Oaks drought-induced responses under root types: gene and microRNA cooperation

Drought is a heavy stressor to plant growth and survival, necessitating resilience strategies to cope with water deficits. This study examines the molecular and hormonal processes involved in the drought response of taproot and lateral roots in oak seedlings of different cultivation techniques, specifically acorn-sown and containerized. RNA-seq analysis revealed differential expression of genes involved in drought responses, including those related to osmoprotection, antioxidant defense, hormonal regulation, and cell wall modification dependent on root system architecture i.e. taproot presence. Key pathways such as starch and sucrose metabolism, glutathione metabolism, and the TCA cycle were enriched, indicating enhanced metabolic activity and stress adaptation. miRNA profiling identified tissue-specific regulation, with miRNAs such as miR172, miR164, miR166 and miR393 playing pivotal roles for regulating the root responses to water shortage in taproots of containerized seedlings. Degradome sequencing revealed 33–45 significant miRNA-mRNA cleavage targets per library, including key regulatory interactions for root development (miR166-ATHB15/REV controlling xylem differentiation), growth regulation (miR396-GRF4/10 modulating meristem activity), and auxin response (miR167b-ARF6 influencing lateral root formation) under drought stress. Hormonal analysis identified that rise in ABA, JA, SA and a decrease in growth-promoting hormones (auxins - IAA, IBA, cytokinins – tZ, 2iP and GA3), reflecting a focus on the protection rather than growth under drought conditions. These findings highlight the complex interplay between genetic, hormonal, and metabolic networks in optimizing drought tolerance, providing insights into the molecular basis of cultivation techniques dependent oak resilience to water shortage.