Deciphering intra-connectivity of gene network response to drought and salinity in apple

Drought and salt stresses severely constrain apple yield and quality. Using <i>in vitro</i> plantlets of apple '<i>Golden Delicious</i>' as experimental materials, we aimed to dissect the stress-responsive mechanisms and provide a basis for the genetic improvement of apple stress resistance. Plantlets under NaCl (salt stress) and PEG (drought stress) treatments, with samples collected at 0, 1, 6, 12 and 24 h post-treatment for transcriptome sequencing. Gene expression levels were quantified as FPKM values to analyze temporal dynamic changes, and Differentially Expressed Genes (DEGs) were screened with |log2(FoldChange)| >1 and padj<0.05. Co-expression analysis was performed to explore the interaction patterns of stress-related genes, coupled with Gene Ontology (GO) (p-value<0.05) and Kyoto Encyclopedia of Genes and Genomes (KEGG) (FDR<0.05) enrichment analyses. The core regulatory network of the "hormone signal-metabolic pathway" in apple in response to salt/drought stresses was identified, with the key nodes of this network clarified as <i>MdAREB3/MdJAZ1</i>, <i>MdPETE1</i>, <i>MdSNF1</i> and <i>MdGH9C2</i>, which are involved in hormone signal transduction, photosynthesis and carbohydrate metabolism, respectively. Stage-specific expression differences of key DEGs at 0, 1, 6, 12 and 24 h post NaCl/PEG treatments were further characterized via comparison of their expression patterns under the two stress conditions. This study systematically identifies the core regulatory network and its key nodes in apple in response to salt and drought stresses, thereby providing a reliable molecular basis for deciphering stress resistance mechanisms, verifying key gene functions, and the genetic improvement of salt/drought-tolerant apple varieties.