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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. Full article

Plant distant grafting can produce stable genetic variation, which is a new method for germplasm innovation. Two chimeras, peach/apricot (PA) and apricot/peach (AP), were created through two-way grafting between peach and apricot. The leaves, flowers and fruit phenotypes of chimeras were significantly different to self-rooted rootstock. In order to investigate the causes of such changes, transcriptome and proteome integrative analyses were conducted on apricots from these two chimeras. Many differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) that may be connected to the development of grafted apricot hybrids were identified and explored based on function. Moreover, we found 76 genes in forward-grafted PA and 46 in reverse-grafted AP that overlapped both in DEGs and DEPs (DEGs/DEPs) via transcriptome–proteome integrative analysis. Mapping the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database in PA and AP, the top significant enrichment pathways of DEGs/DEPs included lipid metabolism (fatty acid elongation, cutin, suberine and wax biosynthesis, fatty acid degradation and alpha-linolenic acid metabolism) and carbohydrate metabolism (glycolysis/gluconeogenesis, starch and sucrose metabolism and galactose metabolism), revealing that lipid metabolism and carbohydrate metabolism may play an irreplaceable role in the development of grafted apricot hybrids. Taken together, this work uncovered numerous candidate transcripts and proteins involved in the development of grafted apricot hybrids. The molecular mechanisms provide new insights into this important process in other heterografting hybrids. Full article