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Table 2 Strategy for Primer Designing

From: Multiplex PCR assay for identification of commonly used disarmed Agrobacterium tumefaciens strains

A. tumefaciens Strain

Chromosome

Antibiotic gene on chromosome

Ti Plasmid

Antibiotic gene on plasmid

Opine

Target gene (Accession Number) (Nucleotide coordinates)

Primers name and sequence

Primer Tm (°C)

Product size (bp)

References

GV3101

C58

Rifampicin

Cured

-

Nopaline

GlyA gene (Accession no. EU334236.1) (1160791-1161213 nt)

C58 GlyA-F: 5′- CCACCACCACGACGCACAAGTCT -3′ C58 GlyA-R: 5′-TGCCGAGACGGACACCCGAC -3′

63.7 64.3

423

(Holsters et al. 1980)

C58C1

C58

-

Cured

-

Nopaline

(Deblaere et al. 1985)

EHA101

C58

Rifampicin

pEHA 101(pTiBo542ΔT-DNA)

Kanamycin

Succinamopine

(Hood et al. 1986)

EHA105

C58

Rifampicin

pEHA 105(pTiBo542ΔT-DNA)

-

Succinamopine

(Hood et al. 1993)

EHA101

C58

Rifampicin

pEHA 101(pTiBo542ΔT-DNA)

Kanamycin

Succinamopine

accF gene (Accession no. NC_010929) (237186-237952 nt)

pTiBo542-F: 5′-CCCGCTGAGAATGACGCCAA-3′ pTiBo452-R: 5′-CCTGCGACACATCGTTGCTGA-3′

60.4 60.2

766

(Hood et al. 1986)

EHA105

C58

Rifampicin

pEHA 101 (pTiBo542ΔT-DNA)

-

Succinamopine

(Hood et al. 1993)

EHA101

C58

Rifampicin

pEHA 101(pTiBo542ΔT-DNA)

Kanamycin

Succinamopine

nptI gene (Accession no. D85525.1) (929-357 nt)

nptI-F: 5′-CTGCGATTCCGACTCGTCCA-3′ nptI-R: 5′-CGGGCAATCAGGTGCGACA-3′

59.4 59.5

572

(Hood et al. 1986)

LBA4404

Ach5

Rifampicin

pAL4404

Spectinomycin & streptomycin

Octopine

FtsZ gene (Accession no. EU334225.1) (48-416 nt)

Ach5FtsZ-F: 5′-GAACTTACAGGCGGGCTGGGT-3′ Ach5FtsZ-R: 5′-CGCCGTCTTCAGGGCACTTTCA-3′

62.0 62.1

369

(Hoekema et al. 1983)

  1. Description of Genetic makeup and target regions for designing PCR primers of various disarmed A. tumefaciens strains used in the study.