Table 3. Summary statistics of functionally annotated and categorized genome wide association hits.
| Category | Genome (count) | GLS GWAS (count) | SE | z-value | p-value |
|---|---|---|---|---|---|
| Cell Cycle | 25777 | 13 | 0.077 | 1.155 | 8.76E-01 |
| Cell Signal | 21016 | 2 | 0.073 | 3.837 | 1.00E+00 |
| Cellular Energy | 805 | 5 | 0.018 | -6.237 | 2.22E-10 |
| Development | 205 | 3 | 0.009 | -7.841 | 2.24E-15 |
| Membrane Transporter | 2896 | 0 | 0.033 | 1.399 | 9.19E-01 |
| Pathogen Defense Related | 4590 | 4 | 0.040 | -0.626 | 2.66E-01 |
| Primary Metabolite | 204 | 1 | 0.009 | -2.391 | 8.39E-03 |
| Secondary Metabolite | 4604 | 8 | 0.041 | -3.027 | 1.23E-03 |
| Structural Components | 3442 | 5 | 0.035 | -1.916 | 2.77E-02 |
Significant GWAS hits were functionally annotated using basic local alignment search tool. These annotations were categorized into biological groups, which include: structural components, secondary metabolites, primary metabolites, genes previously implicated in pathogen-defense, membrane transporter, development, cellular energy, cell signaling, and cell cycle. The genes on the inter-pro hit list (www.maizesequence.org) were also categorized into these same categories. The genome count indicates the total number of genes within the genome in the given category, and the GLS (Count) indicates the number of annotated GLS GWAS hits in a given category. A proportion z-test was used to test the abundance of genes in a given category relative to the overall abundance predicted in the maize genome. SE: standard error.