The transcriptome variations of Panaxnotoginseng roots treated with different forms of nitrogen fertilizers

Xiaohong Ou,Dahui Liu,Binglian Zheng,Yun Zheng,Xiuming Cui,Ye Yang,Shipeng Li,Peiran Liao

doi:10.1186/s12864-019-6340-7

Abstract

BackgroundThe sensitivity of plants to ammonia is a worldwide problem that limits crop production. Excessive use of ammonium as the sole nitrogen source results in morphological and physiological disorders, and retarded plant growth.ResultsIn this study we found that the root growth of Panax notoginseng was inhibited when only adding ammonium nitrogen fertilizer, but the supplement of nitrate fertilizer recovered the integrity, activity and growth of root. Twelve RNA-seq profiles in four sample groups were produced and analyzed to identify deregulated genes in samples with different treatments. In comparisons to NH{~}_{4}^{+} treated samples, ACLA-3 gene is up-regulated in samples treated with NO{~}_{3}^{-} and with both NH_{4}^{+} and NO{~}_{3}^{-}, which is further validated by qRT-PCR in another set of samples. Subsequently, we show that the some key metabolites in the TCA cycle are also significantly enhanced when introducing NO{~}_{3}^{-}. These potentially enhance the integrity and recover the growth of Panax notoginseng roots.ConclusionThese results suggest that the activated TCA cycle, as demonstrated by up-regulation of ACLA-3 and several key metabolites in this cycle, contributes to the increased Panax notoginseng root yield when applying both ammonium and nitrate fertilizer.

Highlights

The sensitivity of plants to ammonia is a worldwide problem that limits crop production
These results suggest that the activated TCA cycle, as demonstrated by up-regulation of ATP-citrate lyase A-3 (ACLA-3) and several key metabolites in this cycle, contributes to the increased Panax notoginseng root yield when applying both ammonium and nitrate fertilizer
By using RNA-seq analysis, this study showed the gene, ACLA-3, played an important role in the TCA cycle, which could involve in the alleviation pathway of ammonium toxicity by regulating the carbon and nitrogen metabolism of P. notoginseng

Summary

Introduction

The sensitivity of plants to ammonia is a worldwide problem that limits crop production. Average N application rate in P. notoginseng cultivation is approximately 250 kg∗hm−2 [8], causes soil available N with an average of 213.65 mg∗kg−1 [9], which is 42.4% higher than the standard of extremely rich level ( 150 mg∗kg−1). Ammonium toxicity is a common phenomenon in agricultural system, and there are a few measures to prevent or alleviate it [10,11,12] Among those measures, ammonium and nitrate combined application is thought to be an effective way to prevent ammonium toxicity, but its mechanism is not unified yet [13]. Roosta et al [14] suggested that nitrate addition can increase cytokinin synthesis and translocation to alleviate ammonium toxicity of cucumber plants. Nitrate-dependent alleviation of ammonium toxicity in A. thaliana is linked to nitrate signaling, uptake and reduction [16], anion channel SLAH3 [13]

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Discussion

Conclusion