Hybridization and detection of digoxigenin probes on RNA blots.

This article describes nonradioactive probing of a Northern blot. The method employs digoxigenin-labeled probes. Antidigoxigenin antibody/alkaline phosphate conjugate, and a chemiluminescent substrate are subsequently used in the detection system.

Nonradioactive probes.

This work concentrates on a single procedure, namely hybridizing Southern blots with nonradioactive probes. Stress is placed on features of the procedures where attention to detail is necessary to obtain strong signals and clear background. Some indications are given to the future development of the technology.

Characterization of a mRNA that accumulates during development of oilseed rape pods.

Dehiscence of oilseed rape pods, commonly known as pod shatter, is a process of agronomic importance that results in seed loss causing yield reductions and carry-over of the crop into the following growing season. In an effort to understand the mechanisms underlying this developmental event, the changes in gene expression that accompany pod shatter have been examined with a view to understanding how the process is regulated. In order to achieve this, cDNA library was constructed using mRNA extracted from the dehiscence zone of developing pods. Differential screening with non-dehiscence zone cDNA led to the isolation of a pod-specific clone, SAC25, with a transcript size of 1100 nucleotide encoding a predicted polypeptide of 34 kDa. The level of SAC25 mRNA accumulation increased during pod development. The sequence shows no significant homology to others within the databases but has two identifiable amino acid motifs, one is an adenine nucleotide binding site for NAD/FAD dehydrogenases and the other is a conserved feature of the ribitol dehydrogenase family. The amino acid sequence has four putative glycosylation sites and contains four cysteine residues. Genomic Southern analysis indicates that SAC25 may be encoded by a single gene or a small gene family. The function of this mRNA is unknown but possible roles in dehiscence and pod development are discussed.

Restriction fragment length polymorphism analysis of loci associated with disease resistance genes and developmental traits in Pisum sativum L.

An F2 population of pea (Pisum sativum L.) consisting of 174 plants was analysed by restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) techniques. Ascochyta pisi race C resistance, plant height, flowering earliness and number of nodes were measured in order to map the genes responsible for their variation. We have constructed a partial linkage map including 3 morphological character genes, 4 disease resistance genes, 56 RFLP loci, 4 microsatellite loci and 2 RAPD loci. Molecular markers linked to each resistance gene were found: Fusarium wilt (6 cM from Fw), powdery mildew (11 cM from er) and pea common Mosaic virus (15 cM from mo). QTLs (quantitative traits loci) for Ascochyta pisi race C resistance were mapped, with most of the variation explained by only three chromosomal regions. The QTL with the largest effect, on chromosome 4, was also mapped using a qualitative, Mendelian approach. Another QTL displayed a transgressive segregation, i.e. the parental line that was susceptible to Ascochyta blight had a resistance allele at this QTL. Analysis of correlations between developmental traits in terms of QTL effects and positions suggested a common genetic control of the number of nodes and earliness, and a loose relationship between these traits and height.

Identification and characterization of a proline-rich mRNA that accumulates during pod development in oilseed rape (Brassica napus L.).

Pod development in oilseed rape (Brassica napus) culminates in a process known as dehiscence (shatter) which can result in the loss of seed before the crop is harvested. In order to investigate the biochemical and the genetic basis controlling this process, a cDNA library was constructed from the dehiscence zone of developing pods. This resulted in the isolation of a cDNA clone (SAC51). The mRNA encoded by SAC51 had a transcript size of ca. 700 nucleotides and was found, by northern analysis, to accumulate preferentially in the dehiscence zone of the pod and in no other part of the plant analysed. The predicted polypeptide is rich in the amino acids proline (14.2%) and leucine (14.2%). The sequence of the polypeptide has more than 40% amino acid sequence identity with polypeptides isolated from carrot embryos, maize roots, soybean seeds and young tomato fruit. The function of these proteins is unknown. Genomic Southern analysis suggests that SAC51 is encoded by a single gene or small gene family. The role of the peptide in the development of pods of oilseed rape is discussed.

Random amplified polymorphic DNA (RAPD) markers for genetic analysis inAllium.

RAPD analysis was applied to onion (Allium cepa) and otherAllium species in order to assess the degree of polymorphism within the genus and to investigate if this approach was suitable for genetic studies of onion. Seven cultivars ofA. cepa, including shallot, and single cultivars of Japanese bunching onion (A. fistulosum), chive (A. schoenoprasum), leek (A. ampeloprasum), and a wild relative of onion (A. roylei), were evaluated for variability using a set of 20 random 10-mer primers. Seven out of the twenty primers revealed scorable polymorphisms between cultivars ofA. cepa and these will be further evaluated for use in genetic mapping. Wide variations in banding profiles between species were observed with nearly every primer tested. These were assessed for use in systematic studies within the genus. Ninety-one band positions were scored (+/-) for all the cultivars studied. Genetic distances between each of the cultivars were calculated and cluster analysis was used to generate a dendrogram showing phylogenetic relationships between them. The resulting analysis was in broad agreement with previous classifications of the species studied, confirming the validity of the method. However, amongst the species studied, it placedA. roylei as the closest relative ofA. cepa, questioning the current classification of the former species in the section Rhizideum.

Stoichiometric differences in DNA molecules containing the atpA gene suggest mechanisms for the generation of mitochondrial genome diversity in maize.

Four genomic arrangements of the maize mitochondrial atpA gene (encoding the alpha subunit of the F(1) ATPase), have been characterized. Most N (fertile) and S (male-sterile) cytoplasms contain two atpA arrangements of equal abundance. Prolonged exposure of blots of maize mitochondrial DNA probed with atpA-specific sequences show that cytoplasms previously reported to lack one of the atpA arrangements do contain the second arrangement but at low levels. Similarly, restriction fragments containing the atpA gene previously thought unique to male-sterile S and T cytoplasms are present in low abundance in fertile cytoplasms. These observations suggest that fertile and male-sterile cytoplasms of maize may be more closely related than previously thought, and suggest possible mechanisms to explain the observed mitochondrial genome diversity.

Transcript termini of messenger RNAs in higher plant mitochondria.

The 3'-termini of the mRNAs for subunit II of the cytochrome oxidase (COX II) and for the alpha-subunit of the mitochondrial ATPase (ATPA) have been determined in Oenothera mitochondria by two independent methods. Analysis of both transcripts by S1 protection experiments and of cloned cDNAs show an identical terminal 50 nucleotide sequence, to which homology is found 3' to some gene sequences in the maize mitochondrial genome. These regions can be folded into potential secondary structures similar to bacterial terminators.

The maize cytochrome c oxidase subunit I gene: sequence, expression and rearrangement in cytoplasmic male sterile plants.

The single copy of the gene for cytochrome c oxidase subunit I (COX I) present in the mitochondrial genome of fertile maize (Zea mays L.) is encoded by a continuous open reading frame of 1584 nucleotides. The predicted polypeptide encoded by the gene has a mol. wt. of 58 219 daltons and shows >60% amino acid sequence homology with the corresponding fungal and animal polypeptides. Two major transcripts of 2400 and 2300 nucleotides can be detected and the 5' end of the larger transcript maps to a sequence from -161 to -153 (relative to the initiator codon) which shows high homology to the yeast mitochondrial promoter. In mitochondrial DNA from the S male-sterile cytoplasm of maize, which also characteristically contain two low mol. wt. linear DNAs (S1 and S2), rearrangements just 5' (at -175) to the COX I gene, generate additional DNA restriction fragments containing entire copies of the gene. These rearrangements involve a sequence identical to the terminal 186 bp of the 208-bp inverted repeat sequence found at either end of the S1 and S2 DNAs.

The mitochondrial genome of fertile maize (Zea mays L.) contains two copies of the gene encoding the alpha-subunit of the F1-ATPase.

In contrast to the situation in animals and fungi the alpha-subunit of the mitochondrial F1-ATPase is encoded by two identical mitochondrial genes (ATP A) in male fertile maize (Zea mays L.). Cytoplasmic male sterile (T, C and S) maize mitochondrial genomes only contain a single copy of the gene. Sequence analysis reveals that the uninterrupted coding region of both copies of the gene is 1,524 bp long and encodes a polypeptide of 508 amino acids with a molecular weight of 55,117. The predicted amino acid sequence shares over 60% homology with the nuclear encoded alpha-subunit from yeast and bovine ATPase and approx. 50% with the corresponding chloroplast and bacterial polypeptides.

Ovarian and fat-body vitellogenin synthesis in Drosophila melanogaster.

The ovary and the fat body of Drosophila melanogaster both synthesise vitellogenins in vivo. The ovary contributes nearly as much vitellogenin to the yolk of an oocyte as does the fat body. Densitometry of fluorographs and gels has been used to compare the amount of the smallest vitellogenin polypeptide, yolk protein 3, synthesised by each tissue. Cell-free translations indicate that the ovary, in contrast to the fat body, contains a much reduced level of the mRNA for yolk protein 3 compared with the mRNAs for the other vitellogenin polypeptides. However, if tissues are cultured in vitro, the underproduction of this protein by the ovary is not significant. Because young embryos have levels of this polypeptide which are expected if the ovary has a low level of its corresponding mRNA, we argue that the ovary genuinely underproduces this protein in vivo and that the relative levels synthesised by the ovary in vitro are an artefact. Egg chambers of previtellogenic stages can synthesise vitellogenins, but the maximum level of vitellogenin synthesis occurs in egg chambers of the early vitellogenic stages. We conclude that the expression of the vitellogenin genes is subject to different controls at each site of synthesis. The possible cell types responsible for ovarian vitellogenin synthesis are discussed; the follicle epithelial cells are tentatively nominated for this role. We also suggest that a specific repression mechanism for vitellogenin gene expression exists in the ovary.