Gene expression networks controlling seedling development and vigour in oilseed rape.
Wagner, Marie Helene
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The aim of the study was to confirm Quantitative trait loci (QTL) candidate genes with putative network regulatory roles during seedling emergence. A transcriptome-based systems analysis of seedling emergence was performed in a panel of 42 winter-type Brassica napus L. accessions with broad genetic and phenotypic diversity. Using weighted gene co-expression network analysis (WGCNA) shoot and root gene co-expression modules from four weeks old seedlings were correlated to in-vitro germination parameters and multi-environment field emergence traits. Combining QTL analysis with gene co-expression network analysis helped to prioritize candidate genes that lie within QTL intervals for seed germination and vigour. Several newly reported genes that were associated to the QTL were strongly supported as candidates by the network analysis. Such genes associated to QTL thousand seed weight were Bna.PME3 and BnaA01g04540D, a cytochrome bd ubiquinol oxidase gene found in gene co-expression module eigengenes correlated to thousand seed weight trait as well as field emergence traits. Seed quality traits including thousand seed weight as well as environmental effects affect establishment in the field. In addition, inside multi-environment field emergence associated modules, top hub genes especially from the auxin signalling pathway suggest a role in germination and seedling development for the genes. This study will aid in selection of markers for improving seedling vigour in B. napus by complementing genomic studies through identification of regulatory and QTL candidate genes involved in seedling development. In the second part of the study, fold change of expressed genes in osmotic stress (PEG) in the same panel of diverse 42 winter-type B. napus accessions were clustered using a WGCNA approach and the module eigengenes were correlated to metabolites and biomass. Clusters of expressed genes associated to metabolites and biomass were enriched for osmotic stress resistance. They contained hub genes involved in metabolite biosynthesis, osmotic stress responses and resistance mechanisms. These results were further supported by another previously published study whose candidate genes from the QTL associated to water stress was supported by the network analysis. The present study has pinpointed the key variations in the response to osmotic stress of a diverse set of genotypes. The genotypes were found to have varied response to osmotic stress at both transcriptional and metabolic level. In addition to previously reported osmolytes such as proline and sugars, glycine and betaalanine were found to be associated to osmotic stress related gene co-expression networks. The study provides markers that aid in the breeding of B. napus genotypes resistant to abiotic stress.