Table 2.
The identified SNPs associated with popping-related traits within annotated gene regions based on GWAS
| Trait | SNP | Effect | P-value | Alleles | Annotation | GeneID | Gene Name | Description | Previous study |
|---|---|---|---|---|---|---|---|---|---|
| Color | S6_44382110 | 0.061 | 1.096E-09 | T/A | synonymous_variant | GRMZM2G086294 | zp15 | Zein-beta Precursor (Zein-2)(16 kDa zein) (Zein clone 15A3) | |
| Color | S6_82019628 | 0.14 | 2.25E-38 | A/G | synonymous_variant | GRMZM2G300348 | y1 | Phytoene synthase, chloroplastic Precursor (EC 2.5.1.32) | |
| Color | S6_86338050 | 0.038 | 1.33E-06 | C/T | 5_prime_UTR_variant | GRMZM2G082874 | uwm3035 | plant-specific domain TIGR01589 family protein | |
| Floury/Vitreous | S4_210389724 | 0.069 | 2.19E-06 | G/A | intron_variant | GRMZM2G040559 | uwm10774 | tubulin alpha-6 chain | |
| PEV | S1_55451772 | -15.95 | 2.34E-06 | T/C | upstream_gene_variant | GRMZM2G056424 | uwm46912 | photosystem II 11 kD protein | qPEV1-1 |
| PEV | S1_253277924 | 23.48 | 4.40E-06 | A/T | upstream_gene_variant | GRMZM5G837732 | CBL-interacting serine/threonine-protein kinase 15 (LOC100285495), mRNA | qPV1-3 | |
| PEV | S1_253277948 | 23.48 | 4.40E-06 | C/T | upstream_gene_variant | GRMZM5G837732 | CBL-interacting serine/threonine-protein kinase 15 (LOC100285495), mRNA | qPV1-3 | |
| PEV | S2_36136426 | 25.052 | 2.88E-06 | C/T | intron_variant | GRMZM2G030598 | kelch motif family protein | ||
| PEV | S3_162805619 | 23.61 | 9.64E-06 | C/T | downstream_gene_variant | GRMZM2G133398 | vp1 | Regulatory protein viviparous-1 | |
| PEV | S3_213803780 | -20.67 | 7.27E-06 | T/C | splice_region_variant&intron_ variant | GRMZM2G047129 | alpha-L-fucosidase 2 | qBPV3-1 | |
| PEV | S5_175731057 | 29.74 | 1.14E-06 | A/G | synonymous_variant | GRMZM2G024739 | cry1 | cryptochrome 1 | |
| IF | S5_160833678 | 0.15 | 9.26E-06 | A/C | synonymous_variant | GRMZM2G077989 | RS21-C6 protein | ||
| IF | S7_106078238 | -0.26 | 9.63E-07 | A/C | missense_variant | GRMZM2G046600 | uwm17845 | catalytic/ hydrolase | |
| IF | S9_153853384 | -0.28 | 3.39E-06 | G/A | upstream_gene_variant | GRMZM2G171466 | nascent polypeptide-associated complex alpha subunit-like protein | ||
| Protein | S7_165744712 | -0.11 | 4.21E-06 | C/A | upstream_gene_variant | GRMZM2G054032 | uwm10642 | F-box protein | |
| Shape | S5_190238066 | -0.14 | 2.18E-06 | T/C | upstream_gene_variant | GRMZM2G169558 | protein kinase APK1A | ||
| Shape | S8_136138158 | 0.14 | 2.97E-06 | A/G | 3_prime_UTR_variant | GRMZM2G100229 | calmodulin binding protein |