Identification of miRNA-mRNA pairs involved in the development of grafted peach hybrids by integrating sRNAome and transcriptome

Abstract

Plant grafting is widely practiced with fruit trees and horticultural crops, and can lead to graft hybrid formation with desirable traits that can solve production problems. MicroRNAs have been identified that play an important role in the formation and development of grafted plants. However, the role of miRNAs in the development of grafted peach hybrids remains unexplored. In this study, we first created two-way grafted peach hybrids (apricot/peach and peach/apricot) with variation phenotypes. We then examined the expression of the biosynthesis of conserved miRNAs in grafted peach hybrids and identified four miRNA biosynthesis genes (PpRDR6, PpAGO5, PpRDR1, and PpDCL8) that were involved in the development of graft hybrids with differential expression. Moreover, miRNAs and their target genes involved in the grafted peach hybrids were identified by high-throughput sequencing. In total, 711 miRNAs, including 307 known and 404 new ones, were obtained from two grafted peach hybrids, and 8198 targets were evaluated. Among the abovementioned miRNAs, 84 showed significant expression differences in grafted peach hybrids when compared with self-rooted peach, and 8118 of their targets were also obtained. According to the expressional profile of mRNA and miRNA, the significant opposite expression between 55 miRNA-mRNA interaction pairs in apricot/peach and 83 miRNA-mRNA interaction pairs in peach/apricot were observed, in which 5 were confirmed by qRT-PCR. Functional annotation of the analysis demonstrates that these interaction pairs are involved in chloroplast development, flower development, cell tip growth, and defense response, as are the key miRNA-mRNA pairs for the development of grafted peach hybrids. Finally, the PC-5p-172,144_25-XM_007199802.2 and miR482-XM_020561265.1 pairs that were involved in the development of grafted peach hybrids were further verified using 5′RACE and dual-luciferase assay. These results supply new insights for the development of grafted peach hybrids and also lay a theoretical basis for future functional exploration of these candidate miRNAs pairs and their targets in fruit tree grafted hybrids and for improving the cultivation of peaches.