Objective  This paper intends to analyze the mobile mRNA in heterologous grafted plants, explore the effects of sequence and functional characteristics on mRNA transfer, reveal the principle of mRNA transfer, and provide a theoretical basis for the directional regulation of grafting.

  Method  With the transcriptome data of the various grafts, the coding region length and GC content of transfer mRNAs were calculated by Tbtools software and their correlation with mRNA transfer was further analyzed by Excel software. The sequence identity analysis via BLASTP was applied to find out the co-transfer mRNAs in different grafts. Function annotation and metabolic pathways analysis of the mRNAs were conducted through GO and KEGG database.

  Result  (1) The average length of root-to-shoot or shoot-to-root transfer mRNA was 1 573 and 1 547, respectively. The mRNA transfer ratio increased progressively along with the mRNA length increasing. Obviously, the transfer ratio of the root-to-shoot mRNA was larger than that of the shoot-to-root mRNAs, and the tendency was more significant with the mRNA length increasing. (2) When the GC content was 52% − 54%, the mRNA transfer rate from stem to root was the highest (3.66%), and when the GC content was 46% − 48%, the mRNA transfer rate from root to stem was the highest (4.71%). (3) Co-transfer mRNA analysis showed 1 032 root to shoot and 1 727 shoot to root mRNA were present in at least 2 grafts, which mainly participated in carbon metabolism, amino acid synthesis, and signal transduction. Even, 5 root-to-shoot mRNA and 2 shoot-to-root mRNA were commonly present in 7 grafts that mainly involved in hormone transport and basic metabolism.

  Conclusion  mRNA transfer in heterologous grafted plants is closely related to mRNA length, GC content, gene function and action position. mRNA differences and exchanges between heterologous plants give grafted plants new phenotypes.