Multi-omics analysis unveils early molecular responses to aluminum toxicity in barley root tip

Barley ( Hordeum vulgare L.) is widely cultivated across diverse soil types, including acidic soils where aluminum (Al) toxicity is the major limiting factor. The relative Al sensitivity of barley highlights the need for a deeper understanding of early molecular responses in root tip (the primary target of Al toxicity) to develop Al-tolerant cultivars. Integrative N 6-methyladenosine (m6A) modification, transcriptomic, and metabolomic analyses revealed that elevated auxin and jasmonic acid (JA) levels modulated Al-induced root growth inhibition by repressing genes involved in cell elongation and proliferation. Additionally, these pathways promoted pectin demethylation via up-regulation of genes encoding pectin methylesterases (PMEs). The up-regulation of citrate efflux transporter genes including Al-activated citrate transporter 1 ( HvAACT1 ), and ATP-binding cassette (ABC) transporters like HvABCB25, facilitated Al exclusion and vacuolar sequestration. Enhanced activity within the phenylpropanoid pathway supported antioxidant defenses and internal chelation through the production of specific flavonoids and altered cell wall composition via lignin unit modulation. Notably, several Al-responsive genes, including HvABCB25 and transcription factors (TFs), exhibited m6A modification changes, with two microtubule associated protein 65 ( MAP65 ) members displaying opposing regulatory patterns at both transcriptional and m6A levels, underscoring the crucial role of m6A modification in gene expression regulation. This comprehensive study provides valuable insights into the epitranscriptomic regulation of gene expression and metabolite accumulation in barley root tip under Al stress.