Table 2.
Significant SNPs for anthocyanin content in rose petals from greenhouse- and field-grown roses.
| Greenhouse | p-value | Effectb | Function (identified gene) | |||
|---|---|---|---|---|---|---|
| Combineda | (E525nm) | Allele A:A | Allele A:B | Allele B:B | ||
| Rh12GR_283_1910Q | 2.35E-09 | −5.412 | − | 77 | 104 | gene31631-v1.0-hybrid_Auxin_response_factor_8_ (putative) |
| RhMCRND_20203_163Q | 7.20E-09 | −4.091 | − | 81 | 102 | gene31669-v1.0-hybrid_Medium-chain-fatty-acid-CoA_ligase_(probable) |
| Rh12GR_20064_1031P | 1.86E-07 | −4.521 | 102 | 75 | − | gene31669-v1.0-hybrid_Medium-chain-fatty-acid-CoA_ligase_(probable) |
| RhK5_7371_202Q | 2.02E-07 | −4.492 | − | 79 | 104 | gene31672-v1.0-hybrid_Glutathione_S-transferase_ (similar_to) |
| RhK5_1258_2078P | 3.75E-07 | −6.674 | 66 | 117 | − | gene08692-v1.0-hybrid_3beta-hydroxysteroid-dehydrogenase/decarboxylase_isoform_2_(At3BETAHSD/D2)_(similar_to) |
| RhMCRND_7128_1021Q | 4.51E-07 | −1.935 | − | 83 | 92 | gene31668-v1.0-hybrid_Medium-chain-fatty-acid–CoA_ligase_(probable) |
| Rh12GR_64257_531Q | 4.62E-07 | −5.776 | − | 61 | 106 | gene16750-v1.0-hybrid_hypothetical_protein |
| RhK5_2615_1401Q | 5.58E-07 | −5.549 | − | 76 | 105 | gene09148-v1.0-hybrid_Cysteine_proteinase _RD21a_ (RD21),_Precursor_(putative) |
| RhK5_15799_993Q | 6.00E-07 | −7.015 | − | 59 | 106 | gene26062-v1.0-hybrid_Formin-like_protein_20_(AtFH20)_(similar_to) |
| RhMCRND_982_2342Q | 1.06E-06 | −5.538 | − | 60 | 117 | gene26062-v1.0-hybrid_Formin-like_protein_20_ (AtFH20)_(similar_to) |
| RhK5_1553_678P | 1.10E-06 | −4.719 | 119 | 65 | − | gene26062-v1.0-hybrid_Formin-like_protein_20_ (AtFH20)_(similar_to) |
| RhK5_9221_621Q | 1.11E-06 | 6.179 | 76 | 85 | − | gene16819-v1.0-hybrid_Thioredoxin_F-type_2, _chloroplastic_(Trx-F2),_Precursor_(similar_to) |
| Rh12GR_77973_217Q | 1.17E-06 | −4.794 | 108 | 75 | − | − |
| RhK5_12663_103Q | 1.32E-06 | −3.628 | − | 69 | 114 | gene24536-v1.0-hybrid_Possible_hemolysin_C_ (probable) |
| Rh12GR_17814_425Q | 1.62E-06 | −3.136 | 104 | 81 | − | gene31679-v1.0-hybrid_Ubiquitin-like_protein_SMT3 _(probable) |
| RhK5_15799_993P | 1.80E-06 | −5.472 | − | 60 | 119 | gene26062-v1.0-hybrid_Formin-like_protein_20_ (AtFH20)_(similar_to) |
| RhMCRND_1369_1182Q | 2.00E-06 | 5.215 | 62 | 121 | gene26062-v1.0-hybrid_Formin-like_protein_20_(AtFH20)_(similar_to) | |
| Rh12GR_283_1910P | 2.38E-06 | 3.516 | − | 81 | 94 | gene31631-v1.0-hybrid_Auxin_response_factor_8_ (putative) |
| RhK5_19460_153P | 2.45E-06 | 4.855 | 123 | 61 | − | gene04292-v1.0-hybrid_Cytokinin-O-glucosyltransferase_2_(AtZOG2)_(probable) |
| Rh12GR_38264_410P | 2.58E-06 | −4.584 | 88 | 79 | − | − |
| Greenhouse | p-value | Effectb (E525nm) | Allele A:A | Allele A:B | Allele B:B | Function (identified gene) |
| Rh12GR_283_1910Q | 9.73E-11 | −5.740 | − | 40 | 52 | gene31631-v1.0-hybrid_Auxin_response_factor_8_ (putative) |
| RhK5_1439_806P | 8.10E-09 | −4.927 | 68 | 19 | − | U3 small nucleolar RNA-associated protein 4/UTP4 |
| RhMCRND_20203_163Q | 1.17E-08 | −5.135 | − | 42 | 51 | gene31669-v1.0-hybrid_Medium-chain-fatty-acid–CoA_ligase_(probable) |
| RhK5_1258_2078P | 9.44E-08 | −7.589 | 33 | 60 | − | gene08692-v1.0-hybrid_3beta-hydroxysteroid-dehydrogenase/decarboxylase_isoform_2_(At3BETAHSD/D2)_(similar_to) |
| Rh12GR_20064_1031P | 1.21E-07 | −5.112 | 51 | 39 | − | gene31669-v1.0-hybrid_Medium-chain-fatty-acid–CoA_ligase_(probable) |
| RhK5_7371_202Q | 1.23E-07 | −5.426 | − | 41 | 52 | gene31672-v1.0-hybrid_Glutathione_S-transferase_ (similar_to) |
| RhMCRND_319_1197P | 7.49E-07 | 4.398 | − | 60 | 26 | Urease_(similar_to) |
| RhK5_12076_566Q | 7.74E-07 | −5.193 | − | 42 | 52 | Photosystem_I_reaction_center_subunit_XI,_ chloroplastic_(PSI-L),_Precursor_ |
| RhMCRND_982_2342Q | 8.43E-07 | −6.928 | − | 30 | 60 | gene26062-v1.0-hybrid_Formin-like_protein_20_ (AtFH20)_(similar_to) |
| Rh12GR_17814_425Q | 8.45E-07 | −4.391 | 52 | 42 | − | gene31679-v1.0-hybrid_Ubiquitin-like_protein_SMT3 _(probable) |
| Rh12GR_92431_4144Q | 8.48E-07 | −3.985 | − | 35 | 58 | gene31646-v1.0-hybrid_Serine/threonine-protein_ kinase_PBS1_(probable) |
| RhK5_2615_1401Q | 8.64E-07 | −5.525 | − | 39 | 53 | gene09148-v1.0-hybrid_Cysteine_proteinase_ RD21a_(RD21),_Precursor_(putative) |
| RhK5_15799_993P | 1.00E-06 | −6.814 | - | 30 | 61 | gene26062-v1.0-hybrid_Formin-like_protein_20_ (AtFH20)_(similar_to) |
| RhK5_5774_854P | 1.11E-06 | 4.321 | − | 62 | 26 | Translation_initiation_factor_IF-2_ |
| RhK5_12663_103Q | 1.37E-06 | 4.258 | − | 33 | 57 | gene24536-v1.0-hybrid_Possible_hemolysin_C _(probable) |
| RhK5_21626_409P | 1.66E-06 | 4.064 | − | 61 | 25 | gene07023-v1.0-hybrid_Anthranilate_ phosphoribosyltransferase_(probable) |
| Rh12GR_3292_1365P | 2.20E-06 | 4.122 | 18 | 68 | − | gene10566-v1.0-hybrid_Putative_indole-3-acetic_acid-amido_synthetase_GH3.9_(AtGH3-9) |
| Field | p-value | Effectb (E525nm) | Allele A:A | Allele A:B | Allele B:B | Function (identified gene) |
| Rh12GR_283_1910Q | 4.51E-08 | −5.451 | − | 37 | 52 | gene31631-v1.0-hybrid_Auxin_response_factor_8_ (putative) |
| RhMCRND_20203_163Q | 5.29E-08 | −2.631 | − | 40 | 51 | gene31669-v1.0-hybrid_ Medium-chain-fatty-acid–CoA_ligase_(probable) |
| RhK5_1258_2078P | 1.30E-07 | −6.511 | 33 | 57 | − | gene08692-v1.0-hybrid_3beta-hydroxysteroid-dehydrogenase/decarboxylase_isoform_2_(At3BETAHSD/D2)_(similar_to) |
| Rh12GR_20064_1031P | 1.82E-06 | 5.051 | 51 | 36 | − | gene31669-v1.0-hybrid_Medium-chain-fatty-acid–CoA_ligase_(probable) |
| RhK5_7371_202Q | 1.94E-06 | 5.100 | − | 38 | 52 | gene31672-v1.0-hybrid_Glutathione_S-transferase_ (similar_to) |
| RhMCRND_7128_1021Q | 2.37E-06 | −1.901 | − | 39 | 48 | gene31668-v1.0-hybrid_Medium-chain-fatty-acid–CoA_ligase_(probable) |
a
Total number of A:A, A:B, and B:B genotypes was counted in two environments and exceeded the number of 96 cultivars.
b
The effect was presented as untransformed values.