Genome-Wide Identification of the NAC Gene Family and Expression Analysis Under Contrasting Salinity in Zostera marina L.

Eelgrass (Zostera marina L.) is a marine angiosperm exposed to substantial salinity fluctuations, yet the transcriptional mechanisms associated with its salinity adaptation responses remain incompletely understood. To characterize the NAC transcription factor family and its potential involvement in salinity responses, we performed genome-wide identification, phylogenetic, structural, duplication, promoter, and expression analyses in Z. marina, followed by quantitative reverse transcription PCR (qRT-PCR) validation. Sixty-three ZmNAC genes were identified and classified into six phylogenetic groups. Most encoded proteins contained a conserved N-terminal NAC domain but varied considerably in length, motif composition, gene structure, and predicted subcellular localization. Duplication analysis classified 55 genes as dispersed duplicates, seven as whole-genome duplication (WGD) or segmental duplicates, and one as a proximal duplicate. Promoter analysis identified 64 cis-acting element types associated mainly with light, phytohormone, and stress responses. RNA-seq analysis of roots, stems, and leaves after 24 h at NaCl concentrations of 0‰, 24‰, and 40‰ revealed distinct salinity- and tissue-dependent expression patterns among the ZmNAC family members. Expression patterns of four candidate genes in leaves, assessed by qRT-PCR, were largely consistent with the RNA-seq results. These findings reveal structural and expression diversification within the ZmNAC family and identify candidate genes for further functional investigation of salinity responses in eelgrass.