Table 3.
Description of some expected MTAs using imputed SNPs for agronomic traits of Iranian wheat accessions in well-watered environment
| No | SNP | Sequence | Trait- Index | Chromosome | Position (bp) | Analysis method | Biological process | Cellular component | Molecular process |
|---|---|---|---|---|---|---|---|---|---|
| 1 | rs15519 | TGCAGCACTCTGCAAGAAAAACGTCAAAGTAAGAACCACCTACCCACATCTGCTCCAATTCAAA | TKW | 1D | 47,767 | pGWAS | lipid biosynthetic process | integral component of membrane | iron ion binding, oxidoreductase activity |
| 2 | rs23792 | TGCAGCCCCTGGTCCTCCTGGTGGGAGAGCGTGTGGAACTCAAGGTAGCTGCCGTCCGTCACAA | SA | 2 A | 11,390 | pGWAS | protein binding | - | - |
| 3 | rs59777 | TGCAGTCTTTCAGAAGTGCAGATGTAAACGTATTGCTATATCAGTGGTTTGAACTACATGGTAA | TKW | 2D | 58,883 | pGWAS, eGWAS(BRR,gBLUP,rrBLUP) | protein ubiquitination, positive regulation of protein catabolic process | Protein binding | - |
| 4 | rs61092 | TGCAGTGCTGCTAGCGATCAGCTTGGTAGTCTGACAGGAAGGAGAGGCGTATCTACCTATTTAT | GY | 3D | 54,810 | pGWAS | carbohydrate binding | - | - |
| 5 | rs23471 | TGCAGCCCCATGGCTGGCCACTGCCCCGCCGACGCCACCTGCGGGTTTGGAGACGCCACCACGC | GY | 5 A | 58,225 | pGWAS, eGWAS(BRR,gBLUP,rrBLUP) | RNA binding | - | |
| 6 | rs31132 | TGCAGCGCTCTCGGCGGTGACTCGTCGTCGCTCGGTGGCATCACCATCAACAAGACACGCGCGC | TKW | 5 A | 58,225 | pGWAS | lipid transport | lipid binding | - |
| 7 | rs55428 | TGCAGGTTTCAATTACGGAGGGAAAAACTCCAAGAAACTTATTGTTAGCAAGACGAAGTGACTG | GY | 5 A | 109,694 | pGWAS, eGWAS(BRR,gBLUP,rrBLUP) | protein binding | - | - |
| 8 | rs31181 | TGCAGCGCTGCATCTCTGGATTGTAGCGACAAGGAACTAAGCATGGATTGGAGGTATTATGTAA | PH | 5B | 26,242 | pGWAS, eGWAS(BRR,gBLUP,rrBLUP) | - | - | - |
| 9 | rs63031 | TGCAGTTCATCAAATTCGAAGGCCTCTCGTGCTAGCATAGCCATCACTTAGTTTGGGAACTGAA | GN | 5B | 45,594 | pGWAS, eGWAS (BRR,gBLUP) | nucleoside metabolic process, UMP salvage, CTP salvage | uridine kinase activity, ATP binding, kinase activity | - |
| 10 | rs11075 | TGCAGCAAATCGTCACTGCCTTCTAGCACGCCCGCCGTCTCTTAGTTGCAGCACCTAGCCGCCG | SH | 6 A | 46,797 | pGWAS, eGWAS(BRR,gBLUP,rrBLUP) | - | - | - |
| 11 | rs44444 | TGCAGGAGCTGAGCAACGAGGCCACAGCCGCCGCAGAAAAGGAGTCCCTGAACGGCACACTGGC | TKW | 6B | 92,187 | pGWAS, eGWAS(BRR,gBLUP,rrBLUP) | ubiquitin-dependent protein catabolic process, protein deubiquitination | intracellular anatomical structure | thiol-dependent deubiquitinase |
| 12 | rs34582 | TGCAGCTACCGCGTGACAAGCTACGTTACGCACGGGGTGCCGCCTCTGGCCGTGGCGGCATGGC | PH | 6B | 58,062 | pGWAS, eGWAS(BRR,gBLUP,rrBLUP) | protein binding | - | - |
| 14 | rs44962 | TGCAGGAGTCGCCACAGGATGTCTCATTTCTTGCCTTTGCTGGAAGCGTGAATTTCTGCCGATT | SA | 1B | 45,574 | eGWAS(rrBLUP) | DNA topological change | chromosome | DNA binding, DNA topoisomerase activity, DNA topoisomerase type I (single strand cut, ATP-independent) activity |
| 15 | rs2390 | TGCAGAAGTTCGACCTTTCAACATCTGTCCTGGCAATGCCAGCCATATGAAAAACTTCACATGG | GN | 1B | 45,574 | eGWAS(gBLUP,rrBLUP) | - | anaphase-promoting complex | |
| 16 | rs64529 | TGCAGTTGTCTATCTCCAGAGAGGCCAGAGACCGTAAACCTCGCAAACAAGTACCCAGCTGCTC | SH | 1B | 47,847 | eGWAS(BRR) | - | ADP binding | |
| 17 | rs9736 | TGCAGATGTGCTTGGCCGTTCGATTGATGCTCTGTTCTTCTTTGCCAGATCCCCAACGGGTGCG | SA | 1B | 47,279 | eGWAS(BRR,gBLUP,rrBLUP) | carbohydrate transport | integral component of membrane | |
| 18 | rs28731 | TGCAGCGAGCAAGAACATGGCCAAAACGCCGTCGCCGAGATCGGAAGAGCGGGATCACCGACTG | SW | 2 A | 92,517 | eGWAS(rrBLUP) | - | - | electron transfer activity |
| 19 | rs3810 | TGCAGACCCAAACAAACAGTGTTCAGCCCATGCAAAGCACGAACGTACGTACTAGTATATGCAA | PH | 2B | 59,184 | eGWAS(BRR,gBLUP) | transmembrane transport | membrane, integral component of membrane | transmembrane transporter activity |
| 20 | rs49651 | TGCAGGGACGGAGACGGAGGTAGGCGGAGGCGTGGTCGGCTTCTTCGCCCTCGTCCTTGGTGGC | SA | 2B | 71,688 | eGWAS(BRR,gBLUP,rrBLUP) | - | - | protein binding |
| 21 | rs7932 | TGCAGATATTTATCGCCCAAGAGCAAAGATGCTTGACCAGGATTTGGATTGCGGACCGAGATCG | SH | 2B | 86,479 | eGWAS(rrBLUP) | transcription, DNA-templated | - | DNA binding, DNA-directed 5’-3’ RNA polymerase activity, ribonucleoside binding |
| 22 | rs41022 | TGCAGCTTCTACAGGTCTCTCGTGCTCCATGCATCAAACATGTGGGGACTGGATTCTTGCAGGC | FS | 7B | 118,551 | eGWAS(BRR,rrBLUP) | - | - | ADP binding |
| 23 | rs38543 | TGCAGCTGCAACCAACACCCTGACGGCGGGCCAGTCGCTCGCCGTCGGCGGCAGCAAGCTCGTC | PH | 2D | 79,343 | eGWAS(BRR) | protein phosphorylation, recognition of pollen | integral component of membrane | protein kinase activity, protein serine/threonine kinase activity, ATP binding |
| 24 | rs54935 | TGCAGGTTCATTGAGAGAGCGCAGGCTCTGATTCATGGAGATCTCCATACTGGTTCCATCATGT | SH | 2D | 82,753 | eGWAS(BRR,gBLUP) | methionine biosynthetic process, phosphorylation | - | S-methyl-5-thioribose kinase activity |
| 25 | rs46842 | TGCAGGCCAGCCAAATTTATTGGCACGCGAACGGGAAAACGAACTGTTAAAATATCTGTAACTA | PH | 3B | 45,525 | eGWAS(BRR,gBLUP) | - | - | oxidoreductase activity, oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor, metal ion binding |
| 26 | rs24758 | TGCAGCCGACGGAGCTCGCGAGCCACATGAGCTCCCGCTGCCCTGCTCTCGAGGACTTGAAACT | PH | 3B | 121,341 | eGWAS(rrBLUP) | - | - | protein binding |
| 27 | rs63419 | TGCAGTTCGAGCGCCGATGGTGCCTCTTGTTGTGTTGTGTCCCCCCTCGCCATGTGTTGTCCAT | GY | 4 A | 61,015 | eGWAS(rrBLUP) | cation transport, calcium ion transport, transmembrane transport | integral component of membrane | cation transmembrane transporter activity, calcium:proton antiporter activity |
| 28 | rs40457 | TGCAGCTTAAACATACAAGCAAGCCATACATGCCACGGATGTGGCGCCATTGGTTTACCTTTTA | SH | 4 A | 146,426 | eGWAS(BRR,gBLUP) | - | integral component of membrane | - |
| 29 | rs62498 | TGCAGTTAATCATTTATTAGTACTAGTTATTAAAAGACCAAGATAGTGAAGACAGAATTCCCTG | SA | 4 A | 147,563 | eGWAS(BRR) | protein phosphorylation | - | protein kinase activity, ATP binding |
Abbreviations: PH Plant height, GY Grain yield, GN Grain number per spike, TKW Thousand kernel weight, SW Spike weight, SA Spike area, SH Spike harvest index, SF Spike fertility