Table 1.
Enrichment of prioritized genes for CornCyc pathway annotations
| PNC | Minimum percentile | Pathway | Enrichment | P-value (FDR) |
|---|---|---|---|---|
| Observed | NA | Triacylglycerol degradation (LIPAS-PWY) | 0.76 | 2.9 × 10−5 (0.0093) |
| Aerobic respiration III (alternative oxidase pathway) (PWY-4302) | 0.70 | 3.7 × 10−5 (0.0093) | ||
| Predicted | 90% | Glycolysis IV (plant cytosol) (PWY-1042) | 1.41 | 7.8 × 10−7 (0.00038) |
| Rubisco shunt (PWY-5723) | 1.40 | 2.1 × 10−4 (0.015) | ||
| Glycolysis I (from glucose 6-phosphate) (GLYCOLYSIS) | 1.36 | 1.0 × 10−5 (0.0025) | ||
| Gluconeogenesis I (GLUCONEO-PWY) | 1.36 | 8.4 × 10−5 (0.0083) | ||
| Glycolysis II (from fructose 6-phosphate) (PWY-5484) | 1.36 | 2.4 × 10−5 (0.0029) | ||
| Triacylglycerol degradation (LIPAS-PWY) | 0.65 | 1.7 × 10−5 (0.0027) | ||
| Very long-chain fatty acid biosynthesis I (PWY-5080) | 0.59 | 3.1 × 10−4 (0.019) | ||
| Trans-zeatin biosynthesis (PWY-2681) | 0.29 | 1.6 × 10−4 (0.013) | ||
| 99% | L-leucine biosynthesis (LEUSYN-PWY) | 3.66 | 9.5 × 10−4 (0.043) | |
| Fatty acid β-oxidation II (peroxisome) (PWY-5136) | 3.59 | 4.8 × 10−4 (0.033) | ||
| Glyoxylate cycle (GLYOXYLATE-BYPASS) | 2.99 | 6.3 × 10−4 (0.033) | ||
| TCA cycle II (PWY-5690) | 2.51 | 5.0 × 10−4 (0.033) | ||
| Gluconeogenesis I (GLUCONEO-PWY) | 2.24 | 2.6 × 10−4 (0.032) | ||
| Glycolysis IV (plant cytosol) (PWY-1042) | 2.16 | 2.0 × 10−4 (0.032) | ||
| Glycolysis II (from fructose 6-phosphate) (PWY-5484) | 2.16 | 2.0 × 10−4 (0.032) | ||
| Glycolysis I (from glucose 6-phosphate) (GLYCOLYSIS) | 2.09 | 4.4 × 10-4 (0.033) | ||
| Aerobic respiration I (cytochrome c) (PWY-3781) | 0.31 | 4.3 × 10−6 (0.0021) | ||
| Triacylglycerol degradation (LIPAS-PWY) | 0.23 | 6.5 × 10−4 (0.033) | ||
| Very long-chain fatty acid biosynthesis I (PWY-5080) | 0 | 6.6 × 10−4 (0.033) |
PNC: Measure of phylogenetic nucleotide conservation (PNC) used to select SNPs in the maize reference panel (Hapmap 3.2.1) and prioritize the genes containing the selected SNPs; SNPs were selected if their observed PNC was 1 or if their predicted PNC was above the 50%, 90%, 99%, or 99.9% percentile; Pathway: name and ID of pathway, retrieved from CornCyc, release 2021/03/25 [31]; Enrichment: ratio of observed over expected counts; P-value, from Fisher’s exact test; FDR, false discovery rate [32] to correct for multiple testing over pathways. Prioritization of genes by SIFT scores did not result in any statistically significant enrichment or depletion for pathway annotations