Detection of transgenic DNA
The authors looked for three specific fragments of transgenic DNA in their PCR analyses:

• the Cauliflower Mosaic Virus 35S promoter (CaMV 35S), which acts as an on-off switch for transgenes in most GE varieties.
• the cryIAb gene, which encodes an insecticidal protein found in many Bt varieties.
• the nos termination sequence used to mark the end of a transgene.

(See How Do You Make a Transgenic Plant? for details of transgene construction).

The CaMV 35S sequence was detected in four of the six landrace samples, although with a weak intensity compared to the sample from the government food agency and the known GE samples. The authors also reported detecting the nos sequence in two of six landrace samples, and the cryIAb sequence in one landrace sample. As expected, these sequences were not detected in the GE-free samples. The weak intensity of CaMV 35S amplification in the landraces indicated, according to the authors, that the transgenic DNA was present in a small proportion of kernels. This is consistent with similar analyses conducted by the Mexican government, which found that 3 to 10% of kernels from the same area contained transgenic DNA (Quist and Chapela, 2001). To confirm the identity of the weak CaMV 35S DNA bands amplified from the landraces, they were subjected to another round of PCR amplification to increase the quantity of DNA, then analyzed to obtain their nucleotide sequences. In all cases, the sequence obtained from the landrace DNA bands matched the sequence of the suspected CaMV 35S promoter.

Evidence for transgene movement in the genome
Quist and Chapela performed inverse PCR (iPCR) to examine the regions flanking the CaMV 35S DNA, and thus to determine where in the genome the transgenic DNA had integrated. The iPCR procedure allows amplification of DNA segments that are adjacent to DNA of known sequence (http://www.pmci.unimelb.edu.au/core_facilities/manual/mb390.asp; Triglia et al., 1988). Sequencing of iPCR products yielded several different results, which the authors claimed indicated insertion of the transgenic DNA into numerous sites in the genome. The authors stated that two of the sequences allegedly flanking CaMV 35S had similarity to part of the adh1 gene used in several Bt maize lines to enhance gene expression, and other sequences were similar to non-transgenic maize DNA. This led Chapela and Quist to conclude that the transgenic construct was capable of inserting into the genome and then moving around either during the original transformation event or during the genetic recombination that occurs each time a seed is produced. This assertion is significant because if the CaMV 35S promoter were to wander through the genome it could turn on genes that are not normally active, and disrupt, and therefore turn off, genes that are necessary for normal growth and development.