Systems biological analysis of seedling vigour and osmotic stress tolerance in oilseed rape (Brassica napus L., Brassicaceae)

Abstract

Oilseed rape (Brassica napus L.) is a globally important oilseed crop. Variation in germination and emergence is a major challenge for oilseed rape breeders, because strong influences from both the seed production environment and the sowing environment infer low heritability. In crops with complex genomes such as B. napus, systems biological approaches involving different levels of information from the genome and transcriptome can give deep insight into the regulation of poorly understood environmentally sensitive traits like emergence and vigour. In this context, the aim of the first part of the thesis was to confirm the 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 B. 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. Drought has occurred frequently in many areas of the world and is predicted to persist in the future. It affects the yield of crops including B. napus. Thus there is a need to breed for drought resistant plants, that is, plants able to produce economic yield in environments deficient in water. Osmotic stress in plants is caused by water deficit or cell dehydration due to drought or salt stress, and disrupts many cellular functions. Due to the complexity of osmotic stress resistance mechanisms in plants, it has been proposed to use analysis to integrate data at multiple levels of genome, phenome, transcriptome and metabolome. In the second part of the thesis, fold change of expressed genes in osmotic stress induced by polyethylene glycol (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 insight into the responses of different B. napus genotypes to osmotic stress to contribute to the improvement of the crop.