Global patterns of gene expression in rice cultivars undergoing a susceptible or resistant interaction with the parasitic plant Striga hermonthica.

Striga hermonthica is a root hemiparasite of cereals that causes devastating loss of yield. Recently, a rice cultivar, Nipponbare, was discovered, which exhibits post-attachment resistance to this parasite and quantitative trait loci (QTL) associated with the resistance were identified. Changes in gene expression in susceptible (IAC 165) and resistant (Nipponbare) rice cultivars were profiled using rice whole-genome microarrays. In addition to a functional categorization of changes in gene expression, genes that were significantly up-regulated within resistance QTL were identified. The resistance reaction was characterized by up-regulation of defence genes, including pathogenesis-related proteins, pleiotropic drug resistance ABC transporters, genes involved in phenylpropanoid metabolism and WRKY transcription factors. These changes in gene expression resemble those associated with resistance to microbial pathogens. Three genes encoding proteins of unknown function, within a major resistance QTL on chromosome 12, were highly up-regulated and are excellent candidate resistance genes. The susceptible interaction was characterized by large-scale down-regulation of gene expression, particularly within the functional categories plant growth regulator signalling and metabolism, biogenesis of cellular components and cell division. Up-regulated genes included nutrient transporters, enzymes of amino acid metabolism and some abiotic stress genes.

Elephantfish proinsulin possesses a monobasic processing site.

Total pancreatic RNA from the holocephalan species Callorhyncus milii (elephantfish) was used to make cDNA as a template for the polymerase chain reaction. Three redundant primers based on the known amino acid sequence of elephantfish insulin were used to amplify a fragment of proinsulin comprising truncated B-chain, complete C-peptide, and complete A-chain. Whereas the C-peptide/A-chain junction contained the expected dibasic cleavage site (-Lys-Arg-), the B-chain/C-peptide junction was found to contain only a single Arg, the first such site to be unequivocally associated with the proteolytic processing of a proinsulin to insulin. Examination of the flanking sequences around this site shows that a typical endocrine/neuroendocrine PC3 conversion enzyme should still be able to cleave, as the general requirements for precursor processing at a monobasic site are satisfied, notably a basic residue (Lys) at the -4 position. An acidic residue (in this case Asp) at the +1 position, which is seen in all known proinsulins, is maintained. The corresponding genomic DNA fragment of elephantfish proinsulin was also amplified by PCR, revealing a 402-bp intron at the conserved IVS-2 position within the C7 codon.

The red deer (Cervus elaphus) contains two expressed major histocompatibility complex class II DQB genes.

The highly variable second exons of the red deer (Cervus elaphus) major histocompatibility complex (MHC) DQB genes were cloned and sequenced. Eight different expressed DQB sequences were isolated from four unrelated red deer. Either two or three different DQB sequences were isolated from each individual, demonstrating that more than one DQB gene is expressed in red deer. This is consistent with other ruminant, which also have multiple expressed copies of the DQB gene. The sequences ranged in similarity from 81.3% to 97.6% with an average similarity of 90.2%; this indicates that at least one of the DQB genes is highly polymorphic.

Cloning and sequencing of expressed DRB genes of the red deer (Cervus elaphus) Mhc.

The expressed major histocompatibility complex (Mhc) class II DRB genes of 50 unrelated deer were examined by reverse transcription polymerase chain reaction, cloning, and sequencing of DRB exon 2. Deer, like other mammals, have at least one highly polymorphic Mhc class II DRB gene. Thirty-four different sequences were identified. Most of the variation in amino acid composition occurred at positions that have been shown to form the peptide binding site (PBS). Eighteen deer-specific substitutions were found, 11 of these occurred in the PBS. Significantly higher rates of replacement substitutions than silent substitutions were found in the deer sequences, indicating strong positive selection pressure for diversity in DRB sequences. Between one and four DRB sequences were found per deer. Inheritance of these sequences in pedigrees showed Mendelian segregation with up to two expressed DRB genes per haplotype. Sheep are the only other ruminant in which the presence of more than one expressed DRB gene has been demonstrated. Phylogenetic trees were constructed in an attempt to assign the deer DRB sequences to specific loci, but no clear segregation of the DRB sequences for different loci was found. It would seem likely that sequence exchange between the loci has occurred. As has been shown in other species, the alpha-helix and beta-sheet regions of exon 2 appeared to have different evolutionary histories.

Sheep linkage mapping: nineteen linkage groups derived from the analysis of paternal half-sib families.

Nineteen linkage groups containing a total of 52 markers have been identified in the sheep genome after typing large paternal half-sib families. The linkage groups range in size from 2 markers showing no recombination to a group containing 6 markers covering approximately 30 cM of the sheep genome. Thirteen of the groups have been assigned to a sheep chromosome. Three groups contain markers from bovine syntenic groups U2, U7 and U29, and one other group contains a marker that has been mapped only in humans. The remaining three groups are unassigned. This information will provide a useful foundation for a genetic linkage map of sheep.

Assignment of five polymorphic ovine microsatellites to bovine syntenic groups.

A panel of bovine somatic cell hybrids was used to map ovine microsatellites. Five of seven microsatellites were assigned to five bovine syntenic groups. These microsatellites were designated D5S10 (MAF23), D1S4 (MAF46), D13S1 (MAF18), D4S3 (MAF50), and DXS2 (MAF45), mapped to syntenic groups U3 (chromosome 5), U10 (chromosome 1), U11, U13, and the X chromosome, respectively. Two remaining sheep microsatellites amplified rodent DNA in the hybrid somatic cell panel, and were not assigned to bovine syntenic groups. Assignment of ovine-derived microsatellites to bovine syntenic groups provides additional evidence of the usefulness of microsatellites for mapping closely related species. The use of ovine and bovine microsatellites will aid in development of comparative genomic maps for these two species.

DNA fingerprinting analysis of Booroola pedigrees: a search for linkage to the Booroola gene.

Seven minisatellite probes from a variety of sources were used to analyse 11 paternal half-sib families in which the Booroola gene was segregating. A total of 402 bands that showed segregation in the pedigrees were examined for linkage to the Booroola gene. None of the bands showed segregation with the Booroola gene. The most likely evidence for a linked band was produced by the HaRas HVR probe in Family 902 (θ=0.0; LOD 2.3). The conclusion, however, is that the minisatellite probes used in this study could not be used as markers for the Booroola gene. The study highlighted problems associated with the use of minisatellite probes in linkage studies in half-sib families. The complex banding patterns found on fingerprinting gels was a major source of scoring error. In a few cases both of the sire's alleles could be identified at a particular locus, but in most cases only one of the alleles could be identified. For the most part, the bands had to be treated as dominant alleles. The contribution of dam alleles to the banding pattern could only be estimated. There was an indication that minisatellite loci in sheep are clustered in particular regions of the sheep genome as the rate at which bands segregated with each other was higher than one would expect from loci randomly distributed throughout the genome.

Lethal osteogenesis imperfecta and skin fragility in newborn New Zealand Romney lambs.

Osteogenesis imperfecta and skin fragility occurred in about 50 New Zealand Romney lambs born in a flock of 450 ewes. Affected lambs had soft bones and multiple intrauterine bone fractures. Long bones had a thickened diaphysis with almost complete absence of a medullary cavity. Other consistent gross findings were moderate brachynathia inferior, subcutaneous oedema, marked joint laxity, dark blue sclera and small pink teeth. Histopathologic and ultrastructural changes were consistent with a defect in collagen production by fibroblasts. DNA finger-printing was used to identify which of the five rams used in the flock was carrying the genetic defect. The disease was inherited as an autosomal dominant trait and was considered to be a new mutation in the testicular germ cell lines of this ram.

MAF45, a highly polymorphic marker for the pseudoautosomal region of the sheep genome, is not linked to the FecXI (Inverdale) gene.

A highly polymorphic dinucleotide repeat, or microsatellite, that shows partial sex-linked inheritance in sheep has been isolated from the sheep genome. Our data indicate that the locus is in the pseudoautosomal region approximately 13 cm from the boundary with the sex-linked regions. The locus, designated MAF45, has 12 alleles with a PIC of 0.84. The same primers amplify a single polymorphic locus in cattle and goats. This locus was not linked to the Inverdale gene, an X-linked gene that increases the ovulation rate in sheep.