Multi-omics analysis revealed that MAPK signaling and flavonoid metabolic pathway contributed to resistance against Meloidogyne incognita in the introgression line cucumber.

Inhibiting giant cells (GCs) development is an important characteristic of introgression line cucumber IL10-1 against Meloidogyne incognita proved by our previous study, but the systematic regulatory pathways were unknown. To reveal the regulation pathways more comprehensively, in the current study, we performed a joint analysis of RNA-Seq and lable-free quantitative proteomics between the IL10-1 (resistant) and the CC3 (susceptible cucumber) after inoculation with M. incognita. The results indicated that flavonoid biosynthesis pathway was specifically enriched in IL10-1. And protein species of Csa5P590220 and Csa5P589940 associated with flavonoid biosynthesis were highly translated in IL10-1 compared with these in CC3 at 3 days post inoculation (dpi), which would resulted in the excess of flavonoids in IL10-1 roots. In addition, phosphoproteomic analysis found that phosphorylated protein species involved in MAPK signaling cascade were enhanced in IL10-1, while they were inhibited in CC3 at 3 dpi. Accordingly, we speculate that the enhanced MAPK cascade signaling plays an important role in signal transduction for IL10-1 regulating the flavonoid biosynthesis. Knowledge from the study provide important regulatory pathways and protein species of introgression line cucumber against M. incognita, which will help in efforts to improve the recognition of the resistance mechanism of plants against nematode. SIGNIFICANCE: The current approach of joint analysis in transcription level, protein level and protein phosphorylation level more comprehensively revealed the different expression patterns at the molecular level of resistant and susceptible cucumber after inoculation with M. incognita. Based on the different expression patterns, we explore the pathway of resistance regulation of resistant cucumber IL10-1. Moreover, our results are helpful for the discovery of key genes and then apply them to M. incognita-resistance breeding.