Comparative transcriptome analysis unravels key factors regulating nitrogen use efficiency in chrysanthemum

Abstract Background: Nitrogen (N) is a limiting factor that determines yield and quality of chrysanthemum. Genetic variation in N use efficiency (NUE) has been reported among genotypes of chrysanthemum. We performed transcriptome analysis of two chrysanthemum genotypes, ‘Nannonglihuang’ (‘LH’, N-efficient genotype) and ‘Nannongxuefeng’ (‘XF’, N-inefficient genotype), under low N (0.4 mM/L N) and normal N (8 mM/L N) treatments for 15 d and 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. Results: The two genotypes exhibited contrasting responses to different N treatments. N-efficient genotype ‘LH’had significant superiority in agronomic traits, N accumulation and glutamine synthase (GS) activity, under normal N and low N treatments. Transcriptome analysis revealed that low N treatment promoted root growth and increased the expression of partial N uptake genes, genes related to auxin, abscisic acid, and gibberellin signal transduction in roots of ‘LH’. N recovery treatment increased the expression of genes related to the cytokinin signal transduction in roots of ‘LH’. The expression of NRT2-1, AMT1-1, Gln1, genes related to gibberellin (GID1B, GID2, GAI) and cytokinin signal transduction (AHK2, AHK3, AHK4, ARR4, ARR5, ARR9) in roots of ‘LH’ was higher than that 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’ were more sensitive to different N treatments than those of ‘XF’. The network analysis also identified hub genes like bZIP43, bHLH93, NPF6.3, IBR10, MYB62, PP2C, PP2C06 and NLP7, which may be the key regulators of N-mediated response in chrysanthemum and play crucial roles in enhancing NUE and resistance to low N stress in the N-efficient chrysanthemum genotype. Conclusion: This study unravels key factors of regulating NUE in chrysanthemum at the genetic level, and could be useful for genotype improvement and breeding of high NUE chrysanthemum genotypes.