Table 2: DEGs with annotated function in defense hormone biosynthesis and signaling.

Apple gene modelFunctional annotationsLog2FC

Ethylene (ET) biosynthesis
 MDP0000286210ACS 7-like+2.0
 MDP0000413933ACS 8-like+2.1
 MDP0000282901ACO 4-like+2.1
 MDP0000593536ACO homolog+2.1
 MDP0000473933ACO 1-like+2.9

Jasmonic acid (JA) biosynthesis
 MDP0000281525Linoleate 13S-lipoxygenase 2-1+3.0
 MDP0000753547Linoleate 13S-lipoxygenase 2-1+2.4
 MDP0000154928Lipoxygenase−2.5

ET/JA signaling
 MDP0000297771ERF 4+4.0
 MDP0000262710ERF 027-like+2.8
 MDP0000128326ERF RAP2-11-like+2.4
 MDP0000246808ERF 1B-like−2.1
 MDP0000447570ERF 1B-like−2.2
 MDP0000825712Topless-related protein 4-like+2.6
 MDP0000313085Topless-related protein 1-like isoforms X3−2.2

Gibberellin (GA) biosynthesis and signaling
 MDP0000769340GA receptor GID1+5.2
 MDP0000682570GA receptor GID1+3.6
 MDP0000161639GA receptor GID 1C-like+2.3
 MDP0000431628DELLA protein RGL1-like+2.5
 MDP0000126248GA 2-beta-dioxygenase 7-like+2.4
 MDP0000226405GA 2-beta-dioxygenase 2-like−2.1

Abscisic acid biosynthesis
 MDP0000300259ABA 8′-hydroxylase 3-like+2.1
 MDP0000326412ABA 8′-hydroxylase 2+3.7

Cytokinin biosynthesis
 MDP0000318353Cytokinin dehydrogenase 1-like+2.6

Apple gene model is based on available Malus_x_domestica.v3.0.a1_gene_set at https://www.rosaceae.org. Function annotation is based on the blastX search against NR database in GenBank. Variations of transcript abundance are based on the comparison between B.9 and G.935 and expressed as Log2fold change; + indicated higher transcript level in the root of G.935 over that in B.9; indicated the opposite.