Nitrogen deficiency differentially affects lignin biosynthesis genes and flavanols accumulation in tolerant and susceptible tea genotypes (Camellia sinensis (L.) Kuntze)

• Phenylpropanoid pathway significantly enriched under nitrogen deficiency. • Greater stability of the cell wall metabolism and secondary metabolism in tolerant genotype. • Lignin biosynthesis is activated by nitrogen deficiency in tea plant. The mechanisms of the nitrogen deficiency (ND) response are complex and not sufficiently studied in evergreen tree crops. The aim of this study was to investigate the nitrogen deficiency response in two contrasting tea genotypes to reveal molecular crosstalk between tea quality and tolerance to ND. The transcriptional response to two- and four-month nitrogen deficiency was analyzed in tolerant (cv. Karatum) and susceptible (cv. Kolkhida) tea genotypes. Both GO and KEGG analyses indicated that phenylpropanoid pathway was significantly enriched under nitrogen deficiency in both cultivars. Most of the transcription factor DEGs were related to ABA-mediated stress responses; the following transcription factors were upregulated in both genotypes and in both stress periods: TEAK026346 ( bZip23 ), TEAK015869 ( RADIALIS -like 3 isoform X1), TEAK022547 ( bHLH78 ) and one was downregulated TEAK030189 (MYB family transcription factor EFM like) indicating their important role for regulation of nitrogen deficiency response. Gene network of phenylpropanoid pathway DEGs indicated the abandoned edges in lignin biosynthesis DEGs. Generally, the results suggest greater stability of the cell wall metabolism and secondary metabolism in tolerant genotype under long term nitrogen deficiency. The revealed lignin biosynthesis genes can be new candidates for molecular breeding to develop tolerant tea genotypes.