Table 4.
Description of some expected MTAs using imputed SNPs for agronomic traits of Iranian wheat accessions in rain-fed environment
| No | SNP | Sequence | Trait- Index | Chromosome | Position (bp) | Analysis method | Biological process | Cellular component | Molecular process |
|---|---|---|---|---|---|---|---|---|---|
| 1 | rs65348 | TGCAGTTTTCCGATCGGATATGTCAGCGGCGTCGAGGACCATGCATGGATCGTTTAAAGGTGAT | SH | 1 A | 44,512 | pGWAS, eGWAS(BRR,gBLUP,rrBLUP) | - | - | protein binding |
| 2 | rs64529 | TGCAGTTGTCTATCTCCAGAGAGGCCAGAGACCGTAAACCTCGCAAACAAGTACCCAGCTGCTC | TKW | 1B | 47,847 | pGWAS, eGWAS(BRR,gBLUP,rrBLUP) | - | - | ADP binding |
| 3 | rs51900 | TGCAGGGTGGGGGCGGAGAAAAAGGAGGAGGGGCGGCCGAGATCGGAAGAGCGGGATCACCGAC | TKW | 2D | 28,183 | pGWAS, eGWAS(BRR,gBLUP,rrBLUP) | vesicle-mediated transport | plasma membrane, integral component of membrane | protein binding |
| 4 | rs56561 | TGCAGTACTGGTACCCGCCGCCGCCGTACCAACCGCACCTGTGCCACCTCGCCGAGGAGGACCC | PH | 2D | 82,753 | pGWAS | metal ion transport | metal ion binding | |
| 5 | rs64448 | TGCAGTTGTAATCTTCCATGGAATCCCAACAAGTTTAGAGCGTGTCGATTCGTGGTAGATGGAT | SW | 3B | 56,892 | pGWAS | - | membrane, integral component of membrane | monooxygenase activity, iron ion binding, oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, heme binding |
| 6 | rs16023 | TGCAGCAGAGGTGGTTTGGAGGTTTGGTGGCGGCAGGATTCCCCTCCCGCGGGCGGCTCGGCTC | GY | 3B | 56,892 | pGWAS | auxin-activated signaling pathway, transmembrane transport, intracellular auxin transport | membrane, integral component of membrane | - |
| 7 | rs51991 | TGCAGGGTTCGCTCGTCGACGTCAACCCTTTGGAAGCGCAGCTCGAGCGCGGCATCCTTCTGGA | GY | 4 A | 129,369 | pGWAS, eGWAS(BRR,gBLUP,rrBLUP) | ATP binding, ATPase | ||
| 8 | rs38090 | TGCAGCTCTGGTTACAGTAGAACGACGAACAAACCTGAACCTGCATCCACACCACCCAGCATTC | TKW | 3B | 7980 | pGWAS, eGWAS(BRR,gBLUP,rrBLUP) | fatty acid biosynthetic process | membrane, integral component of membrane | acyltransferase activity, acyltransferase activity, transferring groups other than amino-acyl groups |
| 9 | rs5942 | TGCAGAGCATGGTCAGCTTCAGCAGTTCGACAAGCACACGCACCATAGGAGAAAGGTTGCACAT | SA | 4B | 93,598 | pGWAS, eGWAS(BRR) | - | - | methyltransferase activity, protein dimerization activity |
| 10 | rs60493 | TGCAGTGCAGACGGTATACTTACTCTAGAGTGCAAGCAAAGGAGAAACCGAGGGGAGGAGGAGG | SA | 5 A | 5684 | pGWAS, eGWAS(BRR,gBLUP,rrBLUP) | proteolysis | - | serine-type endopeptidase activity, peptidase activit, serine-type peptidase activity, hydrolase activity |
| 11 | rs32859 | TGCAGCGGTAGTTCGCTGGCATTGGCATTAGCCAAGGAGCGATGAGCATGGACCCGAGATCGGA | SA | 5 A | 38,892 | pGWAS, eGWAS(BRR,gBLUP,rrBLUP) | - | integral component of membrane | - |
| 12 | rs40738 | TGCAGCTTCATAGGTCGTACTAGATACTGCAAATACTTTGAAAGCTTAGTTACATGGTTTGTGG | SA | 6B | 94,461 | pGWAS, eGWAS(BRR,gBLUP) | - | integral component of membrane | - |
| 13 | rs3733 | TGCAGACCAGCACGCCCGCCGCGGCCGCCGTGGTAACGGCGCCGAGATCGGAAGAGCGGGATCA | FS | 7B | 51,193 | pGWAS, eGWAS(BRR,gBLUP,rrBLUP) | microtubule-based movement | - | microtubule motor activity, ATP binding, microtubule binding, ATP-dependent microtubule motor activity |
| 14 | rs50966 | TGCAGGGGAGGGGCGAGGAAAAGCCTAGCCGCCGAAGCCGTAGAGGGTGCGGCCCTGGCGCTTG | GY | 1 A | 50,198 | eGWAS(rrBLUP) | nucleosome assembly, response to water deprivation | nucleosome, nucleus, chromosome, nucleolus, vacuolar membrane, cytosol, plasma membrane, plasmodesma, chloroplast,thylakoid | DNA binding, protein heterodimerization activity |
| 15 | rs60665 | TGCAGTGCATTCCTAGCAAGTACTAGGTTAGTTTACTCGTTCAAATACCAAAAGGCAATCTAAG | FS | 1 A | 66,684 | eGWAS(BRR,gBLUP,rrBLUP) | - | - | tRNA binding,GTPase activity,GTP binding |
| 16 | rs52091 | TGCAGGGTTTGACATTCTGCAAGTACCACCTCAACACCGAGATCGGAAGAGCGGGATCACCGAC | GN | 1B | 45,574 | eGWAS(BRR,gBLUP,rrBLUP) | - | - | protein binding |
| 17 | rs14671 | TGCAGCACCTTCACGGCAACCATGGAGCCGTCCCGCAGCGTGCCGCGGTACACGCGGCTGTAGC | PH | 5 A | 3411 | eGWAS(BRR,gBLUP) | protein phosphorylation | - | protein kinase activity,ATP binding |
| 18 | rs17744 | TGCAGCAGGAGCTTGCCGATAAGGTGGCTCTCGACCGAAACGTGGACGAGGCAGACCTCAACAA | PH | 1D | 9094 | eGWAS(BRR) | - | - | monooxygenase activity, iron ion binding,oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen,heme binding |
| 19 | rs33741 | TGCAGCGTGCCTGTGGCTATACGTACTGATCGTTTCCCCGTGTTCCTCCACACGGGCAGGTTCG | PH | 2 A | 59,228 | eGWAS(BRR,gBLUP) | biosynthetic process | - | strictosidine synthase activity |
| 20 | rs61008 | TGCAGTGCTACTCACACAGGGGAATCAGGCCTGACATTCGCCATCTTCTTCTGCTCAGCCAACC | SW | 2B | 59,184 | eGWAS(BRR,gBLUP,rrBLUP) | - | integral component of membrane | |
| 21 | rs21291 | TGCAGCCACCTTCGAAATGTGCATCCCCTTTACCCGTATCGGGAGAACGAGGTGTAGCTCAGTT | SH | 2B | 67,141 | eGWAS(BRR) | - | - | ADP binding |
| 22 | rs48315 | TGCAGGCGGATCTGGTCCAGCAGACGGTCCGCCTCGCCCTCGGCGTCGGCGTCGGCGGCGTCGG | TKW | 2D | 27,046 | eGWAS(BRR,gBLUP) | lipid metabolic process, signal transduction,lipid catabolic process,intracellular signal transduction | intracellular anatomical structure | phosphatidylinositol phospholipase C activity,phosphoric diester hydrolase activity |
| 23 | rs16199 | TGCAGCAGCAACCACCACCATGGAAAGAGAGAGACAGAGACGGTGAGCTCCTCTGGACAGCGAG | TKW | 2D | 28,183 | eGWAS(BRR,gBLUP,rrBLUP) | lipid metabolic process | - | oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water |
| 24 | rs25087 | TGCAGCCGCAGAAACATGACCGCGCTGACACCGACCATCCTGCCCGCCGCGCCGTCGCCGACGA | FS | 3 A | 53,669 | eGWAS(BRR,gBLUP) | - | - | protein binding |
| 25 | rs10286 | TGCAGATTGGAATTTCTGAAAGGCCTCCACAAGATGAAGGAAGCAACGATCGATCCG | PH | 5B | 35,359 | eGWAS(BRR,gBLUP) | - | - | hydrolase activity |
| 26 | rs19868 | TGCAGCATGGAGTTTAAAAATATTCAATGGTAATTTACCAGACCGAAAGACAAATAAGCAATGC | PH | 3B | 18,217 | eGWAS(rrBLUP) | - | - | nucleotide binding, nucleic acid binding, RNA helicase activity,helicase activity,ATP binding |
| 27 | rs27041 | TGCAGCCTCTCTACCTTAGAGATCTTGGGGATGACCACCGTGTTCCTCTGGAGGCCCCACCGAG | SW | 3B | 22,764 | eGWAS(rrBLUP) | - | - | oxidoreductase activity, aldose-6-phosphate reductase (NADPH) activity,D-threo-aldose 1-dehydrogenase activity |
| 28 | rs3365 | TGCAGACACTAGTATCATTGGAAGCACAGGATGAGTCCGTTAGACAGTTGGGGGAGCTGAGGCA | TKW | 4 A | 61,015 | eGWAS(rrBLUP) | - | - | ADP binding |
| 29 | rs31074 | TGCAGCGCTATGGTAGCTTTGGTTGGTAGTTACTCTGAACCGAGATCGGAAGAGCGGGATCACC | PH | 4 A | 125,958 | eGWAS(BRR,gBLUP) | - | integral component of membrane | - |
| 30 | rs17272 | TGCAGCAGCGGCGGGAGCATAGGATCGTGGAGAGGGAGCAGGGACGGCGAGCTTACGGAGCGGG | PH | 4 A | 125,958 | eGWAS(gBLUP) | transmembrane transport | integral component of membrane | oligopeptide transmembrane transporter activity |
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