylamide gels. Of the fragments scored, 58.4% were polymorphic. Inheritance of these random amplified microsatellite polymorphic fragments (RAMP) was studied in doubled-haploid lines from the F1of 'Steptoe' × 'Morex'. Fifty percent of the primers generated codominant markers. Genetic similarities between cultivars were estimated from RAMP and RAPD data. Principal coordinate analysis performed on RAMP data revealed a clear separation of winter six-rowed, winter two-rowed, and spring two-rowed barley. The dendograms generated faithfully reflected the genealogies of the barley cultivars. RAPD failed to show clearly the germplasm sources of the experimental cultivars. Key words : simple sequence repeats, microsatellites, amplification, genetic diversity, barley.
Frequencies and sequence characteristics of di-, tri-, and tetra-nucleotide microsatellites in wheat
Authors: Ma Z. Q. , Röder M. , Sorrells M. E.
Published: May 2008

Microsatellites have emerged as an important source of genetic markers for eukaryotic genomes. In this report, two wheat (Triticum aestivum L.) genomic libraries were screened for several di-, tri-, and tetra-nucleotide tandem repeats. Clones containing (AC)n, (AG)n, (TCT)n, and (TTG)nrepeats were isolated and sequenced. On average, there was one (AC)nmicrosatellite every 292 kbp and one (AG)nmicrosatellite every 212 kbp. The trinucleotide tandem repeats (TCT)nand (TTG)nwere about 10 times less common than the two dinucleotide tandem repeats tested and tetranucleotide tandem repeats were rare. Many of the microsatellites had more than 10 repeats. The maximum repeat number found for (AC)nwas 36 and for (TCT)nwas more than 50. The prevailing category of (AG)nmicrosatellites from (AG)nisolates was perfect repeats. About half of the (AC)nmicrosatellites were compound repeats, while most of the (TCT)nmicrosatellites were imperfect repeats. In a small sample, (TTG)nmicrosatellites consisted mainly of compound repeats. The most frequently associated repeats were (AC)nwith (AG)n, (TCT)nwith (TCC)n, and (TTG)nwith (TGG)n. Among 32 pairs of microsatellite primers surveyed, seven produced polymorphic products in the expected size range and these loci were mapped using a hexaploid wheat mapping population or aneuploid stocks. Key words : wheat, Triticum aestivum L., microsatellites, polymorphism, sequence characteristics.
The 5S rRNA gene units in ancestral two-rowed barley (Hordeum spontaneum C. Koch) and bulbous barley (H. bulbosum L.): sequence analysis and phylogenetic relationships with the 5S rDNA units of cultivated barley (H. vulgare L.)
Authors: Baum Bernard R. , Johnson Douglas A.
Published: May 2008

5S rRNA genes from several accessions of Hordeum spontaneum and Hordeum bulbosum, wild relatives of cultivated barley, Hordeum vulgare, have been amplified by the polymerase chain reaction, cloned, and sequenced. Evaluation of aligned sequences along with principal coordinate analysis demonstrates that the two classes of 5S rDNA sequences found in cultivated barley, and subclasses (groups) of these sequences, can also be found in its closest wild relatives. The two classes of units, formerly categorized as containing short or long 5S rDNA repeats, are distinguishable by the presence or absence of a TAG repeating unit. Sequence comparisons of individual clones (units) isolated from different species have allowed us to confirm that orthology exists for several groups. This demonstration of orthologous groups suggests that the 5S rDNA sequence may be useful for further phylogenetic analysis in the genus Hordeum and possibly in the Triticeae. Key words : 5S rDNA, barley, sequence diversity, phylogenetic analysis.
A standard cytogenetic map forAnopheles sundaicus(Diptera: Culicidae) and evidence for chromosomal differentiation in populations from Thailand and Indonesia
Authors: Sukowati S. , Baimai V.
Published: May 2008

A standard photographic map of polytene chromosomes of Anopheles sundaicus was constructed from ovarian nurse cells and is described herein. Polytene chromosomes of wild specimens collected from 9 different geographical areas in Thailand and Indonesia have been analyzed. Specimens from these populations appear to share banding patterns with standard gene arrangements, except for some specimens from Purworejo, in Central Java, and South Tapanuli and Asahan, both of North Sumatra, which exhibited distinct banding patterns at the tip of chromosome X (Xb) compared with the standard sequence (Xa). Moreover, some specimens collected from Asahan, North Sumatra, consistently showed distinct loosely diffuse bands in zone 19 of chromosome arm 2R (2Rb) compared with the standard banding patterns (2Ra). The existence of the 2Rb pattern correlates perfectly with the presence of an extra block of centromeric heterochromatin in autosome 2 as revealed by mitotic karyotype analysis (2n = 6). These cytological differences have led to the recognition of 3 distinct forms, viz., A, B, and C, within the taxon An. sundaicus. In addition, forms A and C show a normal size for chromosome Y, (Y1), while form B has a relatively larger type of chromosome Y, (Y2). Form A is widely distributed in Thailand and Indonesia, while form B has been found in North Sumatra and Central Java. Form C, however, has been found only in Asahan, North Sumatra. Key words : Anopheles sundaicus, polytene chromosome map, mitotic karyotype, chromosomal differentiation.
Distinct expression patterns detected within individual tissues by the GAL4 enhancer trap technique
Authors: Gustafson Kerstin , Boulianne Gabrielle L.
Published: May 2008

To identify genes that are expressed in specific cell types or tissues during development, we generated enhancer-trap lines in which the yeast transcriptional activator, GAL4, was mobilized throughout the Drosophila genome. The GAL4 lines are part of a two-part system involving GAL4 and its target, the upstream activating sequence (UAS). Detection of GAL4 expression patterns was achieved by crossing individual GAL4 lines with flies carrying the reporter gene lacZ under the transcriptional control of the UAS followed by histochemical and immunocytochemical staining. Here, we present the results of this screen and the characterization of GAL4 lines that show distinct patterns of gene expression during Drosophila development, including embryogenesis, oogenesis, and imaginai disc development. However, we were unable to identify GAL4 lines that were expressed within the germ line or during early embryogenesis. Furthermore, consistent with previous results, we found that the GAL4 enhancer trap technique had a much lower frequency of transposition than has been reported for lacZ enhancer trap screens. Taken together, these results demonstrate both the strengths and weaknesses of the GAL4 enhancer trap technique for identifying unique patterns of gene expression during development. Key words : GAL4, enhancer trap, Drosophila, P element.
Genomic organization of ribosomal RNA genes inBromus(Poaceae)
Authors: Pillay M.
Published: May 2008

Restriction site maps of the rDNA genes of nine Bromus species are described. The rDNA repeat units ranged from 8.2 to 11.1 kbp in length. Intraspecific length variation was observed in the BamHI digestions in three of the nine species. Restriction site variation was observed mainly in the intergenic spacer (IGS) but was also detected in the coding region. A unique KpnI site was present in the IGS of Bromus tectorum and Bromus sericeus (subgenus Stenobromus); in addition, B. sericeus contained an extra EcoRI site. An additional DraI site was observed in the IGS of Bromus trinii (subgenus Neobromus). A BstEII site in the IGS, common to seven of the species, was absent in B. tectorum and B. sericeus. In the coding region, a 2.1-kbp BstEII fragment was present in four subgenera represented by Bromus inermis and Bromus erectus (subgenus Festucaria), Bromus marginatus and Bromus carinatus (subgenus Ceratochloa), B. tectorum and B. sericeus (subgenus Stenobromus), and B. trinii (subgenus Neobromus); a similar fragment of only 1.1 kbp was present in Bromus mollis and Bromus arvensis (subgenus Bromus). An additional BamHI site was present in the coding region of B. erectus. Ribosomal DNA data suggested that B. mollis and B. arvensis (subgenus Bromus) are genetically isolated from the other subgenera, which showed a derived relationship. Restriction site mapping of the rDNA genes could provide useful molecular data for species identification and population and evolutionary studies in Bromus. Key words : Bromus, ribosomal DNA, restriction maps, evolutionary relationships.
Detection of cytosine methylation and mapping of a gene influencing cytosine methylation in the genome ofCitrus
Authors: Cai Qinyin , Guy Charles L. , Moore Gloria A.
Published: May 2008

A new method was developed to detect DNA methylation in the Citrus genome using random amplification coupled with restriction enzyme digestion. Genomic DNA from Citrus grandis (L.) Osb., Poncirus trifoliata (L.) Raf., and their F1hybrid was amplified using 7 individual 10-mer random primers. Prior to amplification the DNA templates were digested with 2 pairs of restriction endonucleases (HpaII–MspI and (or) Sau3AI–NdeII) with different sensitivities to cytosine methylation and after PCR amplification their amplified products were further digested with the same enzymes. Using this method, it was possible to detect 28 methylation events involving 23 amplified bands with the 7 random primers and 2 pairs of enzymes. A methylation polymorphism was found at a Sau3AI site in a 1.2-kb band amplified with one primer. One locus influencing cytosine methylation at this restriction site was identified through genetic analysis of a BC1population between C. grandis and P. trifoliata and was mapped to linkage group IV using an already developed core map. This technique for detecting methylation and methylation polymorphisms is simple and should be applicable to any eukaryotic species and to many situations where it is desirable to determine whether a sequence is methylated. Key words : Citrus grandis, Poncirus trifoliata, restriction endonuclease, polymerase chain reaction, RAPD.
Localization ofDs-transposon containing T-DNA inserts in the diploid transgenic potato: linkage to theR1resistance gene againstPhytophthora infestans(Mont.) de Bary
Authors: El-Kharbotly A. , Jacobs J. M. E. , Hekkert B. te Lintel , Stiekema W. J. , Pereira A. , Jacobsen E. , Ramanna M. S.
Published: May 2008

The Dissociation transposable element (Ds) of maize containing NPTII was introduced into the diploid potato (Solanum tuberosum) clone J91-6400-A16 through Agrobacterium tumefaciens mediated transformation. Genomic DNA sequences flanking the T-DNAs from 312 transformants were obtained with inverse polymerase chain reaction or plasmid rescue techniques and used as probes for RFLP linkage analysis. The RFLP map location of 60 T-DNAs carrying Ds–NPTII was determined. The T-DNA distribution per chromosome and the relative distance between them appeared to be random. All 12 chromosomes have been covered with Ds-containing T-DNAs, potentially enabling tagging of any gene in the potato genome. The T-DNA insertions of two transformants, BET92-Ds-A16-259 and BET92-Ds-A16-416, were linked in repulsion to the position of the resistance gene R1 against Phytophthora infestans. After crossing BET92-Ds-A16-416 with a susceptible parent, 4 desired recombinants (Ds carrying T-DNA linked in coupling phase with the R1 gene) were discovered. These will be used for tagging the R1 gene. The efficiency of the pathway from the introduction to localization of T-DNAs is discussed. Key words : Solanum tuberosum, Phytophthora infestans, Ds element, transposon tagging, R genes, euchromatin.
Cytogenetic identification of Triticum peregrinum chromosomes added to common wheat
Authors: Friebe B. , Badaeva E. D. , Gill B. S. , Tuleen N. A.
Published: May 2008

C-banded karyotypes of a complete set of 14 Triticum peregrinum whole chromosome addition lines and 25 telosomic addition lines are reported. The added T. peregrinum chromosomes were not structurally rearranged compared with the corresponding chromosomes of the donor accession. Comprehensive karyotypic analysis confirmed Triticum umbellulatum as the donor species of the Uv genome and identified Triticum longissimum as the donor species of the Sv genome of T. peregrinum. Neither the Uv nor Sv genome chromosomes of the T. peregrinum accession showed large modifications when compared with the ancestral U and S1 genomes. Key words : Triticum aestivum, Triticum peregrinum, Triticum umbellulatum, Triticum longissimum, chromosome addition lines, C-banding.
Simple sequence repeats for germplasm analysis and mapping in maize
Authors: Taramino Graziana , Tingey Scott
Published: May 2008

Simple sequence repeats (SSRs) are a relatively new class of DNA markers consisting of short runs of tandemly repeated sequence motifs evenly distributed throughout eukaryotic genomes. Owing to the high rate of variation in the number of repeat units, the polymorphism level shown by SSRs is high. Furthermore, they are easy to analyze by means of the polymerase chain reaction, using flanking unique sequence primers. In order to establish the utility of SSR markers for genetic mapping and for the analysis of corn germplasm, corn genomic libraries were constructed and screened for clones containing dinucleotide and trinucleotide repeats. One hundred and fifty clones were isolated and 34 of them were used in this study to analyze 15 (AG)nrepeats, 15 (AC)nrepeats, and 4 trinucleotide repeats. Twelve corn inbred lines, representing 87% of the RFLP alleles present in a collection of public corn cultivars, were used to assess the information content of the SSR markers. The expected heterozygosity of each SSR marker was compared with the expected heterozygosity of 100 different RFLP markers. The stability of SSRs was also tested through segregation analysis on an existing mapping population. Key words : simple sequence repeats, microsatellites, maize, germplasm analysis, mapping.
Molecular cloning and characterization of an unusually large intergenic spacer from the Nor-B2 locus of hexaploid wheat
Authors: Sardana R. K. , Flavell R. B.
Published: May 2008

An allelic rDNA variant from the Nor-B2 locus of 'Bezostaya' wheat that forms an especially active nucleolus was cloned and characterized. It carries an unusually large intergenic spacer compared with rDNA units in most other wheat genotypes. The additional intergenic length is in the array of 135-bp A repeats and not in other internal repeats. These A repeats have sequences nearly identical to other A repeats described for other alleles. It is suggested therefore that the more active Nor-B2 locus of 'Bezostaya' may be due to the constituent rDNA units possessing a larger array of A repeats. Key words : ribosomal DNA, nucleolar organizer region, A and B repeats, allelic, spacer length variants.
Characterization of four induced chromosome deficiencies in rice (Oryza sativaL.)
Authors: Wang Z. X. , Iwata N.
Published: May 2008

Four rice (Oryza sativa L.) deficiencies, involving chromosomes 4 (Df4), 8 (Df8), and 11 (Df11-1, Df11-2), were studied. The deficiencies were induced by means of the pseudodominance technique, i.e., strains carrying one or more recessive marker genes were fertilized with irradiated pollen of a strain carrying normal alleles at corresponding loci. No characteristic morphological features were found in the deficiencies, as compared with the normal F1plants in the progeny. The deficiencies showed high or complete seed sterility. Genetic and cytological studies indicated deficiencies in chromosomes 4, 8, and 11. The fragment chromosomes in Df4, Df8, and Df11-2 were short, possibly being derived from the heterochromatin regions of the chromosomes, including kinetochores, and the fragment chromosome in Df11-1 was long, with about 75% of the long arm missing. At metaphase I, Df4, Df8, and Df11-2 showed only the chromosome configuration of 11 II (bivalents) + 2I (univalents), and Df11-1 only that of 12 II. It seems that the short fragments tend to stay as univalents in meiosis, probably because of their shortness. On the other hand, long fragments act as normal chromosomes and associate with their homologues. The deficiencies were not transmitted to the progenies, although only a few offspring were examined. By using the induced deficiencies Df4 and Df11-1, two morphological marker genes, lg (liguleless) and la (lazy growth habit), were located on the long arm of chromosomes 4 and 11, respectively. This is the first report in rice utilizing induced chromosome deficiencies to locate a gene on a specific arm of a chromosome. The use of induced deficiencies for studying the structure of the rice genome is discussed. Key words : rice, chromosome, deficiencies, cytology, transmission.
Segregation analysis of the testis-determining autosomal trait,Tda, that differs between the C57BL/6J and DBA/2J mouse strains suggests a multigenic threshold model
Authors: Eisner James R. , Eales Brenda A. , Biddle Fred G.
Published: May 2008

The testis-determining autosomal trait (Tda) of the mouse was uncovered when the Y chromosome of the poschiavinus variety of Mus musculus domesticus was introduced into the C57BL/6J laboratory strain background. Testis development is normal in the F1generation but, in the backcross and subsequent crosses to C57BL/6J females, XY individuals with the poschiavinus Y chromosome expressed bilateral ovaries or various combinations of an ovotestis with a contralateral ovary or testis or bilateral ovotestes and few had testes bilaterally. In other strain backgrounds, such as DBA/2J, XY individuals with the poschiavinus Y chromosome always expressed normal testes bilaterally. The first breeding analysis of this difference in the interaction of strain background with the poschiavinus Y chromosome suggested that the Tda trait was due to a single gene, but attempts to map it failed. We constructed two strains of C57BL/6J and DBA/2J that are consomic for the poschiavinus Y chromosome in order to conduct a segregation analysis of the Tda trait. In the C57BL/6J.Y-POS consomic strain, liability to express incomplete testis development is normally distributed and thresholds in development specify the probability of different classes of ovary, ovotestis, and testis combinations. Testis development is complete in the DBA/2J.Y-POS consomic strain. We demonstrated previously that the Tda trait of C57BL/6J is recessive to that of DBA/2J and the segregating first backcross generation of embryos rejected the single-gene model. We have extended our analysis to a F2generation of embryos that also rejects a single-gene model. We also report a test mating analysis of the first backcross generation. It was initiated to provide an independent assessment of the single-gene model, but the analysis of the distribution of test mating results suggests that the difference in the Tda trait between C57BL/6J and DBA/2J may be due to a small number of loci, possibly four or five, and that the phenotypic effect between loci may be additive. Key words : mouse, Y chromosome, gonadal hermaphrodites, primary sex determination, autosomal testis-determining genes, multigenic threshold model.