Integrated physiological, element content, transcriptomic and weighted gene co-expression network analysis provide...

Zinc (Zn) and iron (Fe) deficiencies are pervasive abiotic stresses that severely limit the productivity and nutritional quality of tropical crops, including the economically important Areca catechu. To elucidate the comprehensive response mechanisms of areca to Zn/Fe deficiencies, we conducted an integrated multi-omics analysis. This combined physiological assessment, elemental profiling, transcriptomic sequencing, and weighted gene co-expression network analysis (WGCNA) on seedlings subjected to prolonged (45 day) Zn/Fe deficiency. Our results showed that this prolonged stress significantly altered leaf microstructure, reduced photosynthetic carbon (C) assimilation, and triggered tissue-specific compensatory accumulation of Fe (in L3 leaves under Zn deficiency) or Zn (in L3 leaves under Fe deficiency). Transcriptome sequencing revealed that phenylpropanoid/flavonoid biosynthesis and xyloglucan metabolism pathways were consistently enriched among differentially expressed genes (DEGs) across tissues. Seven stress-specific modules and hub genes related to Zn/Fe deficiency in areca were identified by WGCNA. These results demonstrated that phenylpropanoid/flavonoids metabolism and xyloglucan-mediated cell wall remodeling are central to Zn/Fe deficiency adaptation, while identified transporters and transcription factors (TFs) form critical regulatory networks in Zn/Fe homeostasis in A. catechu. Our study demonstrated the core adaptive pathways (phenylpropanoid/flavonoid and xyloglucan metabolism) and regulatory networks for areca's adaptation to Zn/Fe deficiency, providing genetic resources for breeding nutrient-efficient areca varieties.