[F14. R. solanacearum biovar-specific PCR protocol (Pastrik et al. , 2001) U.K.
4.1. Oligonucleotide primers U.K.
| Forward primer Rs-1-F | 5′- ACT AAC GAA GCA GAG ATG CAT TA -3′ |
| Reverse primer Rs-1-R | 5′- CCC AGT CAC GGC AGA GAC T -3′ |
| Reverse primer Rs-3-R | 5′- TTC ACG GCA AGA TCG CTC -3′ |
Expected amplicon size from R. solanacearum template DNA:
with Rs-1-F/Rs-1-R = 718 bp
with Rs-1-F/Rs-3-R = 716 bp.
4.2. PCR reaction mix U.K.
Biovar 1/2-specific PCR
| a Methods have been validated using Taq polymerase from Perkin Elmer (AmpliTaq) and Gibco BRL. | ||
| Reagent | Quantity per reaction | Final concentration |
|---|---|---|
| Sterile UPW | 12,925 µl | |
| 10X PCR Buffer a | 2,5 µl | 1X (1,5 mM MgCl 2 ) |
| BSA (fraction V) (10 %) | 0,25 µl | 0,1 % |
| d-NTP mix (20mM) | 0,125 µl | 0,1 mM |
| Primer Rs-1-F (10 µM) | 2 µl | 0,8 µM |
| Primer Rs-1-R (10 µM) | 2 µl | 0,8 µM |
| Taq polymerase (5U/µl) a | 0,2 µl | 1 U |
| Sample volume | 5,0 µl | |
| Total volume | 25,0 µl | |
Biovar 3/4/5-specific PCR
| a Methods have been validated using Taq polymerase from Perkin Elmer (AmpliTaq) and Gibco BRL. | ||
| Reagent | Quantity per reaction | Final concentration |
|---|---|---|
| Sterile UPW | 14,925 µl | |
| 10X PCR Buffer a | 2,5 µl | 1X (1,5 mM MgCl 2 ) |
| BSA (fraction V) (10 %) | 0,25 µl | 0,1 % |
| dNTP mix (20 mM) | 0,125 µl | 0,1 mM |
| Primer Rs-1-F (10 µM) | 1 µl | 0,4 µM |
| Primer Rs-3-R (10 µM) | 1 µl | 0,4 µM |
| Taq polymerase (5 U/µl) a | 0,2 µl | 1 U |
| Sample volume | 5,0 µl | |
| Total volume | 25,0 µl | |
4.3. PCR reaction conditions U.K.
Run the following programme for both biovar 1/2- and biovar 3/4/5-specific reactions:
| 1 cycle of: | (i) | 5 minutes at 95 °C (denaturation of template DNA) |
| 35 cycles of: | (ii) | 30 seconds at 95 °C (denaturation of template DNA) |
| (iii) | 30 seconds at 58 °C (annealing of primers) | |
| (iv) | 45 seconds at 72 °C (extension of copy) | |
| 1 cycle of: | (v) | 5 minutes at 72 °C (final extension) |
| (vi) | hold at 4 °C. |
NB: This programme was optimised for use with an MJ Research PTC 200 thermal cycler. Modification of the duration steps of cycles (ii), (iii) and (iv) may be required for use with other models. U.K.
4.4. Restriction enzyme analysis of amplicon. U.K.
PCR products amplified from R. solanacearum DNA using primers Rs-1-F and Rs-1-R produce a distinctive restriction fragment length polymorphism with enzyme Bsm I or an Isoschizomere (e.g. Mva 1269 I) after incubation at 65 °C for 30 minutes. PCR products amplified from R. solanacearum DNA using primers Rs-1-F and Rs-3-R have no restriction sites.]