Gene expression and metabolite analysis reveal importance of faster pathogen recognition and reduced pattern triggered immunity based cell death responses for Phytophthora nicotianae tolerance in citrus

Understanding the basis of Phytophthora tolerance is essential for targeted improvement of citrus. Here, we determined the short term and long-term plant (leaf and root tissues) response of Phytophthora tolerant (Swingle citrumelo; SC) and susceptible (rough lemon; RL) citrus genotypes by examining important defense related genes belonging to structural reinforcement, receptors, salicylic acid (SA) & jasmonic acid (JA) pathways. We also estimated downstream activity of the enzymes lipoxygenase (LOX), phenylalanine ammonia lyase (PAL) and total phenols. The plants were artificially inoculated with mycelium and zoospores of P. nicotianae in root zone and studied at 34- and 105- days post inoculation (dpi). SC roots strongly upregulated receptor like genes viz., LecRK-I.9, BIR2, MPK4, MKK1 and TTG2 at 34-dpi; RL in contrast showed delayed (at 105-dpi) upregulation of LecRK-I.9, MKK1 and TTG2. SC also showed higher PAL activity, higher phenolic content and stronger expression of GSL5 in roots at 34-dpi to create barrier against invading pathogen. SC roots upregulated SA pathway genes like ICS1, EDS1, PAD4, CBP60g, PR-1 at 34-dpi, whereas, RL showed higher expression of JA-related genes (LOX2 and AOS) at 105-dpi, suggesting their role in favoring necrotrophic phase. In general, the SC leaf at 105-dpi mimicked the defense response of its roots at 34-dpi. Study results suggest that early perception, preformed barriers and restricting the pathogen in biotrophic phase are the key tolerance mechanisms of Swingle citrumelo to P. nicotianae. The differentially expressing receptor genes (LecRK-I.9, BIR2) and SA mediated defense gene, PR1 in Swingle citrumelo should further be explored for utilization in citrus rootstock improvement.