Table 4. Characteristics of markers significantly associated.
| Marker name | Associated Trait | Genomic position | Nucleotide | Exon / Intron | Strand | SNP | SNP typea | Codon position | Non synonymous substitution / Missense change | PFAM Description | BLAST-P b |
|---|---|---|---|---|---|---|---|---|---|---|---|
| GQ03709-C10.1.1133 | Scen1 | No gene - downstream (13 nt) MA_59794g0010 | 21494 | + | [T/C] | UTR | * | Unknown | |||
| GQ03204-K15.1.405 | Scen2 | No gene - upstream (164 nt) MA_10434266g0010 | 3694 | — | [T/C] | UTR | Leucine Rich Repeat | No significant similarity found. | |||
| 08Pg07115c | RW; RWt; EW | No gene - downstream (297 nt) MA_39636g0010 | 24594 | — | [T/C] | UTR | Transferase family | Hydroxycinnamoyl-CoA shikimate hydroxycinnamoyltransferase | |||
| GQ03709-C10.1.483 | LW | MA_59794g0010 | 20695 | Exon 1 | + | [T/C] | NSS-M | 2 | GCA = A (Alanine) / GTA = V (Valine) | * | Unknown |
| GQ03121-E24.1.494 | LW | MA_6741659g0010 | 1238 | Exon 2 | + | [T/C] | SS | 3 | CG[T/C]=R (Arginine) | * | Kinase |
| PaPHYN-RI420 | LW | MA_73153g0010 | 13476 | Exon 6 | — | [A/C] | NSS-M | 3 | GAA=E (Glutamic acid) | Phytochrome region | Phytochrome |
| GAC=D (Aspartic acid) | PAS fold | ||||||||||
| PAS domain | |||||||||||
| GAF domain | |||||||||||
| Histidine kinase | |||||||||||
| DNA gyrase B | |||||||||||
| HSP90-like ATPase | |||||||||||
| GQ03205-D16.1.1410 | LW | MA_10432182g0010 | 2114 | Intron | — | [A/C] | UTR | Short chain dehydrogenase | Short chain dehydrogenase | ||
| NAD dependent epimerase/dehydratase family | |||||||||||
| NmrA-like family | |||||||||||
| KR domain | |||||||||||
| NADH(P)-binding | |||||||||||
| Enoyl-(Acyl carrier protein) reductase | |||||||||||
| GQ00410.B3-M23.4-2998 | LW | MA_17539g0010 | 1887 | Exon 1 | + | [A/G] § | SS | 3 | GA[T/C]=D (Aspartic acid) | EF hand / EF-hand domain pair | Calcium-binding protein |
| WS-2.0-GQ0036.TB-K03.1-397 | RD;RDt | MA_10426694g0020 | 18480 | Exon 3 | — | [T/C] § | SS | 3 | GG[A/G]=G (Glycine) | Metallopeptidase family M24 | ERBB-3 BINDING PROTEIN 1 |
| 00930-O17-366 | EDt | MA_588952g0010 | 731 | Exon 1 | — | [A/C] | SS | 3 | CT[C/A]=L (Leucine) | * | No significant similarity found. |
| ss538948434 | Rc00 | MA_100637g0010 | 3240 | Exon 3 | + | [A/G] | NSS-M | 1 | GTT = V (Valine) | PPR repeat | Pentatricopeptide repeat-containing protein |
| ATT = I (Isoleucine) | Herpesvirus protein of unknown function (DUF832) | ||||||||||
| Tetratricopeptide repeat | |||||||||||
| Anaphase-promoting complex, cyclosome, subunit 3 | |||||||||||
| PPR repeat family | |||||||||||
| Pentatricopeptide repeat domain | |||||||||||
| c89584_g2_i1_197 | Rc00;Rt03 | No gene - downstream (418 nt) MA_90007g0010 | 15514 | — | [A/C] | UTR | BTB/POZ domain | ARM repeat protein interacting with ABF2 | |||
| PGLM2-0082 | Rc00 | MA_8047450g0010 | 2537 | Exon 2 | — | [A/G] § | SS | 3 | CA[T/C]=H (Histidine) | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | Unknown |
| ROKNT (NUC014) domain | |||||||||||
| WS-2.0-GQ02827.B7-M03.1-1062 | Rs00 | No gene (MA_75479) | 904 | + | [A/G] | UTR | |||||
| NODE-12228-length-276-cov-134.847824-162 | Rs00 | Not in 1kb MA_118377 | 17768 | — | [T/C] | UTR | |||||
| WS-2.0-GQ03417.B7-O19.1-1215 | Rs00,rRs00 | No gene - downstream (104 nt) MA_119424g0010 | 10110 | — | [T/G] | UTR | Short chain dehydrogenase | Anthocyanidin reductase | |||
| 3-beta hydroxysteroid dehydrogenase/isomerase family | |||||||||||
| NAD dependent epimerase/dehydratase family | |||||||||||
| NmrA-like family | |||||||||||
| Male sterility protein | |||||||||||
| KR domain | |||||||||||
| NADH(P)-binding | |||||||||||
| GQ03812-F08.1.123 | Rs00;rRs00 | No gene (MA_7880) | 20633 | — | [A/G] | UTR | |||||
| MA_475589g0010-111-[C_T] | Rs03;Rt03 | MA_475589g0010 | 5299 | Exon 1 | — | [T/C] | SS | 3 | GG[T/C]=G (Glicine) | Leucine Rich Repeat | F-box/LRR-repeat protein |
| ss538948838 | Rt03 | MA_109428g0010 | 15103 | Exon 4 | + | [T/G] | NSS-M | 1 | TCA = S (Serine) | Translocon-associated protein (TRAP), alpha subunit | Translocon-associated protein subunit alpha |
| GCA = A (Alanine) | NICE-3 protein | ||||||||||
| GQ03512-P11.2.1194 | Rt03 | MA_10427719g0010 | 15051 | Intron | — | [T/G] | UTR | 2OG-Fe(II) oxygenase superfamily | |||
| Non-haem dioxygenase in morphine synthesis N-terminal | |||||||||||
| GQ03013-D24.3.551 | Rt03 | MA_10434370g0040 | 13176 | Exon 2 | — | [T/C] | SS | 3 | GA[T/C]=D (Aspartic acid) | * | EGF domain-specific O-linked N-acetylglucosamine transferase-like |
| ss538944271 | Rc03 | MA_161013g0010 | 7889 | Intron | + | [A/G] | UTR | Multicopper oxidase | Multicopper oxidase | ||
| L-ascorbate oxidase homolog | |||||||||||
| GQ0197-K07.1.447 | Rc03 | MA_38472g0010 | 6199 | Exon 6 | — | [T/C] | SS | 3 | AA[T/C]=D (Aspartic acid) | Homeobox domain | Homeodomain protein HB2 |
| GQ0197-K07.1.345 | Rc03 | MA_38472g0010 | 6301 | Exon 6 | — | [A/G] | SS | 3 | GG[A/G]=G (Glicine) | START domain | Homeobox-leucine zipper protein ANTHOCYANINLESS 2-like isoform |
| Homeobox KN domain | |||||||||||
| Mitochondrial ribosomal protein subunit L20 | |||||||||||
| GQ0068-K02.1.644 | Rc03 | MA_47260g0010 | 3906 | Exon 4 | — | [T/C] | SS | 3 | TC[T/C]=S (Serine) | Tetratricopeptide repeat | Clathrin heavy chain 1 |
| Region in Clathrin and VPS | |||||||||||
| Coatomer WD associated region | |||||||||||
| Clathrin-H-link | |||||||||||
| GQ02904-L21.2.961 | Rc03 | MA_10432150g0010 | 33483 | Exon 2 | + | [T/C] | NSS-M | 2 | CCG = P (Proline) | WD domain, G-beta repeat | WD repeat-containing protein VIP3 |
| CTG = L (Leucine) | Cytochrome D1 heme domain | ||||||||||
| Coatomer WD associated region | |||||||||||
| Eukaryotic translation initiation factor eIF2A | |||||||||||
| Lactonase, 7-bladed beta-propeller | |||||||||||
| Nucleoporin Nup120/160 | |||||||||||
| GQ03204-O22.1.645 | CorJunT | MA_6521216g0010 | 1742 | Exon 1 | — | [A/G] | SS | 3 | GA[A/G]= E (Glutamic acid) | * | Dihydropyrimidinase |
| FCL808Contig2-402 | CorJunT | MA_2267030g0010 | 105 | Exon 1 | + | [A/G] | SS | 3 | GT[A/G]=V (Valine) | CutA1 divalent ion tolerance protein | Protein CutA |
| MA_10289324g0010-1023-[G_A] | CorJunT | MA_10289324g0010 | 1649 | Exon 2 | + | [A/G] | SS | 3 | CT[A/G]=L (Leucine) | 2OG-Fe(II) oxygenase superfamily | GA2OX3 (Gibberellin 2-beta-dioxygenase 3) |
| Non-haem dioxygenase in morphine synthesis N-terminal |
a
SS= Synonymous substitution; NSS-M= non synonymous substitution Missense change, UTR= untranslated regions.
b
Putative gene function assigned by BLAST-P (Table S4 for complete BLAST-P output).
*
PFAM ID could not be found.
§
SNP on the complementary strand of a translated protein.