Transcriptome analysis using RNA-Seq revealed the effects of nitrogen form on major secondary metabolite biosynthesis in tea (Camellia sinensis) plants

The effects of the different forms of N, ammonium (NH4 (+)) and nitrate (NO3 (-)), on secondary metabolite biosynthesis in tea plants are well known. However, the mechanisms of underlying these effects are not well understood. This study generated transcriptomic profiles of Camellia sinensis treated with different N forms for 5 min and 96 h using RNA-Seq. Analysis of differentially expressed genes (DEGs) showed that the regulated DEGs involved in the secondary pathways in the NH4 (+)-treatment were more abundant than those in the NO3 (-)- and NH4 (+)+NO3 (-)-treatments, demonstrating the preference of tea plants for NH4 (+) at the gene level. Expression analysis at different treatment times showed that increasing treatment time changed not only the number of DEGs involved in secondary metabolism but also the pathways of secondary biosynthesis. In addition, only a few DEGs involved in secondary metabolism were regulated in more than one treatment. These results suggested that the secondary biosynthesis pathways regulated by N were dependent on the N form and treatment time. The analysis of DEGs related to transport and N metabolism further confirmed this conclusion. Moreover, the change of DEGs in NO3 (-)-treated tea plants suggested increase of treatment time might attenuate the flavonoid biosynthesis and enhance the theanine and caffeine biosynthesis. The identification of differentially expressed transcription factors revealed the possible crosstalk between the secondary metabolic pathways in C. sinensis. These results help facilitate an understanding of the effects of N on tea quality and represent a valuable reference for the rational application of N fertiliser on tea plantations.