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Table 1 QPCR results obtained with screening targets (TaqMan probes) on AOCS and IRMM certified reference material

From: The GMOseek matrix: a decision support tool for optimizing the detection of genetically modified plants

A. Screening targets (promoters and terminators)
Crop species GM events Reference material p35S[50] p35S[51] p35S[52] pFMV[53] pNOS[53] pUbi[53] pSsuAra[53] pTA29[53] pRice Actin[53] tE9[53] tNOS[52] tNOS[39] t35S[53] tOCS[53] tg7[53] Source of impurity
Rapeseed GT73 (>99%) AOCS 0304-B - - - + - N - - N + - - - - - /
  T45 (100%) AOCS 0208-B + + + - - N - - N - - U(+) U(+) - - not identified
  MS8 (100%) AOCS 0306-F2 - - - - - N + + N - + + - - + /
  RF3 (100%) AOCS 0306-G - - - - - N + + N - + + - - + /
  Topas 19/2 (100%) Bayer REF-0019/04 N + + N N N N N N N U(+) - N N N not identified
Soybean GTS 40-3-2 (10%) ERM-BF410gk + + + - N N N N N - + + - N N /
  MON89788 (>99%) AOCS 0906-B R+ R+ - + N N N N N + R+ - - N N GTS 40-3-2
  A2704-12 (100%) AOCS 0707-B + + + - N N N N N - - - + N N /
  A5547-127 (100%) AOCS 0707-C2 + + + - N N N N N - - - + N N /
  305423 (10%) ERM-BF426d R+ R+ R+ - N N N N N - R+ R+ - N N GTS 40-3-2
  356043 (1%) ERM-BF425c R+ - R+ - N N N N N - R+ - - N N GTS 40-3-2
Maize GA21 (4.29%) ERM-BF414f R+ - - - N N N N + N + + - N N Bt176/ MON810
  MON810 (5%) ERM-BF413f + + + - N N N N - N - - - N N /
  Bt176 (1%) ERM-BF411d + + + - N N N N - N - - BS N N /
  TC 1507 (9.85%) ERM-BF418d + + + - N N N N - N - - + N N /
  T25 (100%) AOCS0306-H + + + - N N N N - N - - + N N /
  NK603 (1.96%) ERM-BF415e + + + - N N N N + N + + - N N /
  DAS59122 (0.1%) ERM-BF424b + + + - N N N N - N - - U(+) N N /
  MON88017 (100%) AOCS 0406-D + + + - N N N N + N + + - N N /
  MON89034 (98%) AOCS 0906-E + + + + N N N N R+ N + + - N N MON88017
  CBH351 (1%) Sigma-A. 69407 + + + - N N N N - N + + U(+) N N /
  3272 (9.8%) ERM-BF420c - - - - N N N N - N + + U- N N /
  98140 (10%) AOCS 0607-A U- U- + - N N N N - N - - - N N /
  MIR604 (9.85%) ERM-BF423d - - - - N N N N - N + + - N N /
  MON863 (9.85%) ERM-BF416d + + + - N N N N - N + + - N N MON810 (Table 1.B)
Cotton MON1445 (100%) AOCS 0804-B + + + + N - N N N + + + N N N /
  LL25 (100%) AOCS 0306-E + N N - N - N N N - + N N N N /
  GHB119 (10%) ERM-BF428c + N N - N - N N N - + N N N N /
  281x3006 (>97%) ERM-BF422b - - - R+ N + N N N R+ - - N N N MON1445
  MON531 (100%) AOCS 0804-C + + + R+ N - N N N R+ + + N N N MON1445
  MON15985 (100%) AOCS 0804-D + + + R+ N - N N N R+ + + N N N MON1445
B. Screening targets (genes and junctions)
Crop species GM events Reference material EPSPS1 EPSPS2[54] gox bar bar[54] pat[54] p35S- bar[55] p35S-hsp70[56] p35S- pat[51] CTP2- cp4epsps[57] cry 1Ab Source of impurity
Rapeseed GT73 (>99%) AOCS 0304-B - + + - - - - - - + N /
  T45 (100%) AOCS 0208-B - - - - - + (+) U- + 0 N not identified
  MS8 (100%) AOCS 0306-F2 - - - + + - + - - - N /
  RF3 (100%) AOCS 0306-G - - - + + - - - - - N /
  Topas 19/2 (100%) Bayer REF-0019/04 N N N N - + - - + - N not identified (Table 1.A)
Soybean GTS 40-3-2 (10%) ERM-BF410gk + - N - - - - - - - N /
  MON89788 (>99%) AOCS 0906-B R+ + N - - - - - - + N GTS 40-3-2
  A2704-12 (100%) AOCS 0707-B - - N - - + - - + - N /
  A5547-127 (100%) AOCS 0707-C2 - - N - - + - - + - N /
  305423 (10%) ERM-BF426d R+ - N - - - N N - - N GTS 40-3-2
  356043 (1%) ERM-BF425c R+ - N - - - N N - - N GTS 40-3-2
Maize GA21 (4.29%) ERM-BF414f - - N R+ - - R- + - - + Bt176/ MON810
  MON810 (5%) ERM-BF413f - - N - - - - + - - + /
  Bt176 (1%) ERM-BF411d - - N + + - + - - - + /
  TC 1507 (9.85%) ERM-BF418d - - N - - + - - + - - /
  T25 (100%) AOCS 0306-H - - N - - + - - + - - /
  NK603 (1.96%) ERM-BF415e + - N - - - - + - + - /
  DAS59122 (0.1%) ERM-BF424b - - N - - + - - + - - /
  MON88017 (100%) AOCS 0406-D + - N - - - - - - + - /
  MON89034 (98%) AOCS 0906-E - R+ N - - - - - - - + MON88017
  CBH351 (1%) Sigma-A. 69407 - - N + + - + - - - - /
  3272 (9.8%) ERM-BF420c - - N - - - - - - - - /
  98140 (10%) AOCS 0607-A - - N - - - N N - - - /
  MIR604 (9.85%) ERM-BF423d - - N - - - - - - - - /
  MON863 (9.85%) ERM-BF416d - - N - - - - R+ - - - MON810
Cotton MON1445 (100%) AOCS 0804-B - + N - - - N N - + N /
  LL25 (100%) AOCS 0306-E - - N + N N N N N N N /
  GHB119 (10%) ERM-BF428c - - N + N N N N N N N /
  281x3006 (>97%) ERM-BF422b - R+ N - - + - - - + N MON1445
  MON531 (100%) AOCS 0804-C - R+ N - - - N N - + N MON1445
  MON15985 (100%) AOCS 0804-D - R+ N - - - N N - + N MON1445
  1. GM events: Name of the GM events and its mass/mass content into the tested reference material (in brackets). Reference material: Catalogue reference of the reference material. Sigma-A. = Sigma-Aldrich. Positive and negative screening results are indicated by + and -, respectively. Late signals, with Cq > 37 are indicated by the plus sign between brackets, (+). Unexpected positive and negative results are indicated by U+ and U-, respectively; false positive results due to GM impurities in the reference material (confirmed by event-specific tests) are indicated by R+. BS = bad signal and amplification curves; N = not tested. Late signals and bad amplification curves are presumed to be due to differences of sequences affecting the efficiency of the PCR and the hybridization of the primers and probes. The positive signal for MON89034 maize with cry1Ab primers and probe, indicated by a bold +, is due to the presence of cry1A105 having a sequence similar to the targeted region.
  2. DNA was extracted with the CTAB method following the recommendations of the ISO21571 standard [58] and tested with qPCR using TaqMan probes. Targets used for this verification test included pUbi, pNOS, tE9, pFMV, pRice pActin, pSsuAra, pTA29, t35S, tOCS, tg7 [53], cry1Ab, bar, EPSPS-1, gox (Debode, unpublished), EPSPS-2 [54], CTP2-cp4epsps [57], pat [54], the junction p35S-bar [55], the junction p35S-pat [56], the junction p35S-hsp70 [51], an additional bar sequence [57], three different sequences of p35S [50, 52, 59], and two sequences of tNOS [39, 52]. Contaminations were checked with the available ring-trial validated event-specific methods [60].