On Systems Thinking, Systems Biology, and the in Silico Plant

The recent summary report of a Department of Energy Workshop on Plant Systems Biology (P.V. Minorsky [2003] Plant Physiol 132: 404-409) offered a welcomed advocacy for systems analysis as essential in understanding plant development, growth, and production. The goal of the Workshop was to consider methods for relating the results of molecular research to real-world challenges in plant production for increased food supplies, alternative energy sources, and environmental improvement. The rather surprising feature of this report, however, was that the Workshop largely overlooked the rich history of plant systems analysis extending over nearly 40 years (Sinclair and Seligman, 1996) that has considered exactly those challenges targeted by the Workshop. Past systems research has explored and incorporated biochemical and physiological knowledge into plant simulation models from a number of perspectives. The research has resulted in considerable understanding and insight about how to simulate plant systems and the relative contribution of various factors in influencing plant production. These past activities have contributed directly to research focused on solving the problems of increasing biomass production and crop yields. These modeling approaches are also now providing an avenue to enhance integration of molecular genetic technologies in plant improvement (Hammer et al., 2002).

Survey of Fusarium species associated with crown rot of wheat and barley in eastern Australia

Fusarium species associated with crown rot were isolated and identified from 409 wheat, barley or durum wheat crops from the eastern Australian grain belt between 1996 and 1999. Fusarium pseudograminearum was almost the only species isolated from crops in Queensland and New South Wales. F. pseudograminearum was also the most common species in Victoria and South Australia, but F. culmorum was frequently isolated in these states. F. culmorum accounted for more than 70% of isolates from the Victorian high-rainfall (> 500 mm) region and the South-East region of South Australia. F. culmorum comprised 18% of isolates from the Victorian medium-rainfall (350-500 mm) region, and 7% of isolates from each of the Victorian low-rainfall region and the Mid-North region of South Australia. F. avenaceum, F. crookwellense and F. graminearum were isolated very infrequently. The proportion of F. culmorum among isolates of Fusarium from districts in Victoria and South Australia was strongly correlated with climatic conditions around the end of the growing season, especially with rainfall in November.

Oidiopsis (Erysiphaceae) on Euphorbia spp. in Australia and Vanuatu

One specimen of powdery mildew on Euphorbia cyathophora from Vanuatu and 11 specimens on E. cyathophora, E. dentata, E. heterophylla and E. leucocephala from Australia were studied. All were shown to represent the Oidiopsis anamorph of Leveillula taurica, which is described. This is the first record of Oidiopsis in Vanuatu. E. leucocephala is a new host record for this powdery mildew.

Genome-wide association analysis and differential expression analysis of resistance to Sclerotinia stem rot in Brassica napus

Brassica napus is one of the most important oil crops in the world, and stem rot caused by the fungus Sclerotinia sclerotiorum results in major losses in yield and quality. To elucidate resistance genes and pathogenesis-related genes, genome-wide association analysis of 347 accessions was performed using the Illumina 60K Brassica SNP (single nucleotide polymorphism) array. In addition, the detached stem inoculation assay was used to select five highly resistant (R) and susceptible (S) B. napus lines, 48 h postinoculation with S. sclerotiorum for transcriptome sequencing. We identified 17 significant associations for stem resistance on chromosomes A8 and C6, five of which were on A8 and 12 on C6. The SNPs identified on A8 were located in a 409-kb haplotype block, and those on C6 were consistent with previous QTL mapping efforts. Transcriptome analysis suggested that S. sclerotiorum infection activates the immune system, sulphur metabolism, especially glutathione (GSH) and glucosinolates in both R and S genotypes. Genes found to be specific to the R genotype related to the jasmonic acid pathway, lignin biosynthesis, defence response, signal transduction and encoding transcription factors. Twenty-four genes were identified in both the SNP-trait association and transcriptome sequencing analyses, including a tau class glutathione S-transferase (GSTU) gene cluster. This study provides useful insight into the molecular mechanisms underlying the plant's response to S. sclerotiorum.