Table 3. Carotenoid-related genes identified through genome-wide association study of five kernel colorimeter traits in the Ames maize inbred panel, and the most significant SNP for each trait-by-gene combination.
| Gene ID | Gene | Trait | SNP ID | Chr | Position of SNP | P-value | FDR-adjusted P-value | MAF | R2LR | R2LR-SNP |
|---|---|---|---|---|---|---|---|---|---|---|
| Zm00001d003512 | zep1 | a* | S2_44473748 | 2 | 46,329,893 | 7.30E-07 | 2.44E-02 | 0.141 | 0.414 | 0.423 |
| Zm00001d036345 | y1 | a* | S6_82020346 | 6 | 85,064,521 | 2.65E-07 | 1.58E-02 | 0.061 | 0.414 | 0.423 |
| Zm00001d019060 | dxs2 | a* | S7_14078791 | 7 | 14,495,640 | 3.25E-10 | 8.72E-05 | 0.050 | 0.414 | 0.428 |
| Zm00001d019060 | dxs2 | hue | S7_14078791 | 7 | 14,495,640 | 4.74E-08 | 6.35E-03 | 0.050 | 0.493 | 0.502 |
| Zm00001d011210 | lcyE | hue | S8_138888278 | 8 | 143,026,247 | 2.52E-07 | 2.25E-02 | 0.416 | 0.493 | 0.501 |
Gene ID: Gene designation and position of SNPs from B73 RefGen_v4 (www.maizegdb.org; Andorf et al. 2016); Gene: Annotated gene containing SNP, except zep1, which is 25 kb upstream of the SNP; Position of SNP: Genomic position (bp) of the SNP from B73 Refgen_v4; FDR-adjusted P-value: False discovery rate adjusted P-value; MAF: Minor-allele frequency; R2LR: R2 likelihood ratio value of model without SNP; R2LR-SNP: R2 likelihood ratio value of model with SNP.