Comparative transcriptome analysis identifies key regulators of nitrogen use efficiency in chrysanthemum

Nitrogen (N) is a limiting factor that determines the yield and quality of chrysanthemum. Genetic variation in N use efficiency (NUE) has been reported among chrysanthemum genotypes. We performed a transcriptome analysis of two chrysanthemum genotypes, ‘Nannonglihuang’ (LH, N-efficient genotype) and ‘Nannongxuefeng’ (XF, N-inefficient genotype), under low N (0.4 mmol L^–1 N) and normal N (8 mmol L^–1 N) treatments for 15 d and an N recovery treatment for 12 h (low N treatment for 15 d and then normal N treatment for 12 h) to understand the genetic factors impacting NUE in chrysanthemum. The two genotypes exhibited contrasting responses to the different N treatments. The N-efficient genotype LH had significant superiority in agronomic traits, N accumulation and glutamine synthase activity under both normal N and low N treatments. Low N treatment promoted root growth in LH, but inhibited root growth in XF. Transcriptome analysis revealed that the low N treatment increased the expression of some N metabolism genes, genes related to auxin and abscisic acid signal transduction in the roots of both genotypes, as well as genes related to gibberellin signal transduction in roots of LH. The N recovery treatment just increased the expression of genes related to cytokinin signal transduction in roots of LH. The expression levels of the NRT2.1, AMT1.1, and Gln1 genes related to gibberellin and cytokinin signal transduction were higher in roots of LH than in XF under different N treatments, suggesting that the genes related to N metabolism and hormone (auxin, abscisic acid, gibberellin, and cytokinin) signal transduction in roots of LH are more sensitive to different N treatments than those of XF. Co-expression network analysis (WGCNA) also identified hub genes like bZIP43, bHLH93, NPF6.3, IBR10, MYB62, PP2C, PP2C06 and NLP7, which may be the key regulators of N-mediated responses in chrysanthemum and play crucial roles in enhancing NUE and resistance to low N stress in the N-efficient chrysanthemum genotype. These results revealed the key factors involved in regulating NUE in chrysanthemum at the genetic level, which provides new insights into the complex mechanism of efficient nitrogen utilization in chrysanthemum, and can be useful for the improvement and breeding of high NUE chrysanthemum genotypes.