Incubator initiative: Breeding drought and heat tolerant grapevine using epigenetic tools

Abstract

Plants have acquired the ability to prime their genomes after environmental stress, enabling a faster and stronger response to future environmental cues. This is most immediately tangible for long-lived crops such as grapevine. DNA methylation is an epigenetic mechanism by which plants control their responses to stress. Such epigenetic memory could be used for breeding purposes. We used MC-Seq to determine the genomic regions showing DNA methylation changes in grapevines during/after heat, drought and combined heat/drought stress. A total of 13,968 genes were identified as differentially methylated between control and stressed plants. The methylation status of 233 of these genes was maintained after physiological recovery and was deemed to reflect epigenetic memory of stress

Summary

The Australian wine industry is under pressure to sustain its profitability due to challenges such as climatic anomalies, heatwaves, irregular precipitation and rising input costs. Vitis vinifera is known to be a species of high phenotypic plasticity and hence it adapts to climate and different growing conditions (Sadras et al., 2009). Successful management of such plasticity, to make it adaptable to a changing environment, would help to maintain the leading position of the Australian wine industry. An organism’s cells from different tissues, developmental stages or grown under different environments are generally genetically identical but may present widespread differences in their DNA methylation profiles. Characterisation of such differences may prove suitable for the identification of epigenetic markers linked to useful characters. This project was needed to understand whether DNA methylation and epigenetics could help understand the mechanisms of grapevine plasticity and its potential use for breeding stress tolerance into the vine. The aims of the project were: Phenotypic characterisation of a grapevine glasshouse population with induced methylation changes through a targeted stress (heat and drought) intervention. Identification of epigenetic markers associated with heat and drought stress in grapevine Validation of epigenetic markers controlling drought and heat resistance in grapevine by interrogating gene expression and methyl-capture DNA libraries derived from the intervened population Generation of a database of potential stress tolerance epialleles for future research Publication of the results in a high impact factor journal To fulfil the project objectives a collaboration with Dr Everard Edwards from CSIRO was initiated to collect samples from a glasshouse experiment where grapevines were subjected to water stress, heat stress and a combination of the two. Samples were selected based on plant physiology measurements in order to choose water and heat stress extremes. The results showed that approximately 14,000 genes were differentially methylated in response to water and/or heat stress. Most importantly, more than 200 differentially methylated genes were maintained after stress and recovery. This is an important finding since the methylation differences which are kept after recovery could mean that a ‘memory’ of the stress is retained in the plant and thus could be exploited, for example, to induce stress resistance in the plant through targeted breeding programs, by priming mother vines before propagation in nurseries. This work has served as a proof of concept for what could become a larger project aimed at exploiting epigenetics and the memory of stress as tools to prime grapevine varieties for a changing environment.