Transcriptome of lncRNAs and mRNAs and Their Network Profile in Relation to Phenotypic Variation in Grafted Peach–Apricot Chimeras

Grafted plants carrying DNA from both species are prone to new phenotypes. Specific long non-coding RNA (lncRNA) sequences are known to play roles in the formation and development of grafted plants. However, the roles of lncRNAs in phenotypic variation in grafts between peach and apricot remain unexplored. In this study, mixed tissues (leaves, buds and fully bloomed flowers) of peach branches from heterografts between apricot/peach (A/P) and peach/apricot (P/A) and homografted peach (SP) were collected for transcriptome sequencing. The differentially expressed genes (DEGs) and lncRNAs (DElncRNAs) between A/P and P/A were identified as candidates mediating the formation of divergent traits. Compared with SP, 1115 and 624 DEGs were detected in A/P and P/A, respectively. There were 173 DEGs shared between A/P and P/A, whereas the transcripts of 942 genes were specifically altered in A/P and 451 DEGs were specific to P/A. There were 29 DElncRNAs in A/P and 26 DElncRNAs in P/A, of which, 21 DElncRNAs were specific to A/P and 18 were specific to P/A. The biological functions of the DEGs and DElncRNAs were predicted via GO and KEGG enrichment analyses. A total of 24 co-expressed ‘lncRNA-mRNA’ pairs were identified, including 14 ‘lncRNA-mRNA’ pairs in A/P and 10 ‘lncRNA-mRNA’ pairs in P/A. The ‘MSTRG.17020.2-XM_007210198-2’ pair potentially participates in aminoacyl biosynthesis, and the ‘MSTRG.8395.1-XM_007217967.2’ pair may regulate galactose metabolism. The lncRNA MSTRG.6365.3 may regulate defense response through altering the levels of XM_020556240.1 and XM_020556234.1. These findings provide valuable insights into the molecular mechanisms underlying grafting-induced differential trait formation and establish a foundation for further research on the functional roles of ‘lncRNA-mRNA’ pairs in fruit tree grafting systems.