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Current safety assessment for novel crops, including transgenic crops, uses a targeted approach, which relies on compositional analysis. The possibility that transgene expression could lead to unintended effects remains a debated issue. This study used transcriptome profiling as a nontargeted approach to evaluate overall molecular changes in transgenic soybean cultivars. Global gene expression was measured in the first trifoliate leaves of two transgenic and three conventional soybean cultivars using the soybean Affymetrix GeneChip. It was found that gene expression differs more between the two conventional cultivars than between the transgenics and their closest conventional cultivar investigated and that the magnitudes of differences measured in gene expression and genotype (determined by SSR analysis) do not necessarily correlate. A MySQL database coupled with a CGI Web interface was developed to store and present the results ( http://soyxpress.agrenv.mcgill.ca/). By integrating the microarray data with gene annotations and other soybean data, a comprehensive view of differences in gene expression is explored between cultivars.

In the development of barley (Hordeum vulgare L.) cultivars for malting purposes, it is usually not possible to select for malt quality characteristics in early generations because of the high cost associated with micromalting large numbers of grain samples and assessing quality traits on the resulting malt samples and because of the sensitivity of quantitative malt quality traits to environmental variation. Thus, barley malting quality may be a good candidate for marker-assisted selection. Here, the objective was to use marker-based selection to manipulate a malt quality characteristic, α-amylase activity, in a barley breeding population. Marker-based selection was applied among F 2:3 lines from the cross 'Morex'/'Labelle', targeting Morex alleles in a region of chromosome 7(5H) that had previously been found to affect α-amylase activity in the cross 'Steptoe'/Morex. The target region was represented by two polymerase chain reaction (PCR) markers. Selected lines were grown in field plots in two years. Agronomic and grain quality data were measured. Grain samples were micromalted and assessed for malt quality traits. Selection for the Morex allele at two PCR markers on chromosome 7(5H) was effective in increasing α-amylase activity. It was concluded that marker-based selection for a quantitative trait locus could be effective even when applied in a population other than the mapping population.

Genetic mapping of plants traditionally involves the analysis of large segregating populations. However, not all individuals in a population contribute equal amounts of genetic information. It is thus possible to achieve rough mapping using a subset of the most informative individuals in the population. We have designed a minimal Brassica napus mapping population of 23 doubled-haploid plants and have tested this method using this population in the mapping of disease resistance gene homologues in B. napus. Several groups have identified such homologues in soybean and potato by amplifying sequences corresponding to conserved nucleotide-binding sites from known resistance genes. However, the sequence conservation in the leucine-rich repeat domain that is present in most of the disease resistance genes isolated has not been exploited via the polymerase chain reaction (PCR). We present the genetic mapping of Brassica napus DNA sequences amplified with primers corresponding to both the nucleotide-binding site and the leucine rich-repeat domain of the Arabidopsis thaliana RPS2 gene. We also describe a method for the quick mapping of resistance gene homologues using the polymerase chain reaction.Key words: Brassica napus, disease resistance genes, minimal mapping population, RFLP markers.

Presence of the dominant Tu gene in Lactuca sativa is sufficient to confer resistance to infection by turnip mosaic virus (TuMV). In order to obtain an immunological assay for the presence of TuMV in inoculated plants, the TuMV coat protein (CP) gene was cloned by amplification of a cDNA corresponding to the viral genome using degenerate primers designed from conserved potyvirus CP sequences. The TuMV CP was overexpressed in Escherichia coli, and polyclonal antibodies were produced. To locate Tu on the L. sativa genetic map, F3 families from a cross between cvs "Cobbham Green" (resistant to TuMV) and "Calmar" (susceptible) were genotyped for Tu. Families known to be recombinant in the region containing Tu were infected with TuMV and tested by the indirect enzyme-linked immunosorbent assay (ELISA) using the anti-CP serum. This assay placed Tu between two random amplified polymorphic DNA (RAPD) markers and 3.2 cM from Dm5/8 (which confers resistance to Bremia lactucae). Also, bulked segregant analysis was used to screen for additional RAPD markers tightly linked to the Tu locus. Five new markers linked to Tu were identified in this region, and their location on the genetic map was determined using informative recombinants in the region. Six markers were identified as being linked within 2.5 cM of Tu.

Experimental data are provided for the presence of a plant protein that interacts with the capsid protein (CP) of turnip mosaic potyvirus (TuMV). The receptor-like protein was identified by exploiting the molecular mimicry potential of anti-idiotypic antibodies. A single-chain Fv molecule derived from the monoclonal antibody 7A (Mab-7A), which recognizes the CP of TuMV, was produced in Escherichia coli and the recombinant protein was used to raise rabbit antibodies. The immune serum reacted with Mab-7A but not with a monoclonal antibody of the same isotype, indicating that anti-idiotypic antibodies were produced. These anti-idiotypic antibodies recognized a 37 kDa protein from Lactuca sativa. Complex formation between the anti-idiotypic antibodies and the plant protein was inhibited by the CP of TuMV which indicates that the plant protein interacts with the viral protein. The 37 kDa protein was localized in chloroplasts and was detected in other plant species.

The second largest cluster of resistance genes in lettuce contains at least two downy mildew resistance specificities, Dm5/8 and Dm10, as well as Tu, providing resistance against turnip mosaic virus, and plr, a recessive gene conferring resistance against Plasmopara lactucae-radicis, a root infecting downy mildew. In the present paper four additional genetic markers have been added to this cluster, three RAPD markers and one RFLP marker, CL1795. CL1795 is a member of a multigene family related to triose phosphate isomerase; other members of this family map to the other two major clusters of resistance genes in lettuce. Seven RAPD markers in the region were converted into sequence characterized amplified regions (SCARs) and used in the further analysis of the region and the mapping of Dm10. Three different segregating populations were used to map the four resistance genes relative to molecular markers. There were no significant differences in gene order or rate of recombination between the three crosses. This cluster of resistance genes spans 6.4 cM, with Dm10 1.2 cM from Dm8. Marker analysis of 20 cultivars confirmed multiple origins for Dm5/8 specificity. Two different Lactuca serriola origins for the Du5/8 specificity had previously been described and originally designated as either Dm5 or Dm8. Some ancient cultivars also had the same specificity. Previously, due to lack of recombination in genetic analyses and the same resistance specificities, it was assumed that Dm5 and Dm8 were determined by the same gene. However, molecular marker analysis clearly identified genotypes characteristic of each source. Therefore, Dm5/8 specificity is either ancient and widespread in L. serriola and some L. sativa, or else has arisen on multiple occasions as alleles at the same locus or at linked loci.

Molecular markers linked to loci of interest can be used for fine mapping a particular area of a genome or for marker-assisted selection. We present an approach for screening individual plants with polymorphic markers that facilitates phenotyping in large populations. Polymorphic DNA fragments, amplified by PCR, are labelled with digoxigenin and used as probes on slot blots of amplified DNA from the individual plants to be tested. DNA is obtained by a simple two-tube purification method. The colorimetric detection of alleles on the blots is more reliable, and more amenable to automation, than conventional staining of electrophoresis gels.Key words: molecular markers, RAPD, genetic mapping, breeding.

We investigated random amplified polymorphic DNA (RAPD) in 27 inbred barley lines with varying amounts of common ancestry and in 20 doubled-haploid (DH) lines from a biparental cross. Of 33 arbitrary 10 base primers that were tested, 19 distinguished a total of 31 polymorphisms. All polymorphisms were scored as dominant genetic markers except for 1, where Southern analysis indicated the presence of two codominant amplification products. The inheritance of 19 RAPD polymorphisms and one morphological trait was studied in the DH lines. There was no evidence for segregation distortion, but a group of four tightly linked loci was detected. The frequencies of RAPD polymorphism in pairs of inbred lines were used to compute values of genetic distance (d), which were compared to kinship coefficients (r) between the same pairs of lines. A linear relationship between r and d was evident, but low values of r gave poor predictions of d. Cluster analysis showed that groups of inbred lines based on r were similar to those based on d with some notable exceptions. RAPD markers can be used to gain information about genetic similarities or differences that are not evident from pedigree information.

Des symptômes de mosaïque virale ont été observés dans des champs expérimentaux de lupin (Lupinus albus) dans Test du Canada. Les plants affectés montraient des symptômes de mosaïque, de réduction et de déformation des feuilles, et de nanisme du plant. Les symptômes ont pu être reproduits en serre par inoculation mécanique sur le cultivar de lupin Ultra. Les symptômes observés sur des espèces diagnostiques, l'observation par microscopie électronique, la détection sérologique ELISA et l'analyse immunologique Western ont été utilisés pour identifier le virus présent. Un potyvirus, identifié comme le virus de la mosaïque jaune du haricot (BYMV), a été détecté dans les plants affectés. Ces résultats sont les premiers à caractériser une maladie virale du lupin au Canada. Puisque le virus est transmis par les pucerons et par la graine, la présence du virus peut devenir une limitation à la production du lupin., Virus-like symptoms were observed in fields of white lupine (Lupinus albus) in Eastern Canada. Affected plants displayed mosaic, leaf stunting and deformation, and bunchy growth habit. The disease was successfully reproduced in greenhouse by mechanical inoculation of white lupine cv. Ultra. The causal virus was identified as bean yellow mosaic virus (BYMV) by symptomatology on diagnostic species, electron microscopy, enzyme linked immunosorbent assay (ELISA) and immunodetection after Western blotting. This is the first report of a viral disease of lupine in Canada. BYMV may represent a significant limitation to lupine culture since it is transmitted by aphids and through infected seed.

In an F2 population, the alleles at two loci with a recombination fraction r 2k) of containing only the coupled allele at the second locus. Based on this principle, several methods have been described to detect linkage (using one or two pools) or to estimate r (using a group of n pools). This report compares maximum likelihood and approximate estimators of r for use in pooled-DNA analysis and illustrates the use of this analysis for dominant markers. Expected values and expected mean squares for estimators of r were computed for varying levels of r, k, and n. Both estimators were biased, but the bias and variability were slightly smaller for the maximum-likelihood estimator. Bias was not severe except when k was large relative to r and (or) n. Methods for optimizing k are discussed relative to several criteria: minimizing variance, minimizing bias, minimizing the probability that linkage cannot be detected, and minimizing the number of samples that must be screened.Key words: pooled DNA, linkage analysis, molecular markers, RAPD, genetic mapping.