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Table 2 Primer and probe sequences used in the construct and event specific promoters

From: Genetics, structure, and prevalence of FP967 (CDC Triffid) T-DNA in flax

Primer/probe name

Sequence

Tm

Notes

SAD reference: Amplifies 68 bp of stearoyl-acyl carrier protein desaturase

P1

GCTCAACCCAGTCACCACCT

63

 

P2

TGCGAGGAGATCTGGAGGAG

61

 

prb1

TGTTGAGGGAGCGTGTTGAAGGGA

68

 

Construct specific assay: Used by commercial testing companies to detect 105 bp of FP967 TDNA

P3

AGCGCGCAAACTAGGATAAA

52

In NOS 3’terminator

P4

ACCTTCCGGCTCGATGTCTA

55

In DHFR gene of E.coli SpecR cassette

prb2

CGCGCGCGGTGTCATCTATG

67

 

Event Specific assay: Detects WT gDNA at scaffold261 or the FP967 TDNA RB-flanking scaffold86 junction

P13

CTATCGTCTGACTCTGACTG

49

FFS1 flax genomic region

P14

CAACGCCCACTCTCTTTCTTA

52

FFS2 flax genomic region

P15

CCCTTAATTCTCCGCTCATGATCAG

50

RB region of TDNA

prb3

CACTTCTTCAATTTTATTTCAATATGTCTTTC

60

Specific for FP967 TDNA insertion site on scaffold86

prb5

ATCAAACACTGATAGTTTAAACTGAAGGCGGG

67

Specific for RB region of TDNA

Event specific assay SAT2-LB: Detects internal inverted repeat of E. coli SpecR cassette adjacent to LB

P85

TACATTAAAAACGTCCGCAATGTG

59

Located in LB

P86

CCTGCTCAGGGATCACCGAA

62

In SAT of E.Coli SpecR cassette

prb28

TATCCTGCCAAAAGCCGCGCCA

68

LB/Spec junction