Genome-Wide Identification and Expression Analysis of the NIN-LIKE Protein (NLP) Gene Family in Salvia Miltiorrhiza.

NIN-like proteins (NLPs) are plant-specific transcription factors with a conserved RWP-RK domain that can bind to nitrate-responsive cis-elements (NREs) in target gene promoters. NLPs play essential roles in nitrogen uptake, transport, metabolism, and are also involved in nitrate signaling, root development, and secondary metabolism. Salvia miltiorrhiza is a medicinal plant valued for its roots and rhizomes. It mainly contains two types of active ingredients: tanshinones and salvianolic acids. Previous studies have shown that nitrogen availability significantly affects the growth of S. miltiorrhiza and the accumulation of its active ingredients, but the regulatory mechanism has not yet been fully elucidated. In this study, 11 SmNLPs were identified in the S. miltiorrhiza genome through bioinformatic analyses, and they were found to be distributed across eight chromosomes. Phylogenetic analysis grouped them into three subfamilies, with members in the same clade sharing similar gene structures and conserved domains. Promoter analysis revealed that SmNLPs harbor cis-acting elements involved in stress responses, hormone signaling, development, and light responses. Tissue-specific expression analysis of two-year-old S. miltiorrhiza plants showed that SmNLPs are broadly expressed in roots, stems, leaves, and flowers, exhibiting distinct tissue-specific patterns. Among them, most SmNLPs, particularly SmNLP3 and SmNLP8, were significantly upregulated in nitrogen-deprivation hairy roots. Co-expression analysis based on transcriptome data suggested that SmNLP3, SmNLP8, and SmNLP10 may be involved in the regulation of tanshinone and salvianolic acid biosynthesis. These findings provide new insights into the potential roles of NLPs in nitrogen response and secondary metabolism in S. miltiorrhiza, laying a foundation for future functional studies and metabolic engineering.