Genome-Wide Identification and Expression Profiling of the NAC Transcription Factor Family in the Waterlogging-Tolerant Tree Magnolia sinostellata

Background The NAC transcription factors are master regulators of plant responses to abiotic stresses; however, their functions in woody ornamentals, particularly under waterlogging, remain poorly explored. Magnolia sinostellata , a rare and waterlogging-tolerant species, provides an ideal system to decipher these mechanisms. Results In this study, a genome-wide analysis identified 96 MsNAC genes in M. sinostellata , which were phylogenetically classified into 17 distinct subgroups. Gene structure and motif analyzes revealed considerable diversity, with several members harboring auxiliary functional domains beyond the conserved NAC domain, suggesting potential functional diversification. Promoter cis-acting element analysis uncovered an abundance of stress-responsive elements, among which abscisic acid (ABA, 19.3%) and methyl jasmonate (MeJA, 13.7%) responses were the most prominent, highlighting a complex regulatory landscape intertwined with hormonal and light signaling pathways. Collinearity and evolutionary pressure analyzes demonstrated that the expansion of the MsNAC family was primarily driven by gene duplication events under strong purifying selection (Ka/Ks < 1). Transcriptomic and RT-qPCR analyzes further revealed that MsNAC genes exhibit tissue-specific and temporally dynamic expression patterns under waterlogging stress. Notably, roots, as the primary sensing organ, mounted the most pronounced response. The key candidate MsNAC 66 was significantly and persistently upregulated, while others, including MsNAC 14, MsNAC 16, MsNAC 63, MsNAC 65, and MsNAC 70, displayed transient induction patterns. Conclusions Our study provides the first comprehensive genomic characterization of the NAC family in M. sinostellata and identifies several core candidate genes with putative roles in the root-centric adaptive response to waterlogging, as determined by their expression dynamics. These findings not only advance our understanding of NAC-mediated stress tolerance in woody plants but also offer valuable genetic resources for the molecular breeding of waterlogging-resistant magnolia cultivars.