Table 1.
Reverse-transcription quantitative polymerase chain reaction primers used for quantification of southern rice black-streaked dwarf virus (SRBSDV) and rice ragged stunt virus (RRSV)
| Purpose | Gene name | Target gene (GenBank accession no.) | Primer for RT-qPCR(5′-3′) | Size of expected amplicon (bp) |
|---|---|---|---|---|
| RRSV | RRSV P1 | HM125559 | AGGATCTCTTCTCAATGCAAGC | 70 |
| AACTTCCACCTGGCAACGTC | ||||
| RRSV P2 | HM125560 | GGCGTTCGATCTCGTGTTTAA | 69 | |
| GCGGGAAAATCATTGGCGTG | ||||
| RRSV P3 | AF020336 | TCAAAGCTAGTGATGAGCGTCTGT | 70 | |
| CTGGCATAAAAACGAAGAGTCTGA | ||||
| RRSV P4A | HM125562 | GGCGTCAGTGTGTAGCAGCAT | 66 | |
| ATTGGGTAGAGTTGTTGTTTTGGAT | ||||
| RRSV P4B | HM125562 | CGCCATCCACAAAGCTATCA | 63 | |
| AACACTCTCGTAGCCTGCCAAT | ||||
| RRSV P5 | HM125562 | CGCCATCCACAAAGCTATCA | 59 | |
| AACACTCTCGTAGCCTGCCAAT | ||||
| RRSV S5 | HM125543 | GGCGGCATCGGGTTGT | 59 | |
| CACCTCTATCAAACGCAGTAACCA | ||||
| RRSV S6 | HM125554 | GCTTTCGCGGTGCTCAA | 59 | |
| CTCCCAATTACGCACCGAAT | ||||
| RRSV P7 | HM125555 | TGACGATTACGCCGAGACAAG | 62 | |
| CGGACGACTGGCCAATG | ||||
| RRSV P8 | HM125546 | GGCTGAGCGTGCGGTTA | 66 | |
| TCAGCCTTGATATCGTTGTAGCA | ||||
| RRSV P9 | L79969 | GGTGTGGCTCTACAACAAATGG | 67 | |
| ACGCCTCTTTCTCTGCTCCTCTA | ||||
| RRSV P10 | HM125568 | CCGAGCCGCCATCATAGTA | 63 | |
| ACCTCAAAAACTCCAGACAGCATA | ||||
| SRBSDV | SRBSDV P1 | JQ692572 | TGTGATTTGAACTCAGAGACAGCTTTA | 80 |
| TGACGTTGATAAGTTGATTGTTGAGA | ||||
| SRBSDV P2 | HM585278 | GCGAACGGCTTTCTGCTTT | 71 | |
| GAATGTGCGAGTGATTTCATGAA | ||||
| SRBSDVP3 | HM585277 | TCCCGGTGTTCGAGAAGTTC | 64 | |
| CAGCATTTTCCATCCAACCAT | ||||
| SRBSDV P4 | HM585276 | TCAACGCTCGACAACCAAAA | 72 | |
| TTATCGTGATATCTGCTACGAATACCA | ||||
| SRBSDV P5-1 | HM585275 | ATCAGATGATAACCTCAATCGTACCA | 94 | |
| TGAGCCAGTGAAGGTAATCATCATTA | ||||
| SRBSDV P5-2 | CGCTTAACAATTGTCGTGATATGAA | 75 | ||
| GCGTGCTTCCGAAAAGTAAAGTT | ||||
| SRBSDV P6 | HM585274 | AAGCAACAAACATCAACGTCAAA | 69 | |
| AACTACGTCGGCCCATGAAC | ||||
| SRBSDV P7-1 | HM58527 | CCTAATGAAAACCCATCTACCTGTAAC | 70 | |
| CACGAATAAACATCAGCGACAAA | ||||
| SRBSDV P7-2 | CAAATATTTAGTAGAAGCAGAACGCAAGT | 61 | ||
| ACATCTTTTTCGTCTTTCTCATACTCTTAA | ||||
| SRBSDV P8 | HM585272 | GATTGTCTCCTTTGGATGATGTTG | 72 | |
| CCTGTCCTTCTTGAAATACACGTAAC | ||||
| SRBSDV P9-1 | HM585271 | TGAAAGCGAATCCTCAACTAAAGA | 68 | |
| TTGAATCAGTGGAGGTGGGTTT | ||||
| SRBSDV P9-2 | CGAGATGAGCGATTCTGGTTT | 70 | ||
| TTCGTGAATGATGTTGTTAACCTTTT | ||||
| SRBSDV P10 | EU784840 | TCATCATTAGCGCGACTAGTTCA | 64 | |
| CGTCACTCGGCGTCGATAA | ||||
| Reference | U6 | S83742 | CGATAAAATTGGAACGATACAGA | 72 |
| ATTTGGACCATTTCTCGATTTGT |