bluuebunny/crossref_metadata_2025 huggingface dataset:
A spatial dynamic multistock production model
Authors: Ault Jerald S , Luo Jiangang , Smith Steven G , Serafy Joseph E , Wang John D , Humston Robert , Diaz Guillermo A
Published: April 2011

We developed a generalized spatial dynamic age-structured multistock production model by linking bioenergetic principles of physiology, population ecology, and community trophodynamics to a two-dimensional finite-element hydrodynamic circulation model. Animal movement is based on a search of an environmental-habitat feature vector that maximizes cohort production dynamics. We implemented a numerical version of the model and used scientific data visualization to display real-time results. As a proxy for larger regional-scale dynamics, we applied the model to study the space-time behavior of recruitment and predator-prey production dynamics for cohorts of spotted seatrout (Cynoscion nebulosus) and pink shrimp (Penaeus duorarum) in the tropical waters of Biscayne Bay, Florida.
Space, time, and scale: new perspectives in fish ecology and management
Authors: Mason Doran M , Brandt Stephen B
Published: April 2011

This supplement is the product of a special symposium organized on "Space, time, and scale: new perspectives in fish ecology and management" held during the 127th annual meeting of the American Fisheries Society in Monterey, California, August 1997. The purpose of this supplement is to illustrate the breadth and diversity of ideas and applications being explored for integrating space, time, and scaling issues and to highlight future directions. Topics cover a variety of studies, techniques, and applications from salt water to freshwater, from lotic to lentic habitats, and across various scales that can be used as background for integrating space, time, and scale in ongoing and future fish research and management.
Phytoplankton assemblages in the St. Lawrence River, downstream of its confluence with the Ottawa River, Quebec, Canada
Authors: Hudon Christiane
Published: April 2011

Consistent differences in physical, chemical, and biological characteristics were observed along a transversal river section located 2 km downstream of the confluence of the Ottawa and the St. Lawrence rivers. Phytoplankton sampled at stations subject to the influence of the St. Lawrence River had a lower biomass, smaller cell volume, lower chlorophyll a, and lower taxa richness than did phytoplankton at stations influenced by the Ottawa River. The stations influenced by St. Lawrence River waters showed regular seasonal changes in phytoplankton biomass and composition, reflecting the major impact of the stratification and mixing cycles observed in the Great Lakes. By comparison, at the stations influenced by Ottawa River waters, monthly variations were found in biomass and composition correlated with temperature and water clarity, suggesting the effects of the watershed's morphology. A discharge reduction of 12% in the St. Lawrence River and 46% in the Ottawa River between summer 1994 and summer 1995 coincided, for stations in both water masses, with lower biomass and greater species richness and an increase in taxa that generate noxious smells and odours. Phytoplankton is recommended for use in monitoring the biological impacts of changes in water characteristics resulting from human activities and climate change in the Great Lakes watershed.
Experimental demonstration of differences in sheltering behaviour between Icelandic populations of Atlantic salmon (Salmo salar) and Arctic char (Salvelinus alpinus)
Authors: Valdimarsson Sveinn K , Metcalfe Neil B , Skúlason Skúli
Published: April 2011

Most salmonids, as well as many other freshwater fish species in the Northern Hemisphere, have been reported to show some form of daytime sheltering behaviour over the winter. Previous work has shown that temperatures around 6-8°C trigger the onset of this sheltering behaviour. However, fish from colder environments would be expected to respond differently to temperature than fish from warmer environments. The incidence of sheltering at different temperatures between two Icelandic populations of both juvenile Atlantic salmon (Salmo salar) and juvenile Arctic char (Salvelinus alpinus) was examined by quantifying the use of refuges in identical controlled laboratory conditions. The results showed clear differences in the sheltering response between the different populations. Salmon from a warm, productive stream and riverine char emerged more by day from their shelter at low temperatures (5-8°C) than did either salmon from a cold, unproductive stream or char from a landlocked lake population. These population differences indicate local adaptations that must be kept in mind when managing fish populations; moreover, the differences do not appear to be predictable on the basis of ambient thermal regimes.
Trends in wild adult steelhead (Oncorhynchus mykiss) abundance in British Columbia as indexed by angler success
Authors: Smith Barry D , Ward Bruce R , Welch David W
Published: April 2011

Intraregional similarities and interregional differences in wild steelhead (Oncorhynchus mykiss) abundance trends over time throughout British Columbia were identified using catch-per-angler-day (CpAD) as an index of abundance. This index was calculated using sport angler catch and effort data obtained by an ongoing mail-out questionnaire begun in the fiscal year 1967-1968. Despite high interannual variability in CpAD for individual rivers, its validity as an index of trends over time in wild steelhead abundance for geographic regions or watersheds is reinforced by similar trends yielded by both fishery-dependent and fishery-independent data. Time series methods generally could not build statistical support for the hypotheses that sudden regulation changes, or the gradual introduction over time of a catch and release philosophy, are generally important factors affecting trends over time in CpAD. This bolsters our confidence that the general patterns in mean CpAD over time within regions and watersheds reasonably index actual wild adult in-river steelhead abundance. We propose that the trends that we observe in wild steelhead CpAD are primarily driven by environmental influences. Some candidate environmental time series currently being considered and investigated are coastal upwelling, various ocean and atmospheric climate indices, freshwater discharge histories, and ultraviolet radiation.
Photoinhibition of natural phytoplankton assemblages in Lake Erie exposed to solar ultraviolet radiation
Authors: Marwood Christopher A , Smith Ralph EH , Furgal John A , Charlton Murray N , Solomon Keith R , Greenberg Bruce M
Published: April 2011

Photoinhibition was examined in natural assemblages of phytoplankton from Lake Erie exposed to ambient solar radiation. The impacts on photosynthesis of photosynthetically active radiation (400-700 nm) (PAR), ultraviolet-A radiation (320-400 nm) (UVA), and ultraviolet-B radiation (295-320 nm) (UVB) were assessed at three sites on the lake using pulse amplitude modulated chlorophyll fluorescence. Short exposures (<= 30 min) to sunlight containing UVB (1.8-4.4 mmol·m-2) resulted in the rapid loss of up to 60% of photosystem II efficiency (in the dark-adapted state) (Fv/Fm) and quantum yield (in the light-adapted state) (ΔF/F'm). Exposure to UVA (46-105 mmol·m-2) generally diminished Fv/Fm and, to a lesser extent, ΔF/F'm. Short exposures to PAR (733-1588 mmol·m-2) had no significant effects on electron transport. Recovery from UVA- or UVB-induced photoinhibition was complete for Fv/Fm and 90% complete for ΔF/F'm after 2 h in low light. The results indicate that exposures of phytoplankton to surface radiation need only be short in duration to cause substantial UV inhibition of photosynthesis. However, depending on the kinetics of mixing of the water column, recovery of photosynthesis is possible if there is sufficient time for repair of UV damage. Future elevated levels of solar UVB due to ozone depletion could significantly inhibit primary production in mesotrophic lakes such as Lake Erie.
Estimation of juvenile survival, adult survival, and age-specific pupping probabilities for the female grey seal (Halichoerus gryprus) on Sable Island from capture-recapture data
Authors: Schwarz Carl J , Stobo Wayne T
Published: April 2011

We use a longitudinal capture-recapture study from resightings of grey seals (Halichoerus gryprus) branded as young on Sable Island to estimate (i) the juvenile survival rate from the time of branding to age 4, (ii) the yearly adult survival rate from age 4 to age 9, and (iii) the age-specific pupping probabilities, i.e., the probability that a seal will first give birth at each age. The estimated juvenile survival rate from branding (just after weaning) to age 4 ranged from 70 to 80%; however, the lower values are known to be biased low because the study was terminated early. The estimated yearly adult survival rates for ages 4-9 ranged from 0.88 to 0.92·year-1. The estimated probabilities of first giving birth to a young seal (pupping) at ages 4-9 are 0.28, 0.41, 0.18, 0.06, 0.05, and 0.02, respectively, and the estimated average age of first pupping is 5.2 years.
Effect of introduced piscivores on native minnow communities in Adirondack lakes
Authors: Findlay C Scott , Bert Daniel G , Zheng Ligang
Published: April 2011

We compared the minnow assemblages of Adirondack lakes with top piscivores with those of lakes having similar physiochemical and biotic characteristics but no top piscivores using a subset of data collected from 1984 to 87 by the Adirondack Lake Survey Corporation. Native minnow richness in lakes with top piscivores was about one third that of lakes without piscivores, with piscivore assemblages dominated by introduced species such as northern pike (Esox lucius), largemouth bass (Micropterus salmoides), and smallmouth bass (Micropterus dolomieu). There was strong evidence that at least four minnow species, including creek chub (Semotilus atromaculatus), northern redbelly dace (Phoxinus eos), blacknose dace (Rhinichthys atratulus), and common shiner (Luxilus cornutus), were less likely to occur in lakes with piscivores; for a fifth species (pearl dace (Margariscus margarita)), the evidence is suggestive but not as strong. Of 13 minnow species, only for two nonnative species (bluntnose minnow (Pimephales notatus) and golden shiner (Notemigonus crysoleucas)) was there strong evidence that their occurrence was unaffected by the presence of introduced piscivores. These results add to the growing body of evidence that the introduction of top piscivores to small temperate lakes puts native minnow communities at high extinction risk.
Reference points for coho salmon (Oncorhynchus kisutch) harvest rates and escapement goals based on freshwater production
Authors: Bradford Michael J , Myers Ransom A , Irvine James R
Published: April 2011

We describe a simple scheme for the management of coho salmon (Oncorhynchus kisutch) population aggregates that uses reference points derived from an empirical analysis of freshwater production data. We fit a rectilinear "hockey stick" model to 14 historical data sets of female spawner abundance and resulting smolt production and found that at low spawner abundance, the average productivity was about 85 smolts per female spawner. Variation in productivity among streams may be related to the quality of the stream habitat. We show how freshwater productivity can be combined with forecasts of marine survival to provide a limit reference point harvest rate. Our method will permit harvest rates to track changes in ocean productivity. We also used the historical data to estimate that, on average, a density of 19 female spawners·km-1 is required to fully seed freshwater habitats with juveniles. However, there was considerable variation among the streams that might limit the utility of this measure as a reference point. Uncertainty in the forecasts of marine survival and other parameters needs to be incorporated into our scheme before it can be considered a precautionary approach.
Land use, fishing, climate change, and the decline of Thompson River, British Columbia, coho salmon
Authors: Bradford Michael J , Irvine James R
Published: April 2011

We investigated a recent, major decline in the abundance of a large aggregate of coho salmon (Oncorhynchus kisutch) spawning in the Thompson River, British Columbia, watershed. We found that the decline could be attributed to a declining trend in productivity likely related to changing ocean conditions, overfishing, and freshwater habitat alteration. Among individual watersheds, rates of decline in adult coho salmon abundance were correlated with agricultural land use, road density, and a qualitative measure of stream habitat status but not with the proportion of land recently logged. The recovery of these populations will require the prudent regulation of fishing, the restoration of salmon producing watersheds, and an improvement in ocean conditions.
Cloning and characterization of an extremely conserved satellite DNA family from the root-knot nematode Meloidogyne arenaria
Authors: Castagnone-Sereno Philippe , Leroy Frédéric , Abad Pierre
Published: April 2011

A new satellite DNA family, named pMaE, has been cloned from the genome of the phytoparasitic nematode, Meloidogyne arenaria (Nematoda: Tylenchida). It is represented as tandemly repeated sequences with a monomeric unit of 172 bp. The monomers are present at approximately 15 700 copies per haploid genome, and represent about 5.3% of the total genomic DNA. Twenty-seven independent monomers have been cloned and sequenced. The deduced consensus sequence is 70.9% A + T rich, with frequent stretches of A and (or) T. Several direct or inverted sub-repeats are present in the sequence, which may allow the formation of a dyad structure, suggesting some potential role of this repetitive sequence in heterochromatin condensation. The monomers are very homogeneous in sequence, showing on average 1.8% divergence from their consensus sequence. Moreover, Southern blot experiments and sequence analysis of homologous monomers from the genome of geographically distinct M. arenaria populations have shown that this satellite DNA is uniformly distributed and highly conserved within the species. Therefore, it is hypothesized that this unusually low level of variability, either within the genome of a given population or between populations, could be achieved as the result of some highly effective homogenization mechanism acting upon the nematode genome.

Key words: genomic organization, Meloidogyne arenaria, satellite DNA.
Arabidopsis thaliana: A source of candidate disease-resistance genes forBrassica napus
Authors: Sillito D , Parkin I AP , Mayerhofer R , Lydiate D J , Good A G
Published: April 2011

Common structural and amino acid motifs among cloned plant disease-resistance genes (R genes), have made it possible to identify putative disease-resistance sequences based on DNA sequence identity. Mapping of such R-gene homologues will identify candidate disease-resistance loci to expedite map-based cloning strategies in complex crop genomes. Arabidopsis thaliana expressed sequence tags (ESTs) with homology to cloned plant R genes (R-ESTs), were mapped in both A. thaliana and Brassica napus to identify candidate R-gene loci and investigate intergenomic collinearity. Brassica R-gene homologous sequences were also mapped in B. napus. In total, 103 R-EST loci and 36 Brassica R-gene homologous loci were positioned on the N-fo-61-9 B. napus genetic map, and 48 R-EST loci positioned on the Columbia × Landsberg A. thaliana map. The mapped loci identified collinear regions between Arabidopsis and Brassica which had been observed in previous comparative mapping studies; the detection of syntenic genomic regions indicated that there was no apparent rapid divergence of the identified genomic regions housing the R-EST loci.Key words: RFLP mapping, candidate R genes, R-gene homologues, genomic collinearity, Arabidopsis ESTs.
A matrix attachment region is located upstream from the high-molecular-weight glutenin gene Bx7 in wheat (Triticum aestivum L.)
Authors: Rampitsch C , Jordan M C , Cloutier S
Published: April 2011

A 2.2-kb nucleotide sequence rich in AT, located upstream from the Bx7 allele of the high-molecular-weight glutenin Glu-B1 locus in wheat (Triticum aestivum cv. Glenlea) was cloned following amplification by PCR. The 5prime region of this sequence contains motifs typically found in matrix attachment regions (MARs) in other plants. We have shown that part of the 2.2-kb DNA binds to wheat nuclear matrix (NM) in vitro, at least as strongly as a known MAR (Adh1) from maize suggesting that there is a MAR upstream of Bx7. This MAR is approximately 800 bases in length running from -750 to -1560 bases, relative to the start codon. Although the MAR is associated with a tissue-specific gene and is beside a strong tissue-specific promoter, the MAR sequence did not lead to tissue-specific expression of the beta-glucuronidase marker gene under the control of the rice actin promoter in various tissues. Presence of the MAR was only slightly beneficial with respect to expression levels, which were not greatly altered in transient expression assays in various wheat tissues although a slight increase in the number of foci was observed in leaves, which have low transformation efficiencies.Key words: matrix attachment region, particle bombardment, wheat.
Pairing affinities of the B- and G-genome chromosomes of polyploid wheats with those ofAegilops speltoides
Authors: Rodríguez S , Maestra B , Perera E , Díez M , Naranjo T
Published: April 2011

Chromosome pairing at metaphase I was studied in different interspecific hybrids involving Aegilops speltoides (SS) and polyploid wheats Triticum timopheevii (AtAtGG), T. turgidum (AABB), and T. aestivum (AABBDD) to study the relationships between the S, G, and B genomes. Individual chromosomes and their arms were identified by means of C-banding. Pairing between chromosomes of the G and S genomes in T. timopheevii × Ae. speltoides (AtGS) hybrids reached a frequency much higher than pairing between chromosomes of the B and S genomes in T. turgidum × Ae. speltoides (ABS) hybrids and T. aestivum × Ae. speltoides (ABDS) hybrids, and pairing between B- and G-genome chromosomes in T. turgidum × T. timopheevii (AAtBG) hybrids or T. aestivum × T. timopheevii (AAtBGD) hybrids. These results support a higher degree of closeness of the G and S genomes to each other than to the B genome. Such relationships are consistent with independent origins of tetraploid wheats T. turgidum and T. timopheevii and with a more recent formation of the timopheevi lineage.Key words: Triticum turgidum, Triticum timopheevii, Aegilops speltoides, meiotic pairing, evolution, C-banding.
Comparative physical mapping of the 18S-5.8S-26S rDNA in three sorghum species
Authors: Sang Yijun , Liang George H
Published: April 2011

The physical locations of the 18S-5.8S-26S rDNA sequences were examined in three sorghum species by fluorescence in situ hybridization (FISH) using biotin-labeled heterologous 18S-5.8S-26S rDNA probe (pTa71). Each 18S-5.8S-26S rDNA locus occurred at two sites on the chromosomes in Sorghum bicolor (2n = 20) and S. versicolor (2n = 10), but at four sites on the chromosomes of S. halepense (2n = 40) and the tetraploid S. versicolor (2n = 20). Positions of the rDNA loci varied from the interstitial to terminal position among the four accessions of the three sorghum species. The rDNA data are useful for investigation of chromosome evolution and phylogeny. This study excluded S. versicolor as the possible progenitor of S. bicolor.Key words: Sorghum bicolor, Sorghum versicolor, Sorghum halepense, 18S-5.8S-26S rDNA, fluorescence in situ hybridization.
Molecular characterization and chromosomal distribution of species-specific repetitive DNA sequences from Beta corolliflora, a wild relative of sugar beet
Authors: Gao D , Schmidt T , Jung C
Published: April 2011

Repetitive DNA sequences have been isolated from a Sau3AI plasmid library of tetraploid Beta corolliflora (2n = 4x = 36), a wild relative of sugar beet (B. vulgaris). The library was screened by differential hybridization with genomic DNA of B. corolliflora and B. vulgaris. When used as probes for Southern hybridization of genomic DNA, six clones were determined to represent highly repetitive DNA families present only in the B. corolliflora genome. Five other sequences were highly repetitive in B. corolliflora and low or single copy in B. vulgaris. The insert size varied between 43 bp and 448 bp. Two sequences pBC1279 and pBC1944 displayed strong homology to a previously cloned satellite DNA from B. nana. With one exception, sequences are tandemly arranged as revealed by a typical ladder pattern after genomic Southern hybridization. The chromosomal distribution of five probes was determined by fluorescence in situ hybridization (FISH) of mitotic metaphases from B. corolliflora and a triploid hybrid between B. vulgaris and B. corolliflora. Three sequences were spread along all chromosome arms of B. corolliflora while one sequence was present on only six chromosomes. The chromosome-specific sequence pBC216 was found in close vicinity to the 5S rDNA located on B. corolliflora chromosome IV. This set of species-specific sequences has the potential to be used as probes for the identification of monosomic alien addition lines and for marker-assisted gene transfer from wild beet to cultivated beet.Key words: Beta vulgaris, FISH, repetitive DNA, species-specific sequences.
Dynamic microsatellites in transcribed regions of gastropod mitochondrial 16S rDNA
Authors: Pfenninger Markus , Bugert Monika
Published: April 2011

Length variations of repetitive sequences in different AT-rich loop-coding regions of mitochondrial 16S rDNA in two gastropod species were discovered during intraspecific haplotype surveys. Examination of the discrete length variation of the basic repeat unit in a phylogenetic framework led to the conclusion of a microsatellite-like mutational dynamic. The observations suggest that the presence of a repetitive sequence structure alone is sufficient to trigger this dynamic.Key words: microsatellites, 16S rRNA, mitochondrial genome, repetitive DNA, gastropods.
Candidate disease resistance genes in sunflower cloned using conserved nucleotide-binding site motifs: Genetic mapping and linkage to the downy mildew resistance genePl1
Authors: Gedil Melaku Ayele , Slabaugh Mary B , Berry Simon , Johnson Richard , Michelmore Richard , Miller Jerry , Gulya Tom , Knapp Steven J
Published: April 2011

Disease resistance gene candidates (RGCs) belonging to the nucleotide-binding site (NBS) superfamily have been cloned from numerous crop plants using highly conserved DNA sequence motifs. The aims of this research were to (i) isolate genomic DNA clones for RGCs in cultivated sunflower (Helianthus annuus L.) and (ii) map RGC markers and Pl1, a gene for resistance to downy mildew (Plasmopara halstedii (Farl.) Berl. & de Toni) race 1. Degenerate oligonucleotide primers targeted to conserved NBS DNA sequence motifs were used to amplify RGC fragments from sunflower genomic DNA. PCR products were cloned, sequenced, and assigned to 11 groups. RFLP analyses mapped six RGC loci to three linkage groups. One of the RGCs (Ha-4W2) was linked to Pl1, a downy mildew resistance gene. A cleaved amplified polymorphic sequence (CAPS) marker was developed for Ha-4W2 using gene-specific oligonucleotide primers. Downy mildew susceptible lines (HA89 and HA372) lacked a 276-bp Tsp509I restriction fragment that was present in downy mildew resistant lines (HA370, 335, 336, 337, 338, and 339). HA370 × HA372 F2progeny were genotyped for the Ha-4W2 CAPS marker and phenotyped for resistance to downy mildew race 1. The CAPS marker was linked to but did not completely cosegregate with Pl1 on linkage group 8. Ha-4W2 was found to comprise a gene family with at least five members. Although genetic markers for Ha-4W2 have utility for marker-assisted selection, the RGC detected by the CAPS marker has been ruled out as a candidate gene for Pl1. Three of the RGC probes were monomorphic between HA370 and HA372 and still need to be mapped and screened for linkage to disease resistance loci.Key words: Helianthus, sunflower, downy mildew, Plasmopara, nucleotide-binding site.
An integrated restriction fragment length polymorphism - amplified fragment length polymorphism linkage map for cultivated sunflower
Authors: Gedil Melaku Ayele , Wye Crispin , Berry Simon , Segers Bart , Peleman Johan , Jones Richard , Leon Alberto , Slabaugh Mary B , Knapp Steven J
Published: April 2011

Restriction fragment length polymorphism (RFLP) maps have been constructed for cultivated sunflower (Helianthus annuus L.) using three independent sets of RFLP probes. The aim of this research was to integrate RFLP markers from two sets with RFLP markers for resistance gene candidate (RGC) and amplified fragment length polymorphism (AFLP) markers. Genomic DNA samples of HA370 and HA372, the parents of the F2population used to build the map, were screened for AFLPs using 42 primer combinations and RFLPs using 136 cDNA probes (RFLP analyses were performed on DNA digested with EcoRI, HindIII, EcoRV, or DraI). The AFLP primers produced 446 polymorphic and 1101 monomorphic bands between HA370 and HA372. The integrated map was built by genotyping 296 AFLP and 104 RFLP markers on 180 HA370 × HA372 F2progeny (the AFLP marker assays were performed using 18 primer combinations). The HA370 × HA372 map comprised 17 linkage groups, presumably corresponding to the 17 haploid chromosomes of sunflower, had a mean density of 3.3 cM, and was 1326 cM long. Six RGC RFLP loci were polymorphic and mapped to three linkage groups (LG8, LG13, and LG15). AFLP markers were densely clustered on several linkage groups, and presumably reside in centromeric regions where recombination is reduced and the ratio of genetic to physical distance is low. Strategies for targeting markers to euchromatic DNA need to be tested in sunflower. The HA370 × HA372 map integrated 14 of 17 linkage groups from two independent RFLP maps. Three linkage groups were devoid of RFLP markers from one of the two maps.Key words: amplified fragment length polymorphism (AFLP), restriction fragment length polymorphism (RFLP), Helianthus, sunflower, genetic map.
A restriction fragment length polymorphism based linkage map of a diploidAvenarecombinant inbred line population
Authors: Kremer C A , Lee M , Holland J B
Published: April 2011

A population of 100 F6-derived recombinant inbred lines was developed from the cross of two diploid (2n = 14) Avena accessions, CI3815 (A. strigosa) and CI1994 (A. wiestii). Restriction fragment length polymorphism (RFLP) probes previously mapped in other grass species were used to develop a framework linkage map suitable for comparative genetics. Nine linkage groups were identified among the 181 loci mapped, with an average interlocus distance of 5 cM, and a total genetic map length of 880 cM. A cluster of five tightly linked crown rust resistance genes (Pca) was localized on the map, as were five loci identified by disease resistance gene analogs from maize, sorghum, and wheat. None of the five loci identified by the gene analogs were linked to the Pca locus. The linkage map was compared with previously published diploid and hexaploid linkage maps in an attempt to identify homologous or homoeologous chromosomes between populations. Locus orders and linkage relationships were poorly conserved between the A. strigosa × A. wiestii map and other Avena maps. In spite of mapping complications due to duplications within a basic genome as well as the allopolyploid constitution of many Avena species, such map comparisons within Avena provide further evidence of substantial chromosomal rearrangement between species within Avena.Key words: grasses, oat, genetic mapping, homoeology.
A system of rapid isolation of end-DNA from a small amount of fosmid DNA, with vector-based PCR for chromosome walking
Authors: Chibana Hiroji , Heinecke Elizabeth L , Beckerman Janna L , Magee Paul T
Published: April 2011

The pBAC 108L and pFos 1 vectors were developed as stable propagation vectors which, due to their extremely low copy number, facilitate the cloning of a large-sized insert containing repeated DNA. However, the low copy number requires laborious end-DNA preparation for end sequencing and chromosome walking. Here we describe efficient methods for end-DNA isolation. The entire process, including small-scale DNA preparation, restriction digestion, self-ligation, and PCR with vector-based primers, is carried out in 96-well formats. Using a Fosmid library of genomic DNA of Candida albicans, PCR products ranging in size from 0.1 to 8 kbp were generated from 118 end sequences in 140 reactions from 70 Fosmid clones. A single or a prominent band was found in 101 of these reactions. Twenty-six of these bands were tested for walking and all of them proved to be specific. Thus, the system overcomes the disadvantage caused by low copy number. This system allows rapid physical mapping of genomes, and is adaptable for several other vectors including BAC (bacterial artificial chromosome), PAC (P1-derived artificial chromosome) and YAC (yeast artificial chromosome).Key words: IPCR, LM-PCR, chromosome walk, genome project, contig map.
Melon bacterial artificial chromosome (BAC) library construction using improved methods and identification of clones linked to the locus conferring resistance to melon Fusarium wilt (Fom-2)
Authors: Luo Meizhong , Wang Yi-Hong , Frisch David , Joobeur Tarek , Wing Rod A , Dean Ralph A
Published: April 2011

Utilizing improved methods, two bacterial artificial chromosome (BAC) libraries were constructed for the multidisease-resistant line of melon MR-1. The HindIII library consists of 177 microtiter plates in a 384-well format, while the EcoRI library consists of 222 microtiter plates. Approximately 95.6% of the HindIII library clones contain nuclear DNA inserts with an average size of 118 kb, providing a coverage of 15.4 genome equivalents. Similarly, 96% of the EcoRI library clones contain nuclear DNA inserts with an average size of 114 kb, providing a coverage of 18.7 genome equivalents. Both libraries were evaluated for contamination with high-copy vector, empty pIndigoBac536 vector, and organellar DNA sequences. High-density filters were screened with two genetic markers FM and AM that co-segregate with Fom-2, a gene conferring resistance to races 0 and 1 of Fusarium wilt. Fourteen and 18 candidate BAC clones were identified for the FM and AM probes, respectively, from the HindIII library, while 34 were identified for the AM probe from filters A, B, and C of the EcoRI library.Key words: bacterial artificial chromosome (BAC) library, Fusarium wilt, melon, pCUGIBAC1, resistant gene.
Physical mapping of restriction fragment length polymorphism (RFLP) markers in homoeologous groups 1 and 3 chromosomes of wheat by in situ hybridization
Authors: Ma X -F. , Ross K , Gustafson J P
Published: April 2011

Using wheat ditelosomic lines and in situ hybridization of biotin-labelled DNA probes, 18 restriction fragment length polymorphism (RFLP) markers were physically located on homoeologous groups 1 and 3 chromosomes of wheat. Most of the markers hybridized to chromosome arms in a physical order concordant with the genetic maps. A majority of the markers studied were clustered in non-C-banded, distal euchromatic areas, indicating the presence of recombination hot spots and cold spots in those regions. However, on 1BS the markers were well dispersed, which could be due to the abundance of heterochromatin throughout the arm. An inversion between Xpsr653 and Xpsr953 was observed on 1AL. One new Xpsr688 locus, approximately 2026% from the centromere, was found on 1AS and 1BS. The physical location of Xpsr170 on group 3 chromosomes probably represents an alternative to the loci on the genetic map. Finally, Xpsr313 was mapped to two physical loci on 1DL. Five markers were located to bins consistent with the deletion-based physical maps.Key words: wheat, physical mapping, in situ hybridization.
Construction of a genetic map of barley (Hordeum vulgareL.) cross 'Azumamugi' × 'Kanto Nakate Gold' using a simple and efficient amplified fragment-length polymorphism system
Authors: Mano Y , Kawasaki S , Takaiwa F , Komatsuda T
Published: April 2011

We have devised a simple and efficient amplified fragment-length polymorphism (AFLP) system consisting of small slab gels, a discontinuous buffer system, and silver staining. Using this system, a single worker developed a barley map with 227 polymorphic fragments in 2 months. As a mapping population, 99 recombinant inbred lines of barley cultivars 'Azumamugi' × 'Kanto Nakate Gold' were used. Most of the 227 AFLP fragments showed a Mendelian segregation ratio of 1:1, and all were assigned to the seven barley chromosomes. Thus, these fragments are useful as molecular markers. They were integrated with 40 previously characterized sequence-tagged sites, 3 isozymes, and 2 morphological markers to construct an integrated map. The resulting map covered 925.6 cM with 272 markers (detecting 150 loci) at an average interval of 6.5 cM/locus. This system greatly simplifies map construction.Key words: amplified fragment length polymorphism (AFLP), Hordeum vulgare, linkage map, recombinant inbred line (RIL), sequence-tagged site (STS).
A linkage map of hexaploid oat based on grass anchor DNA clones and its relationship to other oat maps
Authors: Portyanko V A , Hoffman D L , Lee M , Holland J B
Published: April 2011

A cultivated oat linkage map was developed using a recombinant inbred population of 136 F6:7lines from the cross 'Ogle' × 'TAM O-301'. A total of 441 marker loci, including 355 restriction fragment length polymorphism (RFLP) markers, 40 amplified fragment length polymorphisms (AFLPs), 22 random amplified polymorphic DNAs (RAPDs), 7 sequence-tagged sites (STSs), 1 simple sequence repeat (SSR), 12 isozyme loci, and 4 discrete morphological traits, was mapped. Fifteen loci remained unlinked, and 426 loci produced 34 linkage groups (with 243 loci each) spanning 2049 cM of the oat genome (from 4.2 to 174.0 cM per group). Comparisons with other Avena maps revealed 35 genome regions syntenic between hexaploid maps and 1634 regions conserved between diploid and hexaploid maps. Those portions of hexaploid oat maps that could be compared were completely conserved. Considerable conservation of diploid genome regions on the hexaploid map also was observed (8995%); however, at the whole-chromosome level, colinearity was much lower. Comparisons among linkage groups, both within and among Avena mapping populations, revealed several putative homoeologous linkage group sets as well as some linkage groups composed of segments from different homoeologous groups. The relationships between many Avena linkage groups remain uncertain, however, due to incomplete coverage by comparative markers and to complications introduced by genomic duplications and rearrangements.Key words: Avena, linkage map, comparative mapping, homoeology.
Genome size in 21 Artemisia L. species (Asteraceae, Anthemideae): Systematic, evolutionary, and ecological implications
Authors: Torrell Montserrat , Vallès Joan
Published: April 2011

Genome size was estimated by flow cytometry in 24 populations belonging to 22 Artemisia taxa (21 species, 1 with two subspecies), which represent the distinct subgenera, life forms, basic chromosome numbers, and ploidy levels in the genus. 2C nuclear DNA content values range from 3.5 to 25.65 pg, which represents a more than sevenfold variation. DNA content per haploid genome ranges from 1.75 to 5.76 pg. DNA amount is very well correlated with karyotype length and ploidy level. Some variations in genome size have systematic and evolutionary implications, whereas others are linked to ecological selection pressures.Key words: Artemisia, Asteraceae, flow cytometry, genome size, nuclear DNA amount variation, systematics, evolution, ecology.
Construction of a 1.2-Mb contig including the citrus tristeza virus resistance gene locus using a bacterial artificial chromosome library ofPoncirus trifoliata(L.) Raf.
Authors: Yang Zhong-Nan , Ye Xin-Rong , Choi Sandong , Molina Joe , Moonan Francis , Wing Rod A , Roose Mikeal L , Mirkov T Erik
Published: April 2011

The citrus tristeza virus resistance gene (Ctv) is a single dominant gene in Poncirus trifoliata, a sexually compatible relative of citrus. To clone this gene, a bacterial artificial chromosome (BAC) library has been constructed from an individual plant that was homozygous for Ctv. This library contains 45 696 clones with an average insert size of 80 kb, corresponding to 9.6 genome equivalents. Screening of the BAC library with five chloroplast DNA probes indicated that 0.58% of the BAC clones contained chloroplast-derived inserts. The chromosome walk across the Ctv locus was initiated using three closely linked genetic markers: C19, AD8, and Z16. The walk has been completed and a contig of ca. 1.2 Mb was constructed. Based on new data, the genetic map in the Ctv region was revised, with Ctv being located between AD8-Z16 and C19 at distances of 1.2 and 0.6 cM, respectively. Utilizing DNA fragments isolated from the contig as RFLP markers, the Ctv locus was further mapped to a region of ca. 300 kb. This contig contains several putative disease-resistance genes similar to the rice Xa21 gene, the tomato Cf-2 gene, and the Arabidopsis thaliana RPS2 gene. This library will therefore allow cloning of Ctv and other putative disease-resistance genes.Key words: Poncirus, citrus tristeza virus, chromosome walk, resistance gene.
Mitotic-cycle time and the development of embryo and endosperm in compatible and incompatible crosses in tuber-bearingSolanumspecies
Authors: Masuelli R W
Published: April 2011

To understand the relationship between early seed development and the EBN (endosperm balance number) hypothesis, the embryo and endosperm growth rates in crosses among Solanum spp. with the same and different EBNs were analyzed. For the embryo, the differences in the mean cell-doubling time (MCDT) between the compatible species 2x Solanum gourlayi and Solanum acaule was 3.9 h, whereas the incompatible species Solanum commersonii had MCDT differences of 10 and 13.9 h with 2x S. gourlayi and S. acaule, respectively. The embryo growth rates of the 2EBN species S. acaule and S. gourlayi were almost twice as fast as that of the 1EBN species S. commersonii. Nuclei of variable sizes were observed in the endosperms resulting from incompatible crosses. The author discusses the possibility that the collapse of the endosperm in inter-EBN crosses could be caused by differences in the MCDT between the parents that produce hybrid endosperms with high levels of DNA synthesis and transcription activity, resulting in increased nuclear size. A model is proposed to explain the formation of enlarged endosperm nuclei in incompatible crosses in the genus Solanum.Key words: mean cell-doubling time, endosperm balance number, Solanum, endosperm, embryo.
Development of resistance gene analog polymorphism markers for the Yr9 gene resistance to wheat stripe rust
Authors: Shi Z X , Chen X M , Line R F , Leung H , Wellings C R
Published: April 2011

The Yr9 gene, which confers resistance to stripe rust caused by Puccinia striiformis f.sp. tritici (P. s. tritici) and originated from rye, is present in many wheat cultivars. To develop molecular markers for Yr9, a Yr9 near-isogenic line, near-isogenic lines with nine other Yr genes, and the recurrent wheat parent 'Avocet Susceptible' were evaluated for resistance in the seedling stage to North American P. s. tritici races under controlled temperature in the greenhouse. The resistance gene analog polymorphism (RGAP) technique was used to identify molecular markers for Yr9. The BC7:F2 and BC7:F3 progeny, which were developed by backcrossing the Yr9 donor wheat cultivar Clement with 'Avocet Susceptible', were evaluated for resistance to stripe rust races. Genomic DNA was extracted from 203 BC7:F2 plants and used for cosegregation analysis. Of 16 RGAP markers confirmed by cosegregation analysis, 4 were coincident with Yr9 and 12 were closely linked to Yr9 with a genetic distance ranging from 1 to 18 cM. Analyses of nulli-tetrasomic 'Chinese Spring' lines with the codominant RGAP marker Xwgp13 confirmed that the markers and Yr9 were located on chromosome 1B. Six wheat cultivars reported to have 1B/1R wheat-rye translocations and, presumably, Yr9, and two rye cultivars were inoculated with four races of P. s. tritici and tested with 9 of the 16 RGAP markers. Results of these tests indicate that 'Clement', 'Aurora', 'Lovrin 10', 'Lovrin 13', and 'Riebesel 47/51' have Yr9 and that 'Weique' does not have Yr9. The genetic information and molecular markers obtained from this study should be useful in cloning Yr9, in identifying germplasm that may have Yr9, and in using marker-assisted selection for combining Yr9 with other stripe rust resistance genes.Key words: molecular markers, Puccinia striiformis f.sp. tritici, resistance gene analog polymorphism, Triticum aestivum.
Evidence of differential chromosome loss in aneuploid karyotypes of the Pacific oyster, Crassostrea gigas
Authors: Leitão A , Boudry P , Thiriot-Quiévreux C
Published: April 2011

The G-banding technique was performed on aneuploid karyotypes from gill tissue of the Pacific oyster, Crassostrea gigas, to assess whether chromosome losses could be explained by differential chromosomal susceptibility and to clarify the negative correlation between aneuploidy and growth rate previously reported in different populations of this oyster. The study of 95 G-banded aneuploid karyotypes showed that only 4 of the 10 chromosome pairs (viz. 1, 5, 9, and 10) of C. gigas were affected by the loss of one homologous chromosome. Pairs 1, 9, and 10, which were lost in 56, 33, and 44% of cases, respectively, may be considered to be differentially affected. Hypotheses on this differential chromosomal susceptibility are discussed.Key words: aneuploidy, growth, G-banding, karyotype, oyster.
Application of denaturing high-performance liquid chromatography for mapping of single nucleotide polymorphisms in barley (Hordeum vulgare L.)
Authors: Kota Raja , Wolf Markus , Michalek Wolfgang , Graner Andreas
Published: April 2011

Recent advances in DNA sequence analysis and the establishment of high-throughput assays have provided the framework for large-scale discovery and analysis of DNA sequence variation. In this context, single nucleotide polymorphisms (SNPs) are of particular interest. To initiate a systematic approach to develop an SNP map of barley (Hordeum vulgare L.), we have employed denaturing high-performance liquid chromatography (DHPLC) to analyse segregating SNP patterns in a doubled-haploid (DH) mapping population. To this end, SNPs between the parental genotypes were identified using a direct sequencing approach. Once a SNP was established between the parents, the optimal melting temperature of the PCR fragment containing the SNP was predicted for its analysis by DHPLC. Following the detection of the optimal temperature, the DH lines were analysed for the presence of either of the alleles. To test the utility of the analysis, data from previously mapped RFLP markers from which these SNPs were derived were compared. Results from these experiments indicate that DHPLC can be efficiently employed in analysing SNPs on a high-throughput scale.Key words: denaturing high performance liquid chromatography, doubled-haploid lines, restriction fragment length polymorphism, genetic mapping, molecular markers.
RAPD and ISSR fingerprints as useful genetic markers for analysis of genetic diversity, varietal identification, and phylogenetic relationships in peanut (Arachis hypogaea) cultivars and wild species
Authors: Raina S N , Rani V , Kojima T , Ogihara Y , Singh K P , Devarumath R M
Published: April 2011

Twenty-one random and 29 SSR primers were used to assess genetic variation and interrelationships among subspecies and botanical varieties of cultivated peanut, Arachis hypogaea (2n = 4x = 40), and phylogenetic relationships among cultivated peanut and wild species of the genus Arachis. In contrast with the previous generalization that peanut accessions lack genetic variation, both random and SSR primers revealed 42.7 and 54.4% polymorphism, respectively, among 220 and 124 genetic loci amplified from 13 accessions. Moreover, the dendrograms based on RAPD, ISSR, and RAPD + ISSR data precisely organized the five botanical varieties of the two subspecies into five clusters. One SSR primer was identified that could distinguish all the accessions analysed within a variety. Although the polymorphic index content varied from 0.1 to 0.5 for both ISSR and RAPD markers, primer index values were substantially higher for RAPD primers (0.354.65) than for SSR primers (0.351.73). It was possible to identify accessions, particularly those of divergent origins, by RAPD and (or) ISSR fingerprints. Based on these results, marker-based genetic improvement in A. hypogaea appears possible. None of the 486 RAPD and 330 ISSR amplification products were found to be commonly shared among 13 species of section Arachis and one species each of sections Heteranthae, Rhizomatosae, and Procumbentes. Dendrograms constructed from RAPD, ISSR, and RAPD + ISSR data showed overall similar topologies. They could be resolved into four groups corresponding to the species grouped in four taxonomic sections. The present results strongly support the view that Arachis monticola (2n = 4x = 40) and A. hypogaea are very closely related, and indicate that A. villosa and A. ipaensis are the diploid wild progenitors of these tetraploid species.Key words: Arachis hypogaea, genetic markers, varietal identification, DNA polymorphism, Arachis species.
The detection, cloning, and characterisation of WIS 2-1A retrotransposon-like sequences in Triticum aestivum L. and ×Triticosecale Wittmack and an examination of their evolution in related Triticeae
Authors: Muñiz Luis Miguel , Cuadrado Angeles , Jouve Nicolás , González Juan Manuel
Published: April 2011

Retrotransposons and other mobile elements are major components of the repeated DNA fraction in higher-plant genomes. They have undoubtedly played an important role in higher plant genome evolution. The present work details the detection and characterisation of a WIS 2-1A related sequence in direct wheat relatives, and discusses the prevalence and evolution of its copy number in their genomes. An increase in copy number is detected when following the natural hybridisation processes that gave rise to bread and durum wheats. However, the opposite is observed in the development of triticale, a synthetic hybrid.Key words: retrotransposons, WIS 2-1A, Triticeae, triticale, FISH.
Rapid and reliable identification of rice genomes by RFLP analysis of PCR-amplified Adh genes
Authors: Ge Song , Sang Tao , Lu Bao-rong , Hong De-yuan
Published: April 2011

The rice genus (Oryza L.) consists of 24 species with 10 recognized genome types. With the realization of many useful genes in species of wild rice, continuous efforts have been made to understand their genomic composition and relationships. However, the identification of rice genomes has often been difficult owing to complex morphological variation and formation of allotetraploids. Here we propose a rapid and reliable method for identifying rice genomes based on the restriction sites of PCR-amplified Adh genes. The experimental procedure was as follows: (i) amplify a portion of Adh1 and Adh2 genes with the locus-specific PCR primers; (ii) digest PCR products with restriction enzymes that distinguish different genomes; and (iii) run the digested products on 1.4% agarose gel, and photograph. Using various combinations of restriction digestion of the two Adh genes, all of the rice genomes can be identified.Key words: Adh gene, genome, identification, Oryza L., PCRRFLP.