Table 3.
Newly designed assays for detection of strawberry-infecting viruses.
| Virus | Oligo Name | Sequence (5′ to 3′) | 5’ Reporter | Target Region | Length |
|---|---|---|---|---|---|
| Strawberry crinkle virus | SCV-F1 | ATAGGGAGGAAAAACATTATCCG | RdRp | 175 bp | |
| SCV-F2 | ATAGGGAGGAAAAACATCATCCG | ||||
| SCV-F3 | ATAGGGAGGAAAAACATAATCCG | ||||
| SCV-F4 | ATAGGGAGGAAGAATATCATCCG | ||||
| SCV-R1 | CATTGGTGGCAGACCCATCA | ||||
| SCV-R2 | CATTGGTAGCAGATCCATCA | ||||
| SCV-P1 | TGTCACAAGATGCTGGAAG | FAM | |||
| SCV-P2 | TGTCACAGGATGCTGGAA | FAM | |||
| Strawberry mottle virus | SMoV-F1 | GTAGTTTAGTGACAATCCAAGCGGA | 3’ UTR | 112 bp | |
| SMoV-F2 | GTAGTTTAGCGACAATCCAAGCGGA | ||||
| SMoV-R1 | ATCCCACTTAGGGGCAAAGAA | ||||
| SMoV-R2 | ATCCCACTTAGGGGCAGAGGA | ||||
| SMoV-P1 | TAGGACACCGGCTCT | FAM | |||
| Strawberry mild yellow edge virus | SMYEV-F1 | AGGCTTAAAATGGGAGTTTCTTCTC | CP | 83 bp | |
| SMYEV-F2 | AGGCTTTAAATGGGAGTTTCTTCTC | ||||
| SMYEV-F3 | AGGCTTCAAATGGGAGTTTCTTCTC | ||||
| SMYEV-R1 | ACGGTTAAGTAGTACTATATTCACTTCATGG | ||||
| SMYEV-R2 | ACGGTTAAGTAGTACTACATTCACTTCATGG | ||||
| SMYEV-P1 | TTCTTCTACCCAGCTCC | FAM | |||
| Strawberry pallidosis- associated virus | SPaV-F1 | TTTGTATTCTGGTATGAATTTGGAAACT | Polyprotein 1b | 123 bp | |
| SPaV-F2 | TCTTTATTCTGGGATGAATTTAGAGACT | ||||
| SPaV-R1 | ACACCTTGAGATTTATCAAATTTGCT | ||||
| SPaV-R2 | ACACCTTGGGATTTATCGAATTTACT | ||||
| SPaV-R3 | ACACCTTGAGATTTATCGAACTTGCT | ||||
| SPaV-P1 | TTCCAATTCAAGAGTACAGGAC | FAM | |||
| SPaV-P2 | TCCCAATTCAAGAGTATCGAAC | FAM | |||
| Strawberry vein banding virus | SVBV-F1 | TTTCTGTGACTATGAAACCAATCTTCT | CP | 99 bp | |
| SVBV-F2 | TTTCTGTGATTATGAAACCAATCTTCT | ||||
| SVBV-R1 | TCCATCCCGACAAAGGGTATT | ||||
| SVBV-R2 | TCCATTCCCACAAAGGGTATT | ||||
| SVBV-R3 | TCCATCCCAACAAAGGGTATT | ||||
| SVBV-P1 | CCTATAGAAGAATGGCCCAA | FAM | |||
| SVBV-P2 | CCAATAGAAGAATGGCCCAA | FAM | |||
| Strawberry polerovirus 1 | SPV1-F1 | GCCAGACGTCCCAGAGGTT | CP | 61 bp | |
| SPV1-R1 | GTCTTCCGGCATTCTGTTTCTT | ||||
| SPV1-P1 | AGAGGAGGAAAAGGAAA | FAM | |||
| Beet pseudo yellows virus | BPYV-F1 | AACGGTTGCAAGGTCAACATT | CP | 62 bp | |
| BPYV-R1 | GTTTCACGCTGTAGCCAATTTG | ||||
| BPYV-R2 | GTTTCACGCAGTAGCCAATTTG | ||||
| BPYV-R3 | GTTTCGCGCTGTAGCCAATTTG | ||||
| BPYV-P1 | CGGATGATGATTTGACG | FAM | |||
| Tomato ringspot virus | ToRSV-F1 | CCTGCAGAAGCAGATTGGC | CP | 140 bp | |
| ToRSV-F2 | CCTGCAGAAGCTGATTGGC | ||||
| ToRSV-F3 | CCTGCGGAAGCTGATTGGC | ||||
| ToRSV-R1 | GTTGGCCCGCGCCA | ||||
| ToRSV-R2 | GTAGGCCCGCGCCA | ||||
| ToRSV-R3 | GTTGGCCCACGCCA | ||||
| ToRSV-P1 | GGCGGTTCCTTTTATT | FAM | |||
| ToRSV-P2 | CGCCGTTCCTTTTATT | FAM | |||
| Apple mosaic virus | ApMV-F1 | AAGCGAACCCGAATAAGGGT | CP | 202 bp | |
| ApMV-F2 | AGCGAACCCGAACAAGGG | ||||
| ApMV-F3 | GCGAACCCGAATAAGGGTAAA | ||||
| ApMV-F4 | GCGAACCCGAACAAGGGTA | ||||
| ApMV-R1 | CGGAAGACATCGGCAAAGTC | ||||
| ApMV-R2 | ACGAAAGACATCGGCAAAGTC | ||||
| ApMV-P1 | CTTGGGAGGTTAGAGGC | FAM | |||
| ApMV-P2 | CTTGGGAGGTTAGTGTCC | FAM | |||
| Strawberry chlorotic fleck virus | SCFaV-F1 | TGAACTTGATCTGGGGCGTC | CP | 196 bp | |
| SCFaV-R1 | CCTCGAGCCCAGTGTCTCA | ||||
| SCFaV-P1 | AGGTTTGAAAAGAACCC | FAM | |||
| Strawberry crinivirus 3 | SCrV3-F1 | CAACCACCGTCTACAAACATTACAA | Polyprotein 1a | 126 bp | |
| SCrV3-R1 | GGACCACGGTCGGAAGTTG | ||||
| SCrV3-P1 | TTTGTAGAACGCAGGCACAGT | FAM | |||
| Strawberry crinivirus 4 | SCrV4-F1 | TTTGGGATTTCAGATTTGGGC | Polyprotein 1a | 155 bp | |
| SCrV4-F2 | ATAGGAATCTCGGATTTGGGC | ||||
| SCrV4-R1 | CGAGATCCAGATGAAGAAGTAACATAG | ||||
| SCrV4-R2 | CGAGATCCAGAGGAAGAAGTGAC | ||||
| SCrV4-P1 | TGTGAAGGAGAAGAATACCTA | FAM | |||
| Fragaria chiloensis latent virus | FClLV-F1 | CGTACTATCAATGAAACACTATCCAGAT | MP | 189 bp | |
| FClLV-R1 | TGGTTCAATCGGAACATTGTTC | ||||
| FClLV-P1 | CCATGTCTGATTTAGATAAA | FAM | |||
| Fragaria chiloensis cryptic virus | FCCV-F1 | CCTGACATAGCGTTCACACGA | RdRp | 96 bp | |
| FCCV-R1 | AAGTAGGACGTAATGAAACGCCTC | ||||
| FCCV-P1 | CAAATCAAGGTGAAGAGAA | FAM |
Forward primer (F), reverse primer (R), and TaqMan™ MGB probe (P). Coat protein (CP), movement protein (MP), RNA-dependent RNA polymerase (RdRp), and untranslated region (UTR). Default parameters for primer and probe Tm are 58–60 °C and 68–70 °C, respectively.