Weighted Gene Co-Expression Network Analysis Reveals Key Pathways and Hub Genes Associated with Successful Grafting in Pecan (Carya illinoinensis)

Patch budding (bud grafting) is a commonly used method for pecan reproduction; however, the grafting survival rate varies with cultivars. Clarifying the underlying mechanisms of successful grafting is pivotal for graft technique improvement. Here, weighted gene co-expression network analysis (WGCNA) was conducted to dissect the key pathways and genes related to the successful grafting of pecan. Based on the transcriptome data of two contrasting cultivars (an easy-to-survive cultivar ‘Pawnee’ and a difficult-to-survive cultivar ‘Jinhua’) in response to budding, all the genes with variable transcripts were grouped into 18 modules. There were two modules that were significantly correlated with the trait of different cultivars. Enrichment analysis showed that several enriched gene ontology (GO) terms were related to oxidative detoxification and genes associated with hormone signaling pathway occupied a high ratio for the two modules. A total of 52 hub genes were identified, and 48 showed promoter polymorphisms between the two cultivars. Our study suggested that oxidative detoxification and hormone signaling were probably the key pathways for the successful grafting of pecan. The 48 hub genes identified here might be the key genes that led to the divergence of graft survival rates among different pecan cultivars. Our results will lay a foundation for future graft technique improvement in pecan.