BackgroundThe species Brassica rapa includes important vegetable and oil crops. It also serves as an excellent model system to study polyploidy-related genome evolution because of its paleohexaploid ancestry and its close evolutionary relationships with Arabidopsis thaliana and other Brassica species with larger genomes. Therefore, its genome sequence will be used to accelerate both basic research on genome evolution and applied research across the cultivated Brassica species.ResultsWe have determined and analyzed the sequence of B. rapa chromosome A3. We obtained 31.9 Mb of sequences, organized into nine contigs, which incorporated 348 overlapping BAC clones. Annotation revealed 7,058 protein-coding genes, with an average gene density of 4.6 kb per gene. Analysis of chromosome collinearity with the A. thaliana genome identified conserved synteny blocks encompassing the whole of the B. rapa chromosome A3 and sections of four A. thaliana chromosomes. The frequency of tandem duplication of genes differed between the conserved genome segments in B. rapa and A. thaliana, indicating differential rates of occurrence/retention of such duplicate copies of genes. Analysis of 'ancestral karyotype' genome building blocks enabled the development of a hypothetical model for the derivation of the B. rapa chromosome A3.ConclusionsWe report the near-complete chromosome sequence from a dicotyledonous crop species. This provides an example of the complexity of genome evolution following polyploidy. The high degree of contiguity afforded by the clone-by-clone approach provides a benchmark for the performance of whole genome shotgun approaches presently being applied in B. rapa and other species with complex genomes.

Membrane phospholipid abnormalities have been proposed to be involved in the pathogenesis of mood disorders, and in signal transduction and neurotransmitter uptake. Cytosolic phospholipase A₂ (cPLA₂) is not only an essential enzyme in the metabolism of fatty acids but also in signaling process. Therefore, we examined the association between the BanI polymorphism of the cPLA₂ gene and mood disorders. Sixty-two patients with major depressive disorder (MDD), 50 patients with bipolar I disorder (BID) and 117 healthy controls participated in this study. Genotyping was performed by using PCR-based methods. Genotype and allele distributions in MDD patients were significantly different from those of the controls. In particular, the A2 allele was associated with increased risk of MDD development (p = 0.007, odds ratio = 1.827; confidence interval = 1.141–2.927). However, the polymorphism was not different between BID patients and controls in genotype and allele distribution. This preliminary study indicates the need for further studies on the potential role of the cPLA₂ gene polymorphism in the susceptibility to mood disorders.

The association between Glutathione S-Transferase M1 gene (GSTM1) polymorphism and schizophrenia was examined. One hundred and eleven in-patients with schizophrenia and 130 healthy controls were enrolled in this study. Genotyping was performed using a polymerase chain reaction-based method. The GSTM1 null genotype was significantly more frequent in the schizophrenia patients than in the controls (P=0.014, odds ratio=1.93, 95% confidence interval=1.115-3.351). On the other hand, the GSTM1 genotype variants were not associated with tardive dyskinesia or total abnormal involuntary movement scale scores. This study suggests that, at least in the Korean population, the GSTM1 polymorphism may confer susceptibility to the development of schizophrenia but not to tardive dyskinesia.

The association between the quinone oxidoreductase gene (NQO1) polymorphism (609C/T) and schizophrenia was examined to replicate and extend the findings of a previous study (Hori et al., 2003). The study sample was 107 schizophrenia in-patients and 106 healthy controls. The distributions of the NQO1 genotypes and alleles were not different between the schizophrenia patients and the controls. However, the frequency of the variant genotype was significantly higher in the subgroup with tardive dyskinesia (TD) than in the subgroup without (p=0.019). The subjects with allele T were significantly more frequent in the TD patients than in those without (odds ratio 2.256, 95% confidence interval 1.235-4.133). In addition, the Abnormal Involuntary Movement Scale (AIMS) score was significantly higher in the variant genotype group (T/T) than in other genotypic groups (C/C and C/T) (p=0.004). This study suggests that the NQO1 gene polymorphism (609C/T) may confer susceptibility to the development of TD in schizophrenia, at least in the Korean population.

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