Elite genotype selection for Phytophthora cinnamomi resistance in Holm oak based on multi-omic molecular markers

Sustainable management and conservation of forest tree species are crucial for protecting ecosystems and preserving historical legacies. The Holm oak (Quercus ilex subp. ballota (Desf.) Samp.) holds significant historical, environmental, economic and social value. Threatened by anthropogenic and environmental factors, understanding its biology is vital for developing biotechnological strategies to reduce mortality caused by decline syndrome and climate change. This review outlines advancements in multi-omics approaches to identify key genes involved in the response of Q. ilex to the pathogen Phytophthora cinnamomi, the primary cause of the root rot implicated in decline and premature mortality. Based on our research, we propose 29 candidate genes from asymptomatic individuals involved in the carbohydrate metabolism, the phenylpropanoid pathway, redox reactions, protease activity, cellular detoxification processes, stress-related events, and transcription factors. Model organisms, such as Arabidopsis thaliana and Nicotiana benthamiana, can facilitate bridging the gap between gene identification and their functional verification. We argue that forward and reverse genetic analyses of Q. ilex candidate genes in model organisms, including phenotypic characterization and heterologous complementation, offer a promising approach for advancing the breeding of elite, resilient genotypes for reforestation.