Table I. Top scoring genes using a weighted scoring system based on the number of top 1,000, top 100, and top 20 SNPs associated with each gene.
The complete list of top 1,000 SNPs (based on P value) and their associated genes is shown in Supplemental Table S2, and the scores for each gene with regions of interest marked are shown in Supplemental Table S3. SNP plots for each region of interest are shown in Supplemental Figure S1.
| Gene | Top 1,000 SNPs | Top 100 SNPs | Top 20 SNPs | Score | Region | Gene Description |
|---|---|---|---|---|---|---|
| AT4G27720 | 14 | 4 | 0 | 34 | 63 | Major facilitator superfamily |
| AT3G29725 | 3 | 2 | 2 | 33 | 40 | Pseudogene |
| AT3G29727 | 3 | 2 | 2 | 33 | 40 | Transposable element |
| AT4G27730 | 12 | 4 | 0 | 32 | 63 | Oligopeptide transporter6 |
| AT5G54920 | 6 | 3 | 1 | 31 | 97 | Unknown |
| AT5G54930 | 5 | 3 | 1 | 30 | 97 | AT hook motif protein |
| AT5G54940 | 5 | 3 | 1 | 30 | 97 | Translation initiation factor family |
| AT5G54950 | 4 | 3 | 1 | 29 | 97 | Aconitase family |
| AT5G54960 | 4 | 3 | 1 | 29 | 97 | Pyruvate decarboxylase2 |
| AT5G55040 | 3 | 3 | 1 | 28 | 98 | DNA-binding bromodomain |
| AT4G27700 | 12 | 3 | 0 | 27 | 63 | Phosphatase |
| AT4G27710 | 12 | 3 | 0 | 27 | 63 | CYP709B3 |
| AT1G30473 | 15 | 2 | 0 | 25 | 9 | Heavy metal transporter |
| AT3G51050 | 5 | 2 | 1 | 25 | 45 | FG-GAP repeat protein |
| AT3G51090 | 5 | 4 | 0 | 25 | 46 | Unknown |
| AT3G51100 | 5 | 4 | 0 | 25 | 46 | Unknown |
| AT3G51110 | 5 | 4 | 0 | 25 | 46 | Tetratricopeptide repeat |
| AT4G27690 | 10 | 3 | 0 | 25 | 63 | Vacuolar sorting protein26B |
| AT1G30470 | 14 | 2 | 0 | 24 | 9 | SIT4 phosphatase-associated family |
| AT2G36632 | 4 | 2 | 1 | 24 | 29 | Unknown |
| AT2G36640 | 4 | 2 | 1 | 24 | 29 | Embryonic cell protein63 |
| AT4G33240 | 4 | 2 | 1 | 24 | 65 | 1-Phosphatidylinositol-3-phosphate 5-kinase |
| AT1G30475 | 13 | 2 | 0 | 23 | 9 | Embryo-defective1303-like |
| AT2G36620 | 3 | 2 | 1 | 23 | 29 | RPL24 |
| AT2G36630 | 3 | 2 | 1 | 23 | 29 | Sulfite exporter TauE/SafE family |
| AT2G36650 | 3 | 2 | 1 | 23 | 29 | Unknown |
| AT5G35360 | 3 | 2 | 1 | 23 | 81 | Biotin carboxylase subunit |
| AT5G53510 | 3 | 2 | 1 | 23 | 95 | Oligopeptide transporter9 |
| AT5G54970 | 3 | 2 | 1 | 23 | 97 | Unknown |
| AT3G51057 | 2 | 2 | 1 | 22 | 45 | Unknown |
| AT4G33250 | 2 | 2 | 1 | 22 | 65 | Translation initiation factor3k |
| AT5G35405 | 2 | 2 | 1 | 22 | 81 | ECA1 gametogenesis-related protein |
| AT5G53486 | 2 | 2 | 1 | 22 | 95 | Unknown |
| AT5G53487 | 2 | 2 | 1 | 22 | 95 | Pre-tRNA, tRNA-Gly |
| AT5G55020 | 2 | 2 | 1 | 22 | 98 | MYB120 transcription factor |
| AT1G30480 | 10 | 2 | 0 | 20 | 9 | DNA damage-repair/toleration protein111 |
| AT5G54820 | 10 | 2 | 0 | 20 | 96 | F-box protein |