Transcriptomic Analysis Revealed Hormone-Related and Receptor-Like Kinase Genes Involved in Wound Healing of ‘Duli’ and its Resistance to Valsa Pyri

Valsa canker is a destructive fungal disease that results in a serious loss of production. The pathogen Valsa pyri (Vp) usually infiltrates the bark and xylem via the wound. ‘Duli’ (Pyrus betulifolia), a rootstock with high tolerance to this disease and multiple other stresses, is widely planted in northern China. We found that wound healing plays a crucial role in the resistance of ‘Duli’ against Vp infection. Nevertheless, elucidation of the molecular mechanism of this process has been largely limited. Using RNA sequencing (RNA-seq), we investigated dynamic gene expression profiles of ‘Duli’ and ‘Zaosu’ (Pyrus bretschneideri, susceptible) phloem tissues which 0–3 mm around the wounded site that were cultured for 1, 3, and 7 days after wounding. Quantitative real-time PCR (qRT-PCR) was used to confirm data veracity. After wounding at 1, 3, and 7 days, 4930, 4652, and 6279 differentially expressed genes (DEGs) were found from ‘Duli’, compared to 1641, 1968, and 3347 in ‘Zaosu’, respectively. Functional enrichment analysis revealed that the DEGs associated with “cell wall organization and biogenesis”, “biosynthesis of secondary metabolites” and “cell wall organization. pectin” were enriched both in ‘Duli’ and ‘Zaosu’. Additionally, expressions of DEGs encoding receptor-like kinase (RLK) subfamily Extensin, LRR-III, LRR-IV, LRR-IX, LRR-XI-1, LRR-XII-1, RLCK-IXa and RLCK-V, and transcription factor CRE1, TF, ABF, TGA, and MYC2 were rapidly activated in ‘Duli’, but only a subtle induction in ‘Zaosu’. In conclusion, DEGs related to cell wall thickening are rapidly and continuously induced in ‘Duli’, which plays a positive role in the formation of protective tissues. Notably, JA-, SA-, LRR-, RLCK-, and Extensin-related DEGs probably participated in the regulation of multiple molecular networks and contributed to the quick wound healing of ‘Duli’.