Genomic prediction of disease resistance provides a path to marker assisted restoration in a wetland foundation tree species

Summary Tree species worldwide are under threat from non-native pathogens that impact forests and the ecosystem services they provide. Myrtle rust, caused by Austropuccinia psidii , is one example, first detected in Australia in 2010. This fungal pathogen infects immature tissue from a wide range of Myrtaceae hosts, including the wetland foundation species Melaleuca quinquenervia . Durable restoration action for this species would preferentially incorporate disease resistant individuals. Our aim for this study was to provide a molecular assay to identify and select resistant individuals and seed lots for restoration. We conducted artificial inoculation of a panel of seedlings and measured their immune responses to myrtle rust. We then performed whole genome sequencing (3.2M common SNPs) and conducted a Genome Wide Association Study ( N = 492), which revealed clusters of significantly associated SNPs in three chromosomal regions, including clusters of putative R genes. Associated SNPs were filtered to a panel of 1,049 for a highly accurate genomic prediction model ( R = 0.83). This provides a relatively inexpensive approach to identifying resistant individuals or seed lots for restoration and a template for managing myrtle rust impacts while maintaining population genetic diversity.