Comparative Genomic Analysis and Expression Profiling under Cold Stress of NAC Transcription Factors in Rosaceae

The NAC gene family consists of plant-specific transcription factors that regulate organ development and stress responses.Despite their biological importance, NAC genes remain poorly characterized in Rosaceae crops.In this study, we re-annotated NAC genes in apple (Malus domestica), pear (Pyrus pyrifolia), Arabidopsis (Arabidopsis thaliana), and rice (Oryza sativa).A total of 677 NAC genes were identified, including 92 newly annotated genes.Of these, 46 (50.0%) were in apple and 36 (39.1%) in pear, indicating that the majority of newly identified genes are specific to Rosaceae crops.A gene ontology analysis revealed that NAC genes are primarily associated with transcriptional regulation and DNA binding, consistent with their role as transcription factors.Analyses of the domain architecture and sequence conservation showed that several subdomains within the NAC domain are highly conserved across species.Motif and phylogenetic analyses classified NAC genes into nine subfamilies, with lineage-specific expansions observed in apple and pear.An expression analysis under cold stress in pear identified differentially expressed NAC genes co-expressed with cold tolerance-related genes, suggesting their potential regulatory roles.These results provide a comprehensive characterization of NAC genes in Rosaceae and offer a valuable resource for future functional and breeding studies.