Transcriptome analysis for deep understanding the dwarfing mechanism of Malus dwarf mutant rootstock A1d

•Fuji6 scions grafted on A1d stock (A-F) possess higher level of GAs and GA insensitive.•Multiple plant hormone signal transduction and metabolism pathways were affected by A1d stock.•Down-regulation of IAA signal transduction IAA PAT and cell wall degradation in A-F.•Up-regulation of flavonoid biosynthesis and lignin biosynthesis.•Two amino acids in the conserved N-terminal DELLA region of MhRGL3b were mutated in one chromosome of A1d. A1d is dwarf mutant of Pingyi Tiancha (M. hupehensis var. Pinyiensis, PYTC) with dwarfing effect comparable to that of M26. In order to understanding how it affected scion shoot growth at transcriptional level and identify potential useful dwarf genes from it, the transcriptomic differences between the new spring shoots of apple variety “Fuji6” grafted on vigorous rootstock Pingyi Tiancha (P-F) and A1d (A-F) were investigated by RNA-Seq and followed by qRT-PCR verification in two types of scions as well as rootstocks. 494 differentially expressed genes (DEGs) were identified between two samples by RNA-Seq. Plant signal transduction, phytohormone metabolism and IAA polar transportation pathways were greatly affected by the dwarf A1d rootstock. In particular, gibberellin 2-beta-dioxygenase (GA2OX), which encodes a gibberellic acid (GA) inactivating gene, was down-regulated both in A1d rootstock and A-F, while the contents of active GA forms were higher in A-F shoots. The results of qRT-PCR revealed that genes related with IAA signal, IAA polar transportation and cell wall degradation etc. were significantly down-regulated A1d rootstock and its scions. However, down-regulation of these genes in A-F was not retrieved by GA treatment. Sequence analysis showed that two amino acids in the conserved N-terminal DELLA region of Malus domestica RGA-like 3b (MhRGL3b) were mutated in one chromosome of A1d, and designated as Mhrgl3b. We propose that the transportation of the Mhrgl3b from A1d rootstock play a dominant role in controlling the vigor of scion.