Transcriptome-wide characterization of evolutionary adaptation to extreme edaphic conditions in grasses

• Main Author: Young, Ellen
• Published: Queen's University Belfast 2017
• Subjects: 681.7
• Online Access: http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.728837

The wild grass Holcus lanatus is tolerant of a range of edaphic stresses. It possesses genetic adaptations to these conditions which can produce distinct ecotypes and utilises fungal associations to improve stress tolerance. This thesis explores the adaptations and processes employed by two distinct H. lanatus ecotypes from acid bog and limestone quarry soils in response to their soil of origin and the alternate soil type. A de novo RNA-Seq transcriptome was produced for this purpose. Given the role of fungal associations in H. lanatus edaphic adaptation, a novel RNA-Seq assembly, annotation and analysis pipeline was implemented to investigate the root-associated fungal community composition and gene expression response in both soils. Arbuscular mycorrhizal (AM) and non-AM infection was verified using root staining and PCR protocols. Both ecotypes displayed adaptation to their soils of origin with some soil type specific responses indicated. Additionally gene expression in both ecotypes was altered when transplanted to an alternate soil type, although the acid ecotype on lime soil displayed a degree of gene expression similarity to the lime ecotype on lime soil, thereby displaying plasticity in this population. Staining and RNA-Seq analyses detected differences in AM and non-AM infection between soil types, with an ecotype effect detected for non-AM infection on acid soil using root staining. Furthermore the novel RNA-Seq analysis was capable of detecting differences in fungal community composition based on best BLAST alignment, gene expression and gene function, displaying the multifunctional potential of this technique. This thesis identifies putative soil pH adaptations and emphasises the importance of incorporating root fungal community characterisation in studies of stress tolerance between environments whilst introducing a novel RNA-Seq analysis pipeline for studying natural multi-species fungal infections. This technique can incorporate plant-fungal relationships into analyses of stress tolerance adaptations, where the importance of these interactions is increasingly realised.