Table 2.

Candidate anthocyanin regulatory genes in Malus halliana.

Gene family	NO. alla	S1 vs. S2		S1 vs. S3		S2 vs. S3		S1 vs. S2 vs. S3
		NO. upb	NO. downc	NO. up	NO. down	NO. up	NO. down	Profle 0	Profile 7
MYB	111	16	53	31	61	29	31	27	5
NAC	94	18	34	47	32	44	17	10	19
ERF	88	13	36	24	25	40	18	9	4
bHLH	79	9	35	26	36	41	19	18	8
WRKY	57	6	19	39	6	43	2	1	8
WD40	25	4	12	4	13	4	4	5	1
MADS-box	23	3	4	5	15	8	9	3	0
bZIP	20	7	1	6	10	2	12	0	3
Total	497	76	194	182	198	211	112	73	48

^aindicates the total number of regulatory genes in DEGs, ^bindicates the number of upregulated genes in each comparison, and ^cindicates the number of downregulated genes in each comparison. All candidate anthocyanin regulatory genes in this table are screened from DEGs.