WP2 - Identification of DNA and epigenetic polymorphisms for monitoring diversity evolution and for markers assistance in breeding

Although there has been a large investment in the development of biotechnology tools in crop species in the past 20 years (including molecular markers, gene discovery, expression profiles at the transcriptome or proteome level, etc.), their use in plant breeding is still relatively limited, especially in the case of complex traits. Breeding for organic or low-input (LI) farming implies working with such complex traits controlled by many genes interacting with each other and with complex and variable environments. Thus, new approaches are needed to appropriately integrate these new tools into specific breeding for organic and LI conditions.

WP2 objective is to renew the genetic concepts of plant breeding for organic and LI agriculture, by associating knowledge from genomics, quantitative genetics, population genetics and epigenetic approaches to phenotyping under different organic and low-input crop management systems. In contrast to the usual approaches where associations between molecular markers and phenotypes are studied in a specific design optimized for their detection (QTL mapping), WP2 will be focused on populations and plants developed for organic or LI systems under specific systems (plant breeding scheme x crop management) in WP3-5-6. WP2 will analyse responses at different molecular levels in populations in organic and LI conditions, develop methods for association mapping in these populations and propose strategies for integrating molecular tools to monitor