Table 2 List of significant SNPs associated maize yield related traits and the candidate genes and their functional annotations
From: Genome wide association analysis for yield related traits in maize
Trait | SNP | P value | R2% | Candidate gene | Gene annotation |
|---|---|---|---|---|---|
GYP | 9_150257246 | 1.92E-05 | 7.77 | GRMZM2G330945 | Cold regulated gene 27 (COR27) |
GYP | 7_162001602 | 2.86E-05 | 8.50 | GRMZM2G151649 | ARM repeat superfamily protein |
GYP | 3_138419644 | 5.32E-05 | 7.01 | GRMZM5G803355 | MYB transcription factor |
GYP | 2_29336901 | 5.90E-05 | 6.94 | GRMZM5G845736 | Inactive beta-glucosidase |
GYP | 3_138419203 | 6.10E-05 | 6.91 | GRMZM5G803355 GRMZM2G585025 | MYB transcription factor Small RNA degrading nuclease 5 |
GYP | 3_7417157 | 7.15E-05 | 6.79 | GRMZM2G015267 | FAD/NAD(P)-binding oxidoreductase |
GYP | 1_209009744 | 7.45E-05 | 6.76 | GRMZM2G125557 | Auxin-repressed protein putative expressed |
GYP | 2_66831336 | 7.76E-05 | 6.73 | GRMZM2G097406 | Unknown |
GYP | 3_138762178 | 9.58E-05 | 6.58 | GRMZM2G087590 | PsbP domain-containing protein 4 |
GYP | 8_29023337 | 9.72E-05 | 6.57 | GRMZM2G393347 | HOPZ-ACTIVATED RESISTANCE 1 (ZAR1) |
GYP | 10_34938698 | 1.48E-04 | 6.26 | GRMZM2G003090 | Unknown |
KW | 6_77081642 | 3.60E-18 | 32.43 | GRMZM2G328197 GRMZM2G376957 | RING zinc finger domain superfamily protein Histone H3-like 5 |
KW | 1_299177196 | 2.17E-17 | 32.56 | GRMZM2G110851 | Pentatricopeptide repeat-containing protein |
KW | 3_175569291 | 2.86E-12 | 20.42 | GRMZM2G149662 | COV1-like protein |
KW | 1_52,668,969 | 1.42E-10 | 18.58 | GRMZM2G174696 | Mitochondrial import receptor subunit TOM40–1 |
KW | 5_177277411 | 1.02E-08 | 15.00 | GRMZM2G492156 | MADS-box transcription factor 27 |
KW | 9_154673101 | 2.50E-08 | 14.28 | GRMZM2G092741 | ARATH AP-2 complex subunit alpha-2 |
KW | 6_67479669 | 2.53E-08 | 13.00 | GRMZM2G430902 | C3HC4-type RING finger family protein |
KW | 1_38858313 | 5.16E-08 | 12.44 | AC204035.3 | Unknown |
KW | 4_238037247 | 6.29E-08 | 12.28 | GRMZM2G166145 | Apoptosis-inducing factor homolog |
KW | 10_110533455 | 2.82E-07 | 12.31 | GRMZM2G153215 | Membrane-anchored ubiquitin-fold protein 4 |
KW | 2_223591728 | 4.83E-07 | 10.70 | GRMZM2G172101 GRMZM2G052507 | Seryl-trna synthetase Serine carboxypeptidase-like 45 |
KW | 2_36952454 | 6.26E-07 | 11.67 | GRMZM2G102238 | PAP2 family domain containing protein |
KW | 1_13682335 | 6.28E-07 | 10.49 | GRMZM2G417455 | Beta-galactosidase 5 |
KW | 7_130909742 | 6.31E-07 | 10.49 | GRMZM2G464985 | Serine/threonine-protein kinase D6PKL1 |
KW | 4_174067645 | 9.84E-07 | 10.15 | GRMZM2G010933 | Cytochrome c oxidase copper chaperone 1 |
KW | 6_66363963 | 1.72E-06 | 9.72 | GRMZM2G110983 | Ubiquitin-conjugating enzyme E2 |
KW | 1_154806752 | 1.76E-06 | 9.70 | GRMZM2G446047 | Trm32_arath protein trm32 |
KW | 5_179440519 | 2.05E-06 | 9.58 | GRMZM2G003384 | 60S ribosomal protein L6 |
KW | 1_76348752 | 2.30E-06 | 10.62 | GRMZM2G174708 | Polygalacturonase inhibitor 1 |
KW | 6_19391683 | 2.56E-06 | 10.54 | GRMZM2G319397 | Unknown |
KW | 8_71170430 | 2.78E-06 | 10.47 | GRMZM5G887975 | GATA transcription factor 19 |
KW | 2_54135317 | 2.80E-06 | 9.35 | GRMZM2G173218 | Unknown |
KW | 2_233033601 | 3.21E-06 | 9.24 | GRMZM5G843555 GRMZM2G149935 | Putative prolyl 4-hydroxylase 12 Hydroxyproline o-galactosyltransferase galt4 |
KW | 2_153726247 | 3.51E-06 | 9.17 | GRMZM5G800842 | Ubiquitin-activating enzyme E12 |
KW | 7_115163058 | 5.27E-06 | 8.86 | GRMZM2G071059 GRMZM2G171408 | CCR4-NOT transcription complex subunit 7 Spotted leaf protein 11 |
KW | 1_87304388 | 5.56E-06 | 8.82 | GRMZM2G046848 | U-box domain-containing protein kinase family |
KW | 1_233620848 | 6.16E-06 | 8.74 | GRMZM2G001850 | Nucleolin like 2 |
KW | 5_204816347 | 6.48E-06 | 8.70 | GRMZM5G899787 | RNA-binding (RRM/RBD/RNP motifs) protein |
KW | 8_65840306 | 6.66E-06 | 8.68 | GRMZM2G477340 | CDP-diacylglycerol--serine O-phosphatidyltransferase 2 |
KL | 2_200248530 | 4.01E-05 | 7.18 | GRMZM2G435689 | Unknown |
KL | 2_192310952 | 7.72E-05 | 6.70 | GRMZM2G013892 | Zinc finger C3HC4 type domain containing protein |
KL | 7_137256260 | 9.02E-05 | 6.59 | GRMZM2G458164 | Glucan endo-1 3-beta-glucosidase precursor |
KL | 10_34938698 | 1.51E-04 | 6.21 | GRMZM2G003090 | Unknown |
KNR | 1_52253410 | 1.23E-05 | 9.29 | GRMZM2G128644 | VQ motif-containing protein |
KNR | 1_299177196 | 1.58E-05 | 9.09 | GRMZM2G110851 | PPR repeat domain containing protein |
KNR | 6_77081642 | 3.10E-05 | 7.52 | GRMZM2G328197 GRMZM2G376957 | RING zinc finger domain superfamily protein Histone H3-like 5 |
KNR | 6_158099344 | 4.58E-05 | 8.25 | GRMZM2G049091 GRMZM2G138067 | Transcription initiation factor IIF beta subunit Protein LURP-one-related 5 |
KNR | 7_13586175 | 8.49E-05 | 7.77 | GRMZM2G446921 | F-box domain containing protein |
HKW | 2_206427709 | 2.45E-05 | 8.72 | GRMZM2G418343 GRMZM2G117900 | Cell wall protein precursor putative Translation initiation factor family protein |
HKW | 6_67617018 | 4.05E-04 | 5.59 | GRMZM2G430902 | C3HC4-type RING finger family protein |
TBN | 8_139,471,588 | 2.00E-09 | 14.76 | GRMZM2G101664 | Zinc finger protein |
TBN | 8_89433292 | 6.73E-07 | 10.25 | GRMZM5G856067 GRMZM2G063676 | Ribosomal protein L18ae family heat shock 70 kDa protein 4 |
TBN | 1_29024922 | 1.07E-06 | 9.90 | GRMZM2G153611 GRMZM2G180023 | E3 ubiquitin-protein ligase ARI2 serine/threonine receptor-like kinase NFP |
TBN | 10_4247900 | 1.98E-06 | 9.44 | GRMZM5G886547 | Non-specific lipid-transfer protein 3 |
TBN | 8_148198954 | 2.07E-06 | 9.40 | GRMZM2G130586 | Unknown |
TBN | 8_139164894 | 4.92E-06 | 8.76 | GRMZM2G046037 | ubiquitin carboxyl-terminal hydrolase MINDY-2 |
TBN | 3_160368430 | 7.87E-06 | 8.40 | GRMZM2G129114 | Nucleotide-diphospho-sugar transferase |
TBN | 1_270000781 | 1.41E-05 | 7.97 | GRMZM5G857351 | translational activator GCN1 |
TBN | 3_180017439 | 1.20E-05 | 8.09 | GRMZM2G042295 | methyltransferase putative expressed |
TBN | 4_209597837 | 1.39E-05 | 7.98 | GRMZM2G094541 | Receptor-like serine/threonine-protein kinase SD1–6 |
TBN | 7_175448419 | 1.32E-05 | 8.02 | GRMZM2G086628 | early nodulin-like protein 16 |