. 2009 Oct 24;120(3):655–664. doi: 10.1007/s00122-009-1183-2

Table 1.

Primers used, amplification products and PCR conditions

Pathogen and gene involved	Primer name	Sequence (5′–3′)^a	Assay type	Amplification products (bp)			Origin of test
Pathogen and gene involved	Primer name	Sequence (5′–3′)^a	Assay type	R-band	S-band	Other	Origin of test
M. incognita Mi1-2	PMiF3	GGTATGAGCATGCTTAATCAGAGCTCTC	SCAR co-dominant	550	350		Literature El Mehrach et al. (2005)
M. incognita Mi1-2	PMiR3	CCTACAAGAAATTATTGTGCGTGTGAATG	SCAR co-dominant	550	350		Literature El Mehrach et al. (2005)
ToMV Tm-1	SCN20F	GGTGCTCCGTCGATGCAAAGTGCA	SCAR dominant + LAT primers^b	1400	–	92 (Lat product)	Literature Ohmori et al. (1996)
ToMV Tm-1	SCN20R	GGTGCTCCGTAGACATAAAATCTA	SCAR dominant + LAT primers^b	1400	–	92 (Lat product)	Literature Ohmori et al. (1996)
ToMV Tm-2/Tm2 ^c Assay 1 SNP2493/2494	Outer primer TMV-2262F	GGGTATACTGGGAGTGTCCAATTC	Tetra primer ARMS co-dominant	214 (Tm2²) 255 (Tm2)		417	Primer design based on Lanfermeijer et al. (2005)
	Outer primer TMV-2678R	CCGTGCACGTTACTTCAGACAA
	Tm2² SNP 2494F	CTCATCAAGCTTACTCTAGCCTACTTTAGT
	Tm2 SNP2493 R	CTGCCAGTATATAACGGTCTACCG
ToMV Tm-2/Tm2 ^c Assay 2 SNP901	Outer primer TM2-748F	CGGTCTGGGGAAAACAACTCT	Tetra primer ARMS co-dominant	179 (Tm2 or Tm2²)	382 (tm2)	509	Primer design based on Lanfermeijer et al. (2005)
	Outer primer TM2-1256R	CTAGCGGTATACCTCCACATCTCC
	TM2- SNP901misR	GCAGGTTGTCCTCCAAATTTTCCATC
	TM2- SNP901misF	CAAATTGGACTGACGGAACAGAAAGTT
V. dahliae Ve1 Assay SNP2199	Outer primer Ve1_2072F	CCTTGATGGGGTTGATCTTTCGT	Tetra primer ARMS co-dominant	476	158	580	Sequence retrieval (based on Kawchuk et al. 2001) and development of assay this study
	Outer primer Ve1_2651R	GTAGGTGAGTTTCTTGGACAGTCGA
	Ve1_SNP2199Ft	CAGGCCCTTTGGATGAATCACATT
	Ve1_SNP2199Ra	GTTGGACAAAAGAGAGAAAGTGAAGCTAAGT
	Ve1_SNP2199F1t^c	CAGGCCCTTTGGATGAATCACTA T
	Ve1_SNP2199R1a^c	GTTGGACAAAAGAGAGAAAGTGAAGCTTAC T
V. dahliae Ve2 Assay SNP 2827	Outer primer Ve2_2720F	GGATCTTAGCTCACTTTATGTTTTGAAC	Tetra primer ARMS co-dominant	242	131	321	Sequence retrieval (based on Kawchuk et al. 2001) and development of assay this study
	Outer primer Ve2_3040R	GGTGCTGGTTTCAACTCTGAAGT
	Ve2_SNP2827F	CAAATGCTTGAATCACTAGACCTGTGAAC
	Ve2_SNP2827R	GGATCTCCCCGGACAGGTGGATTC
F. oxysporum race 0, I	At2-F3	CGAATCTGTATATTACATCCGTCGT	SCAR dominant + LAT primers^b	130		92 (Lat product)	Literature on map position (Ori et al. 1997; Scott et al. 2004) sequence retrieval of markers and development of assay
F. oxysporum race 0, I	At2-R3	GGTGAATACCGATCATAGTCGAG	SCAR dominant + LAT primers^b	130		92 (Lat product)
F. oxysporum race 1, I2	Z1063F	ATTTGAAAGCGTGGTATTGC	SCAR dominant + Rubisco primers^d	940		1380 (Rub product)	Primer design based on sequences Simons et al. (1998)
F. oxysporum race 1, I2	Z1063R	CTTAAACTCACCATTAAATC	SCAR dominant + Rubisco primers^d	940		1380 (Rub product)	Primer design based on sequences Simons et al. (1998)

^aIn bold SNP-specific base, underlined base deliberately changed to create mismatch with template

^bLat control primers: Lat1-F AGACCACGAGAACGATATTTGC, Lat2-R TTCTTGCCTTTTCATATCCAGACA

^cSecond set of primers with deliberate mismatch closer to 3’-SNP end of primer gives better results at some laboratories

^dRubisco control primers: Rub-F ATGTCACCACAAACAGAGAC, Rub-R CTCACAAGCAGCAGCTAG