Pepper
Capsicum annuum
| Analysis | Locus | Causal Agent (Genus & Species) | Molecular Marker Systems |
| Bacterial Leaf Spot | Bs2 | Xanthomonas campestris pv. vesicatoria | - |
| Bacterial Leaf Spot | Bs3 | Xanthomonas campestris pv. vesicatoria | - |
| Fertility Restorer (male sterility/fertility) | Rf | - | - |
| Cytoplasmic Male Sterility | coxII & atp6 | - | - |
| Tomato Spotted Wilt Virus (TSWV) | Tsw | Tospovirus serogroups | - |
| Pepper Huasteco Geminivirus (PHV) | - | - | |
| Potato Virus Y (PVY) | Pvr4 | Potato Virus Y (PVY) | - |
| Potato Virus Y (PVY) | Pvr1 | Potato Virus Y (PVY) | - |
| Potato Virus Y (PVY) | Pvr11 | Potato Virus Y (PVY) | - |
| Potato Virus Y (PVY) | Pvr12 | Potato Virus Y (PVY) | - |
| Pepper Mild Mottle Virus (PMMoV) | L3 | Pepper mottle virus (PMMoV) | - |
| Pepper Mild Mottle Virus (PMMoV) | L4 | Pepper mottle virus (PMMoV) | - |
| Root Rot | Phyto5.2 | Phytophthora capsici | - |
| Root-Rot & Foliar-Blight | QTLs | Phytophthora capsici | - |
| Pepper Carotenoid Genes | Ggpp,psy,pds,zds,ze,ccs | - | - |
| Pepper Pungency (Capsaicinoids) | C | - | - |
| Variety Identification and Fingerprinting | - | - | SCAR, CAPS, RAPD, STS, SSR, TRAP, SRAP |