Table 2 Details of candidate genes (CGs) associated with significant MTAs and details of putative proteins identified from Ensembl wheat.
S. No. | Associated SNP ID (with trait and location details) | Chr; Genomic Location | Genes in 1 Mb region/Gene IDs (genomic location) | Description; Protein domain name/ID# | GO Annotation (GO IDs) | ||
|---|---|---|---|---|---|---|---|
Biological process | Molecular function | Cellular component | |||||
1. | 1003062 (DTH_E1, DTH_E2, DTM_E1, DTM_E2) | 4B:39758253–39758321 | TraesCS4B02G051500 (4B: 40,074,250–40,078,403) | Basic Helix-loop-helix DNA-binding domain (bHLH) (PF00010) | N/A | protein dimerization activity (GO: 0046983) | N/A |
2. | 1021420 (DTM_E4) | 2A:755679307–755679375 | TraesCS2A02G547600 (2A: 755,736,756–755,738,760) | Gibberellin-Dioxygenases Gene Family (GAox); Non-haem dioxygenase N-terminal domain/PF14226, Oxoglutarate/iron-dependent dioxygenase/PF03171 | oxidation-reduction process (GO:0055114) | oxidoreductase activity (GO:0016491); 2. metal ion binding (GO:0046872 | N/A |
3. | 1026541 (DTH_E2) | 2B:772063506–772063574 | TraesCS2B02G584900 (2B: 771,923,036–771,924,265) | F-box domain (IPR001810) | N/A | protein binding GO:0005515 | N/A |
4. | 1050557 (DTH_E2) | 5B:348450682–348450747 | (a) TraesCS5B02G193100 (5B: 348,448,002–348,450,302) | Trehalose-phosphatase (PF02358) | trehalose biosynthetic process (GO:0005992); dephosphorylation (GO:0016311) | trehalose-phosphatase activity (GO:0004805); catalytic activity (GO:0003824); hydrolase activity (GO:0016787) | N/A |
(b) TraesCS5B02G193200 (5B: 348,570,451–348,572,272) | AP2/ERF gene (AP2 domain; PF00847) | transcription (GO: 0006351), regulation of transcription (GO: 0006355) | DNA-binding transcription factor activity (GO: 0003700) | Nucleus (GO:0005634) | |||
5. | 1063624 (DTH_E2, DTM_E1, DTM_E2) | 3A:84182120–84182188 | TraesCS3A02G116200 (3A: 83,977,019–83,983,489) | WRKY protein domain (PF03106) | regulation of transcription (GO: 0006355) | DNA-binding transcription factor activity (GO: 0003700) | Nucleus (GO:0005634) |
6. | 1065193 (TGW_E4) | 3A:568445450–568445518 | TraesCS3A02G323500 (3A: 568,094,977–568,098,215) | Bulb-type lectin domain (PF01453), S-locus glycoprotein domain (PF00954), PAN/Apple domain (PF08276), Serine-threonine/tyrosine-protein kinase, catalytic domain (PF07714) | protein phosphorylation (GO: 0006468) | protein serine/threonine kinase activity (GO: 0004674) | membrane (GO:0016020) |
7. | 1090844 (PH_E2) | 5A:595082910–595082978 | TraesCS5A02G401800 (5A: 594,770,622–594,772,285) | Dof domain, zinc finger (PF02701) | regulation of transcription (GO: 0006355) | DNA binding (GO:0003677) | Nucleus (GO:0005634) |
8. | 1091457 (GYPP_E3) | 5D:391278717–391278776 | TraesCS5D02G294400 (5D: 391,372,552–391,378,851) | Squamosa promoter binding protein domain (SBP; PF03110) | N/A | DNA binding (GO:0003677) | Nucleus (GO:0005634) |
9. | 1094628 (TGW_E2) | 4A:667344925–667344993 | (a) TraesCS4A02G389600 (4A: 666,980,143–666,983,528) | NB-ARC domain (PF00931) | N/A | ADP binding (GO: 0043531) | N/A |
(b) TraesCS4A02G389900 (4A: 667,174,383–667,174,854) | Cysteine-rich transmembrane CYSTM domain/PF12734 | N/A | N/A | N/A | |||
10. | 1113894 (PH_E4) | 1B:38599717–38599781 | TraesCS1B02G055800 (1B: 38,832,030–38,835,862) | SET, SAD_SRA (PF02182); D2 Pre-SET (PF05033); D3, SET (PF00856) | Histone methylation (GO:0016571); Histone lysine methylation (GO:0034968) | Protein binding (GO:0005515); Zinc ion binding (GO:0008270); 3. Histone-lysine N-methyltransferase activity (GO:0018024) | Nucleus (GO:0005634); Chromosome (GO:0005694) |
11. | 1126379 (GYPP_E1) | 4A:743768873–743768931 | TraesCS4A02G498100 (4A: 743,748,235–743,749,019) | Late embryogenesis abundant protein (LEA2) (PF03168) | N/A | N/A | N/A |
12. | 1127414 (PH_E4) | 3B:95751799–95751867 | TraesCS3B02G123600 (3B: 95,459,819–95,462,522) | Zinc finger C2H2-type (IPR013087) | N/A | nucleic acid binding (GO:0003676) | N/A |
13. | 1134753 (DTH_E3) | 3B:799744734–799744802 | TraesCS3B02G568000 (3B: 799,521,193–799,524,789) | Ubiquitin (PF00240) | N/A | Protein binding (GO:0005515) | N/A |
14 | 3023142 (DTH_E4) | 5B:588883282–588883319 | TraesCS5B02G414400 (5B: 588,831,208–588,832,584) | Cytochrome P450 (PF00067) | Oxidation-reduction process (GO:0055114) | Iron ion binding (GO:0005506); Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705) | N/A |
15 | 977937 (TGW_E4) | 2A:677497865–677497929 | TraesCS2A02G422700 (2A: 677,530,470–677,532,528) | GRF zinc finger (PF06839) | N/A | Zinc ion binding (GO:0008270) | N/A |
16 | 985312 (TGW_E2) | 4B:37529691–37529759 | TraesCS4B02G049000 (4B: 37,296,414–37,297,430) | Protein kinase domain (PF00069) | Protein phosphorylation (GO: 0006468) | protein kinase activity (GO:0004672); ATP binding (GO:0005524) | N/A |
