Table S2 Primer sequence of MdIDD and reference genes in quantitative real-time PCR.

Gene / Forward primer (5’-3’) / Reverse primer (5’-3’) / Sizea / Tm
MdIDD1 / TCCACCTCAGCCTACAACTTCATCA / GCTGCTGCTGCTGCTACGATT / 77 / 60.0
MdIDD2 / ATCTACAACCAGCAACAACCCAGC / GCTCAAGAACAGTGACCCATCTCCA / 130 / 60.0
MdIDD3 / ATCTGCTGCTGTCCTCCTTCCTCA / TAATGCGACTCCTGCGTAGGTGGA / 103 / 60.0
MdIDD4 / ACTCCAACAACCCATCCGCCAG / TGCCTGGTGGTTCTGATAGTTCTGT / 113 / 60.0
MdIDD5 / AGAAGCAGCAACAACCAAGGCA / GCACTACCACCACCTGATTGATGT / 149 / 60.0
MdIDD6 / ACAACCCTTCCCAATGCCCACA / AGTTGCGTGGCGGATAAATGGC / 168 / 60.0
MdIDD7 / ACCGCCTCACACACCGTCAA / GGTGGTGCTGATTGCCGTAGTAG / 139 / 60.0
MdIDD8 / TCAAATCCGACTCCGAGTGCGAAG / CGGTGGTGCTGATTGCCTTGGT / 190 / 60.0
MdIDD9 / ATCAGCATCAGCATCAGCACCAG / TGGAGAATAATGGCGAGGCAGAGA / 138 / 60.0
MdIDD10&11 / CGGATTGGAAGGCACATAGCAAGG / GCCGCCAAAGCATCACAGAAGG / 121 / 60.0
MdIDD12 / GGGCTTGACCGTGGGAGAGTTT / TTCCCAGTGCCATCGCCATTCA / 150 / 60.0
MdIDD13 / GCCTCCGCAAGCAACTCTACGAT / CAGACGCTTGAGGTTGTTGTTGGA / 181 / 60.0
MdIDD14 / TGGAGAGAAGAAGTGGAAGTGCGA / GCTCTCTTCAGTTAGGGCGTCACA / 181 / 60.0
MdIDD15&16 / ACATAATGGGTGGCGGCGATCA / CGGAGAAGCGAGGTGGTGTTGT / 175 / 60.0
MdIDD17 / CAGGGCAGGAGCGTAGGCAATA / GCCAAACCCACGAAGCAATGATG / 125 / 60.0
MdIDD18 / TGCCAGCCTCAATAAACCCACTTC / GAATGAAAGCCACGGAGGAAGGAG / 131 / 60.0
MdIDD19 / CGAGAAGAAGTGGAAGTGCGACAA / GTCCCGCCTTGAGAATAGAGTGC / 130 / 60.0
MdIDD20 / CAAACAACACCACCACCGCCTC / GGCTCTGGTCGGTTTGGTCACT / 138 / 60.0
EF-1α / ATTCAAGTATGCCTGGGTGC / CAGTCAGCCTGTGATGTTCC / 174 / 60.0

a Size means the product length (bp).

Table S3 Composition and physical and chemical characteristics of MdIDD amino acid sequences.

Proteins / Molecular weight(KD) / Isoelectric Point / Instability Index / GRAVYa / Major Amino Acidb / Aliphatic Index
MdIDD1 / 61.87 / 9.07 / 53.94 / -0.492 / S(13.5%)A(10.9%)P(8.4%) / 61.68
MdIDD2 / 47.30 / 9.16 / 51.66 / -0.644 / S(12.2%) N(8.7%) A(7.5%) / 55.62
MdIDD3 / 56.96 / 9.35 / 42.55 / -0.561 / S(8.9%) P(8.7%) L(8.0%) / 63.71
MdIDD4 / 69.47 / 8.53 / 55.18 / -0.836 / S(11.1%)G(8.9%) N(8.5%) / 51.80
MdIDD5 / 54.00 / 9.58 / 43.61 / -0.724 / S(13.5%) N(9.5%) L(8.3%) / 60.58
MdIDD6 / 57.09 / 8.99 / 44.81 / -0.754 / S(9.0%) G(9.0%)N (9.0%) / 56.11
MdIDD7 / 56.72 / 8.59 / 47.02 / -0.443 / S(14.0%) G(9.4%)A (9.0%) / 61.73
MdIDD8 / 55.78 / 8.81 / 50.06 / -0.442 / S(14.8%) G(9.3%)A (9.3%) / 57.74
MdIDD9 / 58.85 / 8.52 / 50.66 / -0.847 / S(12.2%) G(8.1%)P(7.3%) / 53.44
MdIDD10 / 53.00 / 9.2 / 50.16 / -0.705 / S(12.3%) N(7.9%)T(7.7%) / 52.21
MdIDD11 / 58.09 / 9.38 / 47.73 / -0.602 / S(12.5%) T(8.0%)N(7.9%) / 59.10
MdIDD12 / 51.23 / 9.20 / 42.62 / -0.619 / S(9.4%) P(8.4%)T(8.2%) / 60.17
MdIDD13 / 63.52 / 8.46 / 56.97 / -0.820 / S(13.0%) N(8.7%)G(7.8%) / 52.37
MdIDD14 / 51.25 / 9.40 / 43.91 / -0.706 / S(14.4%) N(9.3%)L(8.2%) / 56.77
MdIDD15 / 66.54 / 9.10 / 52.95 / -0.709 / S(14.4%)G(10.0%)A(7.6%) / 51.23
MdIDD16 / 64.60 / 9.28 / 52.99 / -0.723 / S(14.6%)G(10.1%)A(7.8%) / 50.98
MdIDD17 / 49.51 / 9.02 / 63.18 / -0.461 / S(14.8%)G(11.2%)P(8.7%) / 60.72
MdIDD18 / 58.74 / 8.54 / 51.85 / -0.804 / S(12.8%) L(7.7%)Q(7.7%) / 55.09
MdIDD19 / 62.17 / 9.14 / 48.16 / -0.797 / S(13.0%) G(9.8%)L(8.6%) / 54.81
MdIDD20 / 77.11 / 9.10 / 54.19 / -0.789 / S(13.9%) G(9.8%)L(7.9%) / 52.56

aGrand average of hydropathicity.

bThe three most abundant amino acids in each protein: A, Ala; P, Pro; S, Ser; G, Gly; L, Leul N, ASN; T, Thr.

Table S4 Motif sequences identified by MEME tools

Motif / Width / Multilevel consensus sequence
1 / 50 / GIKKHFSRKHGEKKWKCEKCSKKYAVQSDWKAHSKVCGTREYRCDCGTLF
2 / 50 / DPDAEVIALSPKTLLATNRFVCEICNKGFQRDQNLQLHRRGHNLPWKLKQ
3 / 29 / TKEPKRKVYLCPEPTCVHHDPSRALGDLT
4 / 29 / SRKDSFITHRAFCDALAAEQSARFCSAST
5 / 32 / NGGSSLSSITGAAQMSATALLQKAAKMGATAS
6 / 15 / GPKQTTLDLLGLGMA
7 / 15 / AAPPQKKRRNQPGTP
8 / 50 / HLLSSPSMGSSFRPAQSSAASFFMTGASDHDQSNQQQYHDQDKSFHGLMQ
9 / 50 / LRSFGSSSSTTTKPDRPGTLVPSSLGRMFGSDQTDQSHLQDLMNSFASGG
10 / 41 / NPSFMNGSIANNTHKPQRIPHFIPMFQPEFAGSDHLAANNH

Fig. S1 Distribution of conserved motifs of MdIDDs. The putative motifs are represented by different boxes. P-value means the significant difference. Details of motifs are given in Supplementary Table 3.

Fig. S2 Protein-protein interactions of IDD proteins identified in apple and Arabidopsis with STRING.org. The names shown in red in brackets are apple MdIDD orthologs in Arabidopsis. Different colored nodes shows the query proteins and first shell of interactors. Different lines between different nodes showed different interactions. Green (gene neighborhood), red (gene fusions), and blue lines (gene cooccurrence), yellow (text mining), black (co-expression), cyan lines(protein homology) was used to performed the predicted interactions.

Fig. S3 Flowering rates of various treatment and groups. (a) Comparison among control, GA and sugar treatments in 2016; (b) Comparison between Changfu No. 2 and Yanfu No. 6 in 2016; (c) Flowering rate of alternate bearing apple trees in 2014; (d) Flowering rate of the alternate bearing apple trees in 2015.