Integrative physiological, transcriptome, and metabolome analysis reveals the effects of nitrogen sufficiency and deficiency conditions in apple leaves and roots

Abstract Nitrogen (N) is an essential element for plant growth and development. In this study, physiological, transcriptome and metabolite analyses of apple leaves and roots were compared under different N conditions. The results indicated that different N stresses influenced plant growth, the content of soil plant analytical development (SPAD) value and photosynthesis in apple seedlings. The content of hydrogen peroxide (H2O2), and the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS) and glutamine antinotransferase (GOGAT) were also affected by different N stresses. RNA-Seq was used to analysis the influence of different N tolerances in apple seedlings. Gene Ontology (GO) analysis of differentially expressed genes (DEGs) indicated that apple trees might affect the responses to photosynthesis, organic hydroxy compound biosynthetic process, and secondary metabolite biosynthetic process under N stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that DEGs focused on photosynthesis and secondary metabolite biosynthetic process. There were 527 differential metabolites in LNL/CKL, 157 in HNL/CKL, 477 in LNR/CKR, and 232 in HNR/CKR. The metabolome analysis indicated that total of 1004 and 389 significant differential metabolites were identified under low N and high N conditions in apple. Apple seedlings regulate the carbon metabolism, nitrogen metabolism and flavonoid pathway to adapt the different nitrogen environments. This research provide understanding for the metabolic processes underlying different N responses and provide a foundation for improving the efficiency of N use in apple trees.