bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid and coupled phenotypic and genetic divergence in Icelandic Arctic char (Salvelinus alpinus)
Authors: Gíslason Davíð , Ferguson Moira M , Skúlason Skúli , Snorrason Sigurður S
Published: April 2011

Resource polymorphism has been proposed as an important phase of diversification and speciation in vertebrates. Studies of fish in young lakes of the Northern Hemisphere indicate variably advanced cases of adaptive trophic diversification. We have previously proposed a scheme describing this variation in terms of a gradient of resource-based polymorphic traits, emphasizing flexible behaviour in early phases and morphological divergence in more advanced phases. Here, we present data on Arctic char (Salvelinus alpinus) in Icelandic lakes exhibiting a variable degree of phenotypic and genotypic segregation. We show that (i) the morphs are at different levels of phenotypic segregation and reproductive isolation and in one case completely reproductively isolated, (ii) morphs within lakes appear to be of intralacustrine origin, and (iii) the morphological and genetic divergence of morphs is correlated, suggesting a role for trophic adaptation as a driving force in morph segregation.
Midsummer plankton development along a large temperate river: the St. Lawrence River
Authors: Basu Ben K , Kalff J , Pinel-Alloul B
Published: April 2011

Midsummer planktonic communities were sampled in 1997 along a 425-km reach of the St. Lawrence River between Lake Ontario and Trois-Rivières (Quebec) to describe longitudinal patterns of plankton development. Chlorophyll a (Chl a) quickly declined as water flowed from Lake Ontario into the river. Thereafter, in the reach upstream from Montreal, Chl a was ~1 µg·L-1and total phosphorus (TP) was ~10 µg·L-1. Downstream from Montreal, TP increased to 20-40 µg·L-1and Chl a rose to 2-5 µg·L-1. Although Chl a increased concomitant with TP, phytoplankton may have been light limited at the more turbid downstream stations. Zooplankton biomass decreased from 40 µg dry mass·L-1in Lake Ontario to 16 µg dry mass·L-1at Brockville, 90 km downstream. Zooplankton biomass continued to decline and downstream from Montreal remained <10 µg dry mass·L-1, despite the increased TP and Chl a. Rotifers dominated the zooplankton community, but as in other temperate rivers, total zooplankton biomass was low (<10 µg dry mass·L-1). There was no longitudinal pattern in heterotrophic bacterial or flagellate abundance. A comparison of the inflow and outflow biomass of two fluvial lakes showed the lakes to contribute little to the downstream river plankton during summer.
Total mercury in the water and sediments of St. Lawrence River wetlands compared with inland wetlands of Temagami - North Bay and Muskoka-Haliburton
Authors: Thompson-Roberts E S , Pick F R
Published: April 2011

The concentration of total Hg was compared among 45 wetlands in three regions of Ontario. Twenty-two of these wetlands were located in the Muskoka-Haliburton Highlands and Temagami - North Bay regions and included bogs, fens, and marshes. Twenty-three were riverine marshes along the St. Lawrence River, near Cornwall, a Great Lakes area of concern, where Hg has been released through industrial activity. Overall, significant but weak negative relationships were found between pH and alkalinity of the surface waters and total water Hg concentrations (r2 = 0.28-0.30, p < 0.001). A significant positive relationship was found between dissolved organic C and total water Hg (r2 = 0.30). On average, St. Lawrence wetlands had lower total water Hg when compared with the inland wetlands. While a strong positive relationship was found between sediment organic matter and total sediment Hg concentrations (p < 0.001), the relationship was significantly different between the St. Lawrence and inland wetlands. In general, the St. Lawrence wetlands, despite the proximity to point sources of Hg, actually had lower sediment Hg, likely because of the lower organic matter. However, the St. Lawrence wetlands had twice the amount of Hg per unit of organic matter; the consequences of this difference for methyl mercury production and bioaccumulation need to be addressed.
Cadmium sorption and toxicity in autotrophic biofilms
Authors: Hill Walter R , Bednarek Angela T , Larsen I Lauren
Published: April 2011

Autotrophic biofilms (periphyton) accumulate substantial quantities of metals from contaminated water. In this study, we measured the time course of biofilm cadmium sorption, examined the effects of current, biomass, and light on short-term cadmium sorption by biofilms, and tested the toxicity of cadmium to biofilm photosynthesis. The time course of cadmium sorption appeared to be a linear function of time over the 48-h measurement period. Biofilms in current [Formula: see text]2 cm·s-1sorbed three to five times more cadmium than biofilms in still water. Cadmium sorbed after 4 h was 75% greater in high-biomass biofilm (2.5 mg dry mass·cm-2) than in low-biomass biofilm (0.5 mg dry mass·cm-2), but only in moving water. Light enhanced the sorption of cadmium 40% in one biofilm type. Cadmium toxicity to photo synthesis was evident after 24 h in thin biofilms exposed to initial cadmium concentrations [Formula: see text]10 μg·L-1; photosynthesis by thicker biofilms was not significantly impaired even at the highest concentration (100 μg·L-1). Variations in current, biofilm biomass, and light are likely to influence the movement of metals in flowing systems.
Role of satiation in the functional response of a piscivore, largemouth bass (Micropterus salmoides)
Authors: Essington Timothy E , Hodgson James R , Kitchell James F
Published: April 2011

We evaluated whether satiation regulates the predation rates of a piscivore, largemouth bass (Micropterus salmoides), in natural settings. A functional response model indicated that predation rates can be reduced by satiation when mean prey density is high or when prey encounters are highly patchy. We then used bioenergetics modeling to estimate the predation rates of individual bass in four lakes during a 16-year period and used stomach content mass in diet samples to evaluate the variability in daily predation rates. Predation rates, expressed as the proportion (p) of the maximum daily consumption rate, were low (mode = 0.3, mean = 0.4). Stomach fullness (s), expressed as the proportion of the stomach fullness associated with the maximum sustainable consumption rate, was highly variable, and 13% of all bass diets had s > 1, indicating that bass could opportunistically forage at rates exceeding their maximum sustainable rate. The low predation rates and the ability to consume prey at rates exceeding the maximum sustainable rate make it unlikely that satiation was an important constraint on bass predation rates. Thus, satiation effects widely represented in modeling studies may be a rare component in piscivore-prey interactions, while prey behavior may be a more important component governing predation rates.
Behavior of sex chromosomes, autosomes, and the spindle during nonrandom segregation in a flea beetle
Authors: Kupfer Holly , Wise Dwayne
Published: April 2011

We have analyzed autosome, sex chromosome, and spindle behavior in spermatocytes of the flea beetle, Alagoasa bicolor. In this species, males have very large X and Y chromosomes, which, although they are never physically connected, always segregate to opposite spindle poles at anaphase I, thus preserving the sex ratio in the next generation. We find that the sex chromosomes are partitioned to a peripheral spindle domain early in prometaphase I and that their segregation can be accounted for mainly by their reorientation from the parallel to the linear configuration, and little by chromosome-to-pole movement. Further, the behavior of the autosomes and that of the sex chromosomes seem to have little to do with each other. Spindle elongation is minimal; barely segregating the large sex chromosomes into the daughter cells at telophase I.Key words: nonrandom segregation, sex chromosomes, kinetochores.
Inheritance and mapping of 2n-egg production in diploid alfalfa
Authors: Barcaccia G , Albertini E , Rosellini D , Tavoletti S , Veronesi F
Published: April 2011

The production of eggs with the sporophytic chromosome number (2n eggs) in diploid alfalfa (Medicago spp.) is mainly associated with the absence of cytokinesis after restitutional meiosis. The formation of 2n eggs through diplosporic apomeiosis has also been documented in a diploid mutant of M. sativa subsp. falcata (L.) Arcang. (2n = 2x = 16), named PG-F9. Molecular tagging of 2n-egg formation appears to be an essential step towards marker-assisted breeding and map-based cloning strategies aimed at investigating and manipulating reproductive mutants of the M. sativa complex. We made controlled crosses between PG-F9 and three wild type plants of M. sativa subsp. coerulea (Less.) Schm. (2n = 2x = 16) and then hand-pollinated the F1progenies with tetraploid plants of M. sativa subsp. sativa L. (2n = 4x = 32). As a triploid embryo block prevents the formation of 3x progenies in alfalfa because of endosperm imbalance, and owing to the negligible selfing rate, seed set in 2x-4x crosses was used to discriminate the genetic capacity for 2n-egg production. F1plants that exhibited null or very low seed sets were classified as normal egg producers and plants with high seed sets as 2n-egg producers. A bulked segregant analysis (BSA) with RAPD (random amplified polymorphic DNA), ISSR (inter-simple sequence repeat), and AFLP (amplified fragment length polymorphism) markers was employed to identify a genetic linkage group related to the 2n-egg trait using one of the three F1progenies. This approach enabled us to detect a paternal ISSR marker of 610 bp, generated by primer (CA)8-GC, located 9.8 cM from a putative gene (termed Tne1, two-n-eggs) that in its recessive form determines 2n eggs and a 30% recombination genomic window surrounding the target locus. Eight additional RAPD and AFLP markers, seven of maternal, and one of paternal origin, significantly co-segregated with the trait under investigation. The minimum number of quantitative trait loci (QTLs) controlling seed set in 2x-4x crosses was estimated by ANOVA and regression analysis. Four maternal and three paternal independent molecular markers significantly affected the trait. A paternal RAPD marker allele, mapped in the same linkage group of Tne1, explained 43% of the variation for seed set in 2x-4x crosses indicating the presence of a major QTL. A map of the PG-F9 chromosome regions carrying the minor genes that determine the expression level of 2n eggs was constructed using selected RAPD and AFLP markers. Two of these genes were linked to previously mapped RFLP loci belonging to groups 1 and 8. Molecular and genetic evidence support the involvement of at least five genes.Key words: Medicago spp., meiotic mutants, molecular markers.
Molecular cytogenetic analysis of intergeneric chromosomal translocations between wheat (Triticum aestivum L.) and Dasypyrum villosum arising from tissue culture
Authors: Li Hong-Jie , Guo Bei-Hai , Li Yi-Wen , Du Li-Qun , Jia Xu , Chu Chih-Ching
Published: April 2011

Fluorescence in situ hybridization (FISH) was applied with total genomic DNA extracted from Dasypyrum villosum (L.) Candargy as a probe to characterize chromosome translocations arising from tissue culture in hybrids of Triticum aestivum × (T. durum - D. villosum, amphiploid). Chromosome translocations between wheat and D. villosum occurred in callus cells at an average frequency of 1.9%. Translocations existed not only in callus cells but also in regenerants. Three plants with translocation chromosomes were characterized among 66 regenerants of T. aestivum 'Chinese Spring' × 'TH1W' and 'NPFP' × 'TH1'. One of them proved to be a reciprocal translocation with an exchange of about one third of a wheat chromosome arm with about one half of a chromosome arm of D. villosum. The breakpoints of the other two translocations were located at, or near centromeres. The results are similar for both callus cells and regenerants and provide further evidence that translocations take place in tissue culture. Other structural chromosomal changes, for example, fragments, telocentrics, dicentromeres, and deletions, as well as numerical alterations including aneuploidy and polyploidy were recorded both in callus cells and regenerants.Key words: wheat, Dasypyrum villosum, translocation, genomic in situ hybridization, tissue culture.
Identification and characterization of wheat-wheatgrass translocation lines and localization of barley yellow dwarf virus resistance
Authors: Crasta O R , Francki M G , Bucholtz D B , Sharma H C , Zhang J , Wang R -C , Ohm H W , Anderson J M
Published: April 2011

Stable introgression of agronomically important traits into crop plants through wide crossing often requires the generation and identification of translocation lines. However, the low efficiency of identifying lines containing translocations is a significant limitation in utilizing valuable alien chromatin-derived traits. Selection of putative wheatgrass-wheat translocation lines based on segregation ratios of progeny from γ-irradiated seed using a standard phenotypic analysis resulted in a low 4% success rate of identifying barley yellow dwarf virus (BYDV) resistant and susceptible translocation lines. However, 58% of the susceptible progeny of this irradiated seed contained a Thinopyrum intermedium chromosome-specific repetitive sequence, which indicated that γ-irradiation-induced translocations occurred at high rate. Restriction fragment length polymorphism (RFLP) analysis of susceptible lines containing alien chromatin, their resistant sister lines and other resistant lines showed that more than one third of the progeny of γ-irradiated double monosomic seeds contained wheatgrass-wheat translocations. Genomic in situ hybridization (GISH) analysis of selected lines confirmed that these were wheatgrass-wheat translocation lines. This approach of initially identifying BYDV susceptible deletion lines using an alien chromosome-specific repetitive sequence followed by RFLP analysis of their resistant sister lines efficiently identified resistant translocation lines and localized the BYDV resistance to the distal end of the introgressed Th. intermedium chromosome.Key words: gene introgression, wide crosses, chromosome, repetitive elements, RFLP, Thinopyrum intermedium.
Identification of DNA polymorphism in cultivated groundnut using random amplified polymorphic DNA (RAPD) assay
Authors: Subramanian V , Gurtu S , Rao R C Nageswara , Nigam S N
Published: April 2011

Construction of a genetic linkage map is necessary to apply marker-assisted selection tools in a crop improvement program. Except for the recent studies from two laboratories, most of the previous studies have shown little or no DNA polymorphism in cultivated groundnut (Arachis hypogaea L.). In the present study, 70 selected genotypes, representing variability for several morphological, physiological, and other characters, were studied for polymorphism employing random amplified polymorphic DNA (RAPD) assay with 48 oligonucleotide primers. Of the 48 oligonucleotide primers only 7 (14.6%) yielded polymorphic amplification products. The total number of bands from the 7 primers was 408, of which 27 were polymorphic. Detection of polymorphism in cultivated groundnut opens up the possibility of development of its molecular map by judicious selection of genotypes that show DNA polymorphism. This approach will be useful for developing marker-assisted selection tools for genetic enhancement of groundnut for desirable traits.Key words: Arachis hypogaea L., RAPD, DNA polymorphism, oligonucleotide, random primers.
Comparative analysis of microsatellite loci in chicken and turkey
Authors: Reed Kent M , Mendoza Kristelle M , Beattie Craig W
Published: April 2011

Cross-species amplification of 520 chicken microsatellite markers was tested by polymerase chain reaction with genomic DNA of the turkey (Meleagris gallopavo). Each primer pair was tested at six different combinations of annealing temperature and MgCl2concentration. A total of 280 (54%) of the primer pairs produced amplification products. The majority of these products were similar, if not identical in size to those expected based on the fragment sizes of the corresponding chicken loci. Structure of the dinucleotide repeat and flanking sequences was examined for 13 turkey fragments (amplified with chicken primers) and 5 chicken fragments (amplified with turkey primers). Sequence analysis found a wide array of mutations between species in addition to differences in repeat length. To estimate the usefulness of the amplified loci for genetic mapping in the turkey, allelic polymorphism was determined for 57 of the 280 amplified loci. A total of 20 of 57 markers (35%) were polymorphic with an average of 1.4 alleles per locus. The results of this study suggest that approximately 20% of the chicken microsatellite markers will be useful for mapping the turkey genome.Key words: microsatellite, chicken, turkey, Meleagris gallopavo.
Construction of a binary bacterial artificial chromosome library ofPetunia inflataand the isolation of large genomic fragments linked to the self-incompatibility (S-) locus
Authors: McCubbin Andrew G , Zuniga Carmen , Kao Teh-hui
Published: April 2011

The Solanaceae family of flowering plants possesses a type of self-incompatibility mechanism that enables the pistil to reject self pollen but accept non-self pollen for fertilization. The pistil function in this system has been shown to be controlled by a polymorphic gene at the S-locus, termed the S-RNase gene. The pollen function is believed to be controlled by another as yet unidentified polymorphic gene at the S-locus, termed the pollen S-gene. As a first step in using a functional genomic approach to identify the pollen S-gene, a genomic BAC (bacterial artificial chromosome) library of the S2S2genotype of Petunia inflata, a self-incompatible solanaceous species, was constructed using a Ti-plasmid based BAC vector, BIBAC2. The average insert size was 136.4 kb and the entire library represented a 7.5-fold genome coverage. Screening of the library using cDNAs for the S2-RNase gene and 13 pollen-expressed genes that are linked to the S-locus yielded 51 positive clones, with at least one positive clone for each gene. Collectively, at least 2 Mb of the chromosomal region was spanned by these clones. Together, three clones that contained the S2-RNase gene spanned ~263 kb. How this BAC library and the clones identified could be used to identify the pollen S-gene and to study other aspects of self-incompatibility is discussed.Key words: bacterial artificial chromosome, Petunia inflata, pollen-pistil interactions, self-incompatibility, S-locus.
Reverse transcriptase can stabilize or destabilize the genome
Authors: Haoudi Abdelali , Mason James M
Published: April 2011

Telomeres, the eukaryotic chromosome termini, are deoxyribonucleoprotein structures that distinguish natural chromosome ends from broken DNA. In most organisms, telomeres are extended by a reverse transcriptase (RT) with an integrated RNA template, telomerase; in Drosophila melanogaster, however, telomere-specific retrotransposons, HeT-A and TART, transpose specifically to chromosome ends. Whether telomeres are extended by a telomerase or by retrotransposons, an RT is a key component. RT has been studied extensively, both for its important role in converting RNA genomes to DNA, which has great evolutionary impact, and as a therapeutic target in human retroviral diseases. Here we discuss a few important aspects of RT usage during retrotransposition and telomere elongation.Key words: telomeres, telomerase, retrotransposons, reverse transcriptase.
Production and meiotic pairing behaviour of new hybrids of winter wheat (Triticum aestivum) × winter barley (Hordeum vulgare)
Authors: Molnár-Láng M , Linc G , Logojan A , Sutka J
Published: April 2011

New winter wheat (Triticum aestivum L.) × winter barley (Hordeum vulgare L.) hybrids produced using cultivated varieties (wheat 'Martonvásári 9 kr1'(Mv9 kr1) × barley 'Igri', Mv9 kr1 × 'Osnova', 'Asakazekomugi' × 'Manas') were multiplied in tissue culture because of the high degree of sterility and then pollinated with wheat to obtain backcross progenies. Meiotic analysis of the hybrids Mv9 kr1 × 'Igri' and 'Asakazekomugi' × 'Manas' and their in vitro regenerated progenies with the Feulgen method revealed 1.59 chromosome arm associations per cell in both initial hybrids. The number of chromosome arm associations increased after in vitro culture to 4.72 and 2.67, respectively, in the two combinations. According to the genomic in situ hybridization (GISH) analysis, wheat-barley chromosome arm associations made up 3.6% of the total in the initial Mv9 kr1 × 'Igri' hybrid and 6.6% and 16.5% of the total in in vitro regenerated progenies of the 'Asakazekomugi' × 'Manas' and Mv9 kr1 × 'Igri' hybrids, respectively. The demonstration by GISH of wheat-barley chromosome pairing in the hybrids and especially in their in vitro regenerated progenies proves the possibility of producing recombinants between these two genera, and thus of transferring useful characters from barley into wheat. In vitro conditions caused an increase in chromosome arm association frequency in both combinations and in fertility in some regenerants.Key words: wheat, barley, intergeneric hybridization, meiotic chromosome pairing, GISH.
Inheritance of microsatellite loci in the polyploid lake sturgeon (Acipenser fulvescens)
Authors: Pyatskowit Jonathan D , Krueger Charles C , Kincaid Harold L , May Bernie
Published: April 2011

Inheritance in the expression of amplicons for four microsatellite primer pairs was determined using 10 families created from gametes of wild lake sturgeon (Acipenser fulvescens). Loci Afu34 and Afu68 expressed a maximum of two even-intensity bands per individual and had progeny genotype ratios that fit disomic inheritance (P > 0.05). Some variation exhibited at Afu34 and Afu68 was attributable to a null allele. Genotype expression at both loci also indicated that one female parent had transmitted unreduced gametes. Primer Afu39 amplified products that exhibited four gene doses, where genotype counts fit expected ratios for disomic inheritance (P > 0.05) indicating amplification of products from two disomic loci that share alleles. Meiotic drive was evident at the Afu39 loci based on a test for random segregation (P < 0.05). Only the expression of Afu19 gave evidence of tetrasomic inheritance based on a single progeny potentially produced by a double reduction gamete. No evidence for proposed octoploid inheritance was observed.Key words: diploid, tetraploid, octoploid, meiotic drive.
Maternal inheritance of plastids in Encephalartos Lehm. (Zamiaceae, Cycadales)
Authors: Cafasso D , Cozzolino S , Caputo P , Luca P De
Published: April 2011

The mode of inheritance of chloroplast DNA has been determined in Encephalartos by employing a restriction fragment length polymorphism analysis of chloroplast DNA. Artificial F1 hybrids were produced between a female specimen of E. natalensis and a male specimen of E. woodii. The hybridization patterns of all hybrids correspond, in all cases, with that of E. natalensis, and are different from that of E. woodii, thus indicating the maternal inheritance of cpDNA in cycads.Key words: chloroplast DNA, maternal inheritance, restriction fragment length polymorphism (RFLP), cycads, Encephalartos.
5S ribosomal and U1 small nuclear RNA genes: A new linkage type in the genome of a crustacean that has three different tandemly repeated units containing 5S ribosomal DNA sequences
Authors: Pelliccia Franca , Barzotti Rita , Bucciarelli Elisabetta , Rocchi Angela
Published: April 2011

We investigated the 5S ribosomal RNA (rRNA) genes of the isopod crustacean Asellus aquaticus. Using PCR amplification, three different tandemly repeated units containing 5S rDNA were identified. Two of the three sequences were cloned and sequenced. One of them was 1842 bp and presented a 5S rRNA gene and a U1 small nuclear RNA (snRNA) gene. This type of linkage had never been observed before. The other repeat consisted of 477 bp and contained only an incomplete 5S rRNA gene lacking the first eight nucleotides and a spacer sequence. The third sequence was 6553 bp long and contained a 5S rRNA gene and the four core histone genes. The PCR products were used as probes in fluorescent in situ hybridization (FISH) experiments to locate them on chromosomes of A. aquaticus. The possible evolutionary origin of the three repeated units is discussed.Key words: Asellus, isopoda, crustacea, 5S rDNA, U1 snDNA.
Relationship of hepatocyte ploidy levels with body size and growth rate in mammals
Authors: Vinogradov A E , Anatskaya O V , Kudryavtsev B N
Published: April 2011

To elucidate possible causes of the elevation of genome number in somatic cells, hepatocyte ploidy levels were measured cytofluorimetrically and related to the organismal parameters (body size, postnatal growth rate, and postnatal development type) in 53 mammalian species. Metabolic scope (ratio of maximal metabolic rate to basal metabolic rate) was also included in 23 species. Body masses ranged 105 times, and growth rate more than 30 times. Postnatal growth rate was found to have the strongest effect on the hepatocyte ploidy. At a fixed body mass the growth rate closely correlates (partial correlation analysis) with the cell ploidy level (r = 0.85, P < 106), whereas at a fixed growth rate body mass correlates poorly with ploidy level (r = 0.38, P < 0.01). The mature young (precocial mammals) of the species have, on average, a higher cell ploidy level than the immature-born (altricial) animals. However, the relationship between precocity of young and cell ploidy levels disappears when the influences of growth rate and body mass are removed. Interspecies variability of the hepatocyte ploidy levels may be explained by different levels of competition between the processes of proliferation and differentiation in cells. In turn, the animal differences in the levels of this competition are due to differences in growth rate. A high negative correlation between the hepatocyte ploidy level and the metabolic scope indicates a low safety margin of organs with a high number of polyploid cells. This fact allows us to challenge a common opinion that increasing ploidy enhances the functional capability of cells or is necessary for cell differentiation. Somatic polyploidy can be considered a "cheap" solution of growth problems that appear when an organ is working at the limit of its capabilities.Key words: genome number, somatic polyploidy, nuclear ploidy, multinuclearity, metabolic scope.
The specific isolation of complete 5S rDNA units from chromosome 1A of hexaploid, tetraploid, and diploid wheat species using PCR with head-to-head oriented primers
Authors: Campenhout S Van , Stappen J Vander , Volckaert G
Published: April 2011

The presence of 5S rDNA units on chromosome 1A of Triticum aestivum was shown by the development of a specific PCR test, using head-to-head oriented primers. This primer set allowed the amplification of complete 5S DNA units and was used to isolate 5S-Rrna-A1 sequences from polyploid and diploid wheat species. Multiple-alignment and parsimony analyses of the 132 sequences divided the sequences into four types. The isolates from T. aestivum and the tetraploid species (T. dicoccoides, T. dicoccum, T. durum, T. araraticum, and T. timopheevi) were all of one type, which was shown to be closely related to the type mainly characteristic for T. urartu. The other two types were isolated exclusively from the diploid species T. monococcum, T. aegilopoides, T. thaoudar, and T. sinskajae and the hexaploid species T. zhukovski. Triticum monococcum was the only species for which representatives of each of the four sequence types were found to be present. Further, we discuss the possible multicluster arrangement of the 5S-Rrna-A1 array.Key words: Triticum, A genome, PCR markers, 5S ribosomal RNA locus.
Genome analysis ofElytrigia pycnanthaandThinopyrum junceiformeand of their putative natural hybrid using the GISH technique
Authors: Refoufi Aïcha , Jahier Joseph , Esnault Marie-Andrée
Published: April 2011

Genomic in situ hybridization (GISH), using genomic DNA probes from Thinopyrum elongatum (Host) D.R. Dewey (E genome, 2n = 14), Th. bessarabicum (Savul. & Rayss) A. Löve (J genome, 2n = 14), Pseudoroegneria stipifolia (Czern. ex Nevski) Löve (S genome, 2n = 14), and Agropyron cristatum (L.) Gaertner (P genome, 2n = 14), was used to characterize the genome constitution of the polyploid species Elytrigia pycnantha (2n = 6x = 42) and Thinopyrum junceiforme (2n = 4x = 28) and of one hybrid population (2n = 5x = 35). GISH results indicated that E. pycnantha contains S, E, and P genomes; the first of these was closely related to the S genome of Ps. stipifolia, the second was closely related to to the E genome of Th. elongatum, and the third was specifically related to A. cristatum. The E and P genomes included 2 and 10 chromosomes, respectively, with S genome DNA sequences in the centromeric region. GISH analysis of Th. junceiforme showed the presence of two sets of the E genome, except for fewer than 10 chromosomes for which the telomeric regions were not identified. Based on these results, the genome formula SSPSPSESESis proposed for E. pycnantha and that of EEEE is proposed for Th. junceiforme. The genomic constitution of the pentaploid hybrid comprised one S genome (seven chromosomes), one P genome (seven chromosomes), and three E genomes (21 chromosomes). The E and P genomes both included mosaic chromosomes (chromosomes 1 and 5, respectively) with the centromere region closely related to S-genome DNA. On the basis of these data, the genome formula SPSESEE is suggested for this hybrid and it is also suggested that the two species E. pycnantha and Th. junceiforme are the parents of the pentaploid hybrid.Key words: GISH, Elytrigia pycnantha, Thinopyrum junceiforme, pentaploid hybrid, P genome.
Soybean genomic survey: BAC-end sequences near RFLP and SSR markers
Authors: Marek Laura Fredrick , Mudge Joann , Darnielle Laura , Grant David , Hanson Nadja , Paz Margie , Huihuang Yan , Denny Roxanne , Larson Karin , Foster-Hartnett Dawn , Cooper Anne , Danesh Dariush , Larsen Dana , Schmidt Tina , Staggs Rod , Crow John A , Retzel Ernest , Young Nevin D , Shoemaker Randy C
Published: April 2011

We are building a framework physical infrastructure across the soybean genome by using SSR (simple sequence repeat) and RFLP (restriction fragment length polymorphism) markers to identify BACs (bacterial artificial chromosomes) from two soybean BAC libraries. The libraries were prepared from two genotypes, each digested with a different restriction enzyme. The BACs identified by each marker were grouped into contigs. We have obtained BAC-end sequence from BACs within each contig. The sequences were analyzed by the University of Minnesota Center for Computational Genomics and Bioinformatics using BLAST algorithms to search nucleotide and protein databases. The SSR-identified BACs had a higher percentage of significant BLAST hits than did the RFLP-identified BACs. This difference was due to a higher percentage of hits to repetitive-type sequences for the SSR-identified BACs that was offset in part, however, by a somewhat larger proportion of RFLP-identified significant hits with similarity to experimentally defined genes and soybean ESTs (expressed sequence tags). These genes represented a wide range of metabolic functions. In these analyses, only repetitive sequences from SSR-identified contigs appeared to be clustered. The BAC-end sequences also allowed us to identify microsynteny between soybean and the model plants Arabidopsis thaliana and Medicago truncatula. This map-based approach to genome sampling provides a means of assaying soybean genome structure and organization.Key words: Glycine max, sequencing, physical map, contig.
Molecular and cytogenetic analysis of repetitive DNA in pea (Pisum sativumL.)
Authors: Neumann Pavel , Nouzová Marcela , Macas Jirí
Published: April 2011

A set of pea DNA sequences representing the most abundant genomic repeats was obtained by combining several approaches. Dispersed repeats were isolated by screening a short-insert genomic library using genomic DNA as a probe. Thirty-two clones ranging from 149 to 2961 bp in size and from 1000 to 39 000/1C in their copy number were sequenced and further characterized. Fourteen clones were identified as retrotransposon-like sequences, based on their homologies to known elements. Fluorescence in situ hybridization using clones of reverse transcriptase and integrase coding sequences as probes revealed that corresponding retroelements were scattered along all pea chromosomes. Two novel families of tandem repeats, named PisTR-A and PisTR-B, were isolated by screening a genomic DNA library with Cot-1 DNA and by employing genomic self-priming PCR, respectively. PisTR-A repeats are 211212 bp long, their abundance is 2 × 104copies/1C, and they are partially clustered in a secondary constriction of one chromosome pair with the rest of their copies dispersed on all chromosomes. PisTR-B sequences are of similar abundance (104copies/1C) but differ from the "A" family in their monomer length (50 bp), high A/T content, and chromosomal localization in a limited number of discrete bands. These bands are located mainly in (sub)telomeric and pericentromeric regions, and their patterns, together with chromosome morphology, allow discrimination of all chromosome types within the pea karyotype. Whereas both tandem repeat families are mostly specific to the genus Pisum, many of the dispersed repeats were detected in other legume species, mainly those in the genus Vicia.Key words: repetitive DNA, plant genome, retroelements, satellite DNA, Pisum sativum.
Contrasting genome organisation: two regions of theBrassica oleraceagenome compared with collinear regions of theArabidopsisthalianagenome
Authors: Ryder C D , Smith L B , Teakle G R , King G J
Published: April 2011

Brassica crop species are of worldwide importance and are closely related to the model plant Arabidopsis thaliana for which the complete genome sequence has recently been established. We investigated collinearity of marker order by comparing two contrasting regions of the Brassica oleracea genome with homologous regions of A. thaliana. Although there is widespread replication of marker loci in both A. thaliana and B. oleracea, we found that a combination of genetic markers mapped in B. oleracea, including RFLPs, CAPS, and SSRs allowed comparison and interpretation of medium-scale chromosomal organisation and rearrangements. The interpretation of data was facilitated by hybridising probes onto the whole A. thaliana genome, as represented by BAC contigs. Twenty marker loci were sampled from the whole length of the shortest B. oleracea linkage group, O6, and 21 from a 30.4-cM section of the longest linkage group, O3. There is evidence of locus duplication on linkage group O6. Locus order is well conserved between a putative duplicated region of 10.5 cM and a discrete region comprising 25 cM of A. thaliana chromosome I. This was supported by evidence from seven paralogous loci, three of which were duplicated in a 30.6-cM region of linkage group O6. The pattern of locus order for the remainder of linkage group O6 and the sampled section of linkage group O3 was more complex when compared with the A. thaliana genome. Although there was some conservation of locus order between markers on linkage group O3 and approximately 9 cM of A. thaliana chromosome I, this was superimposed upon a complex pattern of additional loci that were replicated in both A. thaliana and B. oleracea. The results are discussed in the context of the ability to use collinear information to assist map-based cloning.Key words: comparative mapping, BAC, physical contig, MADS box.
Construction and characterization of a BAC library for the molecular dissection of a single wild beet centromere and sugar beet (Beta vulgaris) genome analysis
Authors: Gindullis Frank , Dechyeva Daryna , Schmidt Thomas
Published: April 2011

We have constructed a sugar beet bacterial artificial chromosome (BAC) library of the chromosome mutant PRO1. This Beta vulgaris mutant carries a single chromosome fragment of 6-9 Mbp that is derived from the wild beet Beta procumbens and is transmitted efficiently in meiosis and mitosis. The library consists of 50 304 clones, with an average insert size of 125 kb. Filter hybridizations revealed that approximately 3.1% of the clones contain mitochondrial or chloroplast DNA. Based on a haploid genome size of 758 Mbp, the library represents eight genome equivalents. Thus, there is a greater than 99.96% probability that any sequence of the PRO1 genome can be found in the library. Approximately 0.2% of the clones hybridized with centromeric sequences of the PRO1 minichromosome. Using the identified BAC clones in fluorescence in situ hybridization experiments with PRO1 and B. procumbens chromosome spreads, their wild-beet origin and centromeric localization were demonstrated. Comparative Southern hybridization of pulsed-field separated PRO1 DNA and BAC inserts indicate that the centromeric region of the minichromosome is represented by overlapping clones in the library. Therefore, the PRO1 BAC library provides a useful tool for the characterization of a single plant centromere and is a valuable resource for sugar beet genome analysis.Key words: Beta vulgaris, BAC library, Beta procumbens minichromosome, centromere, FISH.
TheDrosophilaaeroplanemutant is caused by an I-element insertion into a tissue-specificteashirtenhancer motif
Authors: Soanes Kelly H , Bell John B
Published: April 2011

In Drosophila melanogaster, aeroplane (ae) is a regulatory allele of teashirt (tsh), and the mutant wing posture phenotype of homozygous ae flies is caused by a defect in the hinge region of the wing, whereby the base of the wing at the proximal ventral radius is fused to the thorax in the region of the pleural wing process. The apparent paralysis of the wings and the drooping halteres are caused by an I-element insertion into a 3' noncoding sequence of tsh. The cis-acting regulatory element interrupted by the I element is required, to drive tsh expression in the regions of the developing adult that give rise to proximal wing and haltere tissues. Loss of this expression results in the fusion of the proximal structures of the wing and halteres to the thoracic cuticle. Further characterization of this tsh regulatory motif has now identified an additional enhancer activity directing tsh expression in tissues forming portions of the midgut. Subdivision of this midgut enhancer activity has identified putative negatively acting motifs.Key words: Drosophila melanogaster, enhancer, development, wing posture, I element, teashirt, wing hinge, tissue-specificity.
Maternal inheritance of the chloroplast genome inEucalyptus globulusand interspecific hybrids
Authors: McKinnon Gay E , Vaillancourt René E , Tilyard Paul A , Potts Brad M
Published: April 2011

The utility of chloroplast DNA (cpDNA) in Eucalyptus, either as a molecular marker for genetic studies or as a potential vehicle for genetic manipulation, is based on knowledge of its mode of inheritance. Chloroplast inheritance in angiosperms can vary among and within species, and anomalous inheritance has been reported in some interspecific-hybrid combinations. In Eucalyptus, abnormalities of pollen-tube growth occur in a number of interspecific-hybrid combinations, and this might increase the likelihood of anomalous chloroplast transmission. We used a rapid PCR technique to determine chloroplast heritability in 425 progeny of Eucalyptus, comprising 194 progeny of the premier pulpwood species E. globulus and 231 interspecific hybrids between E. globulus and E. nitens (F1, F2, and backcrosses). At this sampling intensity, no pollen-mediated transmission of cpDNA was found in any of the 40 families tested. The results are discussed with reference to chloroplast engineering and the use of cpDNA as a seed-specific marker in phylogeographic studies of Eucalyptus.Key words: organelle, plastids, uniparental, maternal inheritance, interspecific hybrids.
Genetic diversity in Bambara groundnut (Vigna subterranea L.) germplasm revealed by RAPD markers
Authors: Amadou H I , Bebeli P J , Kaltsikes P J
Published: April 2011

Random amplified polymorphic DNA (RAPD) markers were used to assess genetic diversity in Bambara groundnut (Vigna subterranea L.) germplasm using 25 African accessions from the collection in the International Institute for Tropical Agriculture, Ibadan, Nigeria. Fifty random decamer primers were screened to assess their ability to detect polymorphism in bambara; 17 of them were selected for this study. Considerable genetic diversity was found among the V. subterranea accessions studied. The relationships among the 25 accessions were studied by cluster analysis. The dendrograms showed two main groups of accessions mainly along the lines of their geographic origin. It is concluded that RAPD can be used for germplasm classification in bambara groundnut and hence for improving this crop.Key words: germplasm, PCR, RAPD, Vigna subterranea.
Synaptonemal complex analysis in spermatocytes and oocytes of turbot, Scophthalmus maximus (Pisces, Scophthalmidae)
Authors: Cuñado N , Terrones J , Sánchez L , Martínez P , Santos J L
Published: April 2011

A surface-spreading synaptonemal complex (SC) technique was used to analyze spermatocytes and oocytes of turbot (Scophthalmus maximus) to visualize the process of chromosome synapsis. The total SC length was 205 ± 12 µm in males and 172 ± 29 µm in the only female analyzed. A representative SC karyotype of turbot was obtained. Each SC showed lateral elements of equal length. No bivalent exhibiting atypical synaptic behaviour that could be associated with heteromorphic sex chromosomes was observed, either in males or in the female. The DNA content of turbot was evaluated in eight individuals of both sexes by flow cytometry analysis. The 2C mean DNA content of turbot (1.308 ± 0.009 pg/cell) was among the lowest observed within fishes. No statistical differences in DNA content were revealed between the sexes [Wilcoxon/MannWhitney test; P(Wx = 0.243)]. The SC/DNA content ratio observed in turbot was the highest reported to date in bony fishes (Osteichthyes).Key words: Scophthalmus maximus, fish, DNA content, meiosis, synaptonemal complex.
A bacterial artificial chromosome (BAC) library ofMalus floribunda821 and contig construction for positional cloning of the apple scab resistance geneVf
Authors: Xu Mingliang , Song Junqi , Cheng Zhukuan , Jiang Jiming , Korban Schuyler S
Published: April 2011

The apple scab resistance gene Vf, originating from the wild species Malus floribunda 821, has been incorporated into a wide variety of apple cultivars through a classical breeding program. With the aim of isolating the Vf gene, a bacterial artificial chromosome (BAC) library consisting of 31 584 clones has been constructed from M. floribunda 821. From the analysis of 88 randomly selected BAC clones, the average insert size is estimated at 125 kb. If it is assumed that the genome size of M. floribunda 821 is 769 Mb/haploid, the library represents about 5× haploid genome equivalents. This provides a 99% probability of finding any specific sequence from this library. PCR-based screening of the library has been carried out using eight random genomic sequence-characterized amplified regions (SCARs), chloroplast- and mitochondria-specific SCARs, and 13 high-density Vf-linked SCAR markers. An average of five positive BAC clones per random SCAR has been obtained, whereas less than 1% of BAC clones are derived from the chloroplast or mitochondrial genomes. Most BAC clones identified with Vf-linked SCAR markers are physically linked. Three BAC contigs along the Vf region have been obtained by assembling physically linked BAC clones based on their fingerprints. The overlapping relatedness of BAC clones has been further confirmed by cytogenetic mapping using fiber fluorescence in situ hybridization (fiber-FISH). The M. floribunda 821 BAC library provides a valuable genetic resource not only for map-based cloning of the Vf gene, but also for finding many other important genes for improving the cultivated apple.Key words: apple, resistance Vf gene, BAC library, sequence-characterized amplified regions (SCARs), fiber fluorescence in situ hybridization (fiber-FISH), positional cloning.
Isolation by improved thermal asymmetric interlaced PCR and characterization of a seed-specific 2S albumin gene and its promoter from grape (Vitis vinifera L.)
Authors: Li Zhijian T , Gray D J
Published: April 2011

A seed-specific 2S albumin gene and its promoter region of grape (Vitis vinifera L.) were isolated using an improved thermal asymmetric interlaced PCR that allowed efficient amplification of target sequence of up to 3 kbp in length directly from genomic DNA. The 2S albumin VvAlb1 (for V. vinifera 2S albumin 1) gene from different grape cultivars encompasses a coding region of 504-540 nucleotides corresponding to a deduced amino acid sequence of 167-179 residues. This deduced protein contains up to 30% glutamine residues and eight cysteine residues arranged in a pattern highly conserved among 2S albumins for disulfide bond formation. DNA sequence alignment revealed that the same VvAlb1 gene among different grape cultivars varied greatly, including an insertion of up to 36 bp near the 3' end of the gene sequence isolated from 'Thompson Seedless'. DNA sequence analysis indicated that several conserved seed-specific regulatory motifs were clustered within a 0.6-kbp region 5' upstream of the transcription start site. To further test promoter activity, the sequence of this region was used to drive a bifunctional EGFP/NPTII fusion gene in Agrobacterium-mediated transformation of grape somatic embryos and leaf discs of grape and tobacco (Nicotiana tabacum L.). A high level of GFP expression, comparable with that derived from an enhanced double CsVMV promoter, was observed in the cotyledonary but not hypocotyl and vegetative tissues of grape and tobacco. These results suggest that the VvAlb1 gene promoter isolated is capable of conferring seed-specific gene expression.Key words: grape, Vitis vinifera, genomic DNA, gene isolation, promoter, seed-specific expression.
Molecular mapping of the chlorophyll retainer (cl) mutation in pepper (Capsicum spp.) and screening for candidate genes using tomato ESTs homologous to structural genes of the chlorophyll catabolism pathway
Authors: Efrati Ari , Eyal Yoram , Paran Ilan
Published: April 2011

The chlorophyll retainer (cl) mutation causes inhibition of chlorophyll degradation during pepper fruit ripening and is controlled by a single recessive gene. The retention of chlorophyll in mature red or yellow fruits produces brown- or green-colored ripe fruits, respectively. We mapped CL on chromosome 1 of pepper corresponding to chromosome 8 in tomato in which a homologous mutation, green flesh, was previously assigned. To test whether known structural genes from the chlorophyll catabolism pathway could correspond to CL, we mapped tomato expressed sequence tag clones corresponding to three loci of CHLOROPHYLLASE and one locus of PHEOPHORBIDE A OXYGENASE in the tomato introgression lines population. The three CHLOROPHYLLASE loci mapped to chromosomes 6, 9, and 12, while PHEOPHORBIDE A OXYGENASE mapped to chromosome 11, indicating that CL may correspond to an as yet unavailable gene from the chlorophyll catabolism pathway or to a regulator of the pathway.Key words: fruit color, pepper, tomato, molecular mapping, chlorophyll catabolism.