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Our team is a part of WP1 (WP leader Maria-Jose Manzanares) named “Crop characteristics and bioindicators associated with plant sustainability and DUS criteria”. The general objective of WP1 is to identify crop characteristics and bioindicators associated with plant resources use efficiency (RUE), adaptation to sustainable cropping systems under greenhouse and resilience to variable and more challenging environment conditions (including drought stress). WP1 will also explore methods to efficiently discriminate between (epi)mutants. For apple, WP1 will evaluate epigenetic changes between varieties and between sports for fruit coloration grown at three different locations with contrasted climates. 

We are leader of Task 1.4 named “Exploring the use of epigenetic marks for variety identification and adaptation to environment”: Epigenetic changes in apple grown under different environments will be assessed in sports and in varieties grown at different locations. In the case of sports, INRA-Angers will measure differentially methylated regions (DMR) through whole-genome bisulfite sequencing (BS) in three distinct sports of the variety Gala grown at three locations with contrasted climates (France, Spain and Italy). ‘Gala’ genome and DNA methylation data produced in an ongoing CPVO-funded project will provide the basis for this study. For apple varieties, IRTA will analyse the effect of environment on whole-genome DNA methylation (WGM) and will explore the use of variations on WGM level as a bioindicator for crop adaptation. For this, IRTA will evaluate at least three low-cost methods for measuring WGM (ELISA-base kits) in 10 apple varieties from the apple REFPOP grown at Spain, Italy and Switzerland. The variation on WGM levels between environments will be compared with yield stability. In the case of potato, genetic and epigenetic changes will be identified at WU by comparing 10 potato clones (Cara, Desiree and Agria and their sports) at the genetic and epigenetic level by whole genome and by BS sequencing. This will identify somatic variation in SNPs, novel insertions and quantify their copy numbers as well as those regions differentially methylated.