Host and pathogen genomics: the molecular repertoire of soybean and Sclerotinia interactions

Sclerotinia sclerotiorum (Lib.) de Bary is an economically important soybean pathogen in the U.S. and worldwide. Understanding the disease caused by this fungus can help in controlling it. In the present study, genome-wide screenings were carried out to identify soybean mRNAs and small RNAs that change in expression during early infection stages with S. sclerotiorum or its primary virulence factor, oxalic acid. Microarray expression data was obtained from a transgenic soybean line expressing oxalate oxidase (OxO), an enzyme that degrades oxalic acid, and from its parent, the soybean cultivar ‘AC-Colibri’. Treatments included direct inoculations with S. sclerotiorum and leaf infiltrations with oxalic acid. Taking advantage of novel technologies, the profiling of gene expression was later expanded by subjecting the RNA samples used in the microarrays to deep sequencing using the Illumina/Solexa SBS platform. These studies allowed for the identification of a set of genes that may play important roles during pathogenicity, including several known defense-related genes. The data also suggested the possible involvement of iron homeostasis during disease development. In a second study, the Illumina/Solexa platform was used to query the small RNA composition of control and inoculated soybean stems, and of S. sclerotiorum mycelia grown on liquid media. In addition to these global RNA expression studies, a gene-specific study was carried out on the role of a putative G protein-coupled receptor possibly implicated in the plant interactions with pathogens. The gene was identified, cloned and an RNAi vector was constructed and transformed into soybean with the objective of carrying future functional analyses