Table 4.
Significant SNPs associated with Phytophthora capsici KPC-7 resistance in the pepper population.
| Chr. | Position (bp) | p-Value | Ref.* | Alt.* | Type | Gene name/symbol | Function | Primer design |
|---|---|---|---|---|---|---|---|---|
| chr01 | 18,309,131 | 3.12E-07 | T | A | missense_variant | LOC107869375 | Protein NRT1/PTR FAMILY 7.3-like | No |
| chr01 | 18,541,809 | 5.90E-07 | T | A | intergenic_region | – | – | No |
| chr01 | 18,541,871 | 5.37E-07 | C | G | intergenic_region | – | – | No |
| chr02 | 112,632,207 | 4.85E-07 | T | C | upstream_gene_variant | LOC107858831 | Protein WVD2-like 7 | Yes |
| chr02 | 115,557,669 | 8.66E-07 | G | A | intergenic_region | – | – | Yes |
| chr02 | 118,473,950 | 8.83E-07 | A | C | downstream_gene_variant | LOC107858923 | Uncharacterized | Yes |
| chr02 | 165,074,534 | 8.84E-08 | C | A | synonymous_variant | LOC107860606 | Peroxidase 63 mRNA | Yes |
| chr02 | 165,083,237 | 1.09E-06 | C | A | upstream_gene_variant | LOC107860605 | U-box domain-containing protein 40 | Yes |
| chr02 | 165,083,291 | 1.10E-08 | T | C | upstream_gene_variant | LOC107860605 | U-box domain-containing protein 40 | Yes |
| chr03 | 26,843,710 | 2.82E-07 | G | T | synonymous_variant | LOC107864116 | Protein TIME FOR COFFEE | Yes |
| chr03 | 92,882,787 | 1.46E-07 | G | C | intergenic_region | – | No | |
| chr03 | 203,119,513 | 4.45E-07 | T | C | upstream_gene_variant | LOC107863456 | luc7-like protein 3 | Yes |
| chr03 | 273,929,454 | 1.06E-06 | A | G | intron_variant | Signal recognition particle 54 kDa | Yes | |
| chr03 | 281,084,163 | 1.07E-07 | A | T | synonymous_variant | LOC107864287 | F-box/Kelch-repeat protein At3g06240-like | No |
| chr03 | 281,374,819 | 3.75E-07 | T | C | intergenic_region | – | – | Yes |
| chr03 | 281,374,880 | 3.77E-07 | T | G | intergenic_region | – | – | Yes |
| chr04 | 9,578,255 | 2.47E-24 | G | A | intergenic_region | – | – | Yes |
| chr06 | 1,385,184 | 2.39E-08 | A | T | intergenic_region | – | – | No |
| chr06 | 3,204,310 | 7.86E-07 | G | A | intergenic_region | – | – | Yes |
| chr06 | 184,471,306 | 4.83E-07 | G | A | missense_variant | LOC107873008 | Uncharacterized | Yes |
| chr07 | 9,144,225 | 3.23E-07 | A | G | intergenic_region | – | – | Yes |
| chr07 | 205,297,202 | 1.85E-07 | C | T | downstream_gene_variant | LOC107879742 | Pentatricopeptide repeat-containing | Yes |
| chr08 | 126,466,421 | 3.57E-08 | T | A | downstream_gene_variant | LOC107879742 | Hevamine-A-like mRNA | No |
| chr08 | 138,930,210 | 1.86E-07 | C | A | upstream_gene_variant | LOC107839408 | Phosphomannomutase | Yes |
| chr09 | 3,642,467 | 8.34E-07 | T | C | downstream_gene_variant | LOC107843160 | Uncharacterized | Yes |
| chr09 | 16,370,729 | 9.33E-07 | C | T | missense_variant | LOC107842944 | Phosphatidate phosphatase PAH1 | Yes |
| chr10 | 19,168,172 | 6.50E-07 | C | G | intergenic_region | – | – | No |
| chr12 | 208,357,955 | 6.52E-07 | T | A | downstream_gene_variant | LOC107851575 | Endoglucanase 6 mRNA | No |
| chr12 | 232,050,702 | 1.24E-10 | T | C | downstream_gene_variant | LOC107851266 | Succinate dehydrogenase subunit 5 | Yes |
Chr., Chromosome; Ref., Reference sequence; Alt., Alternate sequence. *p < 0.05.