Table 7: DEGs encoding pathogenesis-related proteins and cell wall metabolism enzymes.

Apple gene modelFunctional annotationsLog2FC

Pathogenesis-related protein 1-like
 MDP0000202342Pathogenesis-related protein 1-like+5.5
 MDP0000144351Pathogenesis-related protein 1-like+3.8

Chitinase family protein
 MDP0000202342Chitinase family protein−3.2
 MDP0000144351Chitinase family protein−2.9
 MDP0000171646Acidic endochitinase SE2-like−2.6
 MDP0000282918Acidic mammalian chitinase-like−2.1

Thaumatin-like protein
 MDP0000916930Thaumatin-like protein 1a+4.9
 MDP0000205389Thaumatin-like protein 1a+2.9
 MDP0000552328Thaumatin-like protein 1a+2.3
 MDP0000218699Thaumatin-like protein 1a+2.1
 MDP0000293451Thaumatin-like protein 1-like+2.1
 MDP0000124752Thaumatin-like protein 1a−3.3

Glucan endo-1,3-beta-glucosidase
 MDP0000908326Glucan endo-1,3-beta-glucosidase 9-like−2.2
 MDP0000231628Glucan endo-1,3-beta-glucosidase 4-like−2.0
 MDP0000237685Glucan endo-1,3-beta-glucosidase 12-like−5.8

Pectin esterase inhibitor
 MDP0000188907Pectin esterase inhibitor 16+3.1
 MDP0000161463Pectin esterase inhibitor 35+3.0
 MDP0000299506Pectin esterase inhibitor 24+2.5
 MDP0000611653Pectin esterase inhibitor 24+2.4
 MDP0000299884Pectin esterase inhibitor 24+2.2
 MDP0000503248Pectin esterase inhibitor family protein+3.0

Polygalacturonase
 MDP0000845683Polygalacturonase+2.3
 MDP0000845685Polygalacturonase+2.6

Cellulose synthase-like protein
 MDP0000208533Cellulose synthase-like protein E2+4.1
 MDP0000172542Cellulose synthase-like protein G3+2.4
 MDP0000223480Cellulose synthase-like protein E1−2.1

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.