What are farmers really planting? Measuring the presence and effectiveness of Bt cotton in Pakistan

Genetically modified, insect-resistant Bacillus thuringiensis (Bt) cotton is cultivated extensively in Pakistan. Past studies, however, have raised concerns about the prevalence of Bt cotton varieties possessing weak or nonperforming insect-resistance traits conferred by the cry gene. We examine this issue using data drawn from a representative sample of cotton-growing households that were surveyed in six agroclimatic zones spanning 28 districts in Pakistan in 2013, as well as measurements of Cry protein levels in cotton tissue samples collected from the sampled households’ main fields. The resultant dataset combines information from 593 sampled households with corresponding plant tissue diagnostics from 70 days after sowing, as well as information from 589 sampled households with corresponding diagnostics from 120 days after sowing. Our analysis indicates that 11 percent of farmers believed they were cultivating Bt cotton when, in fact, the Cry toxin was not present in the tested tissue at 70 days after sowing (i.e., a Type I error). The analysis further indicates that 5 percent of farmers believed they were cultivating non-Bt cotton when, in fact, the Cry toxin was present in the tested tissue (i.e., a Type II error). In addition, 17 percent of all sampled farmers were uncertain whether or not they were cultivating Bt cotton. Overall, 33 percent of farmers either did not know or were mistaken in their beliefs about the presence of the cry gene in the cotton they cultivated. Results also indicate that toxic protein levels in the plant tissue samples occurred below threshold levels for lethality in a significant percentage of cases, although these measurements may also be affected by factors related to tissue sample collection, handling, storage, and testing procedures. Nonetheless, results strongly suggest wide variability both in farmers’ beliefs and in gene expression. Such variability has implications for policy and regulation in Pakistan’s transgenic cotton seed market.


S2 Appendix: Using ELISA Results to Validate Strip Test Results
To validate the findings described in Section 4.2, we compare strip test results with ELISA results. We assume that a positive strip test is validated by ELISA results when the latter detect the Bt protein at some level greater than zero. Table S2A below describes the classification criteria used to determine whether a tissue sample from Punjab or Sindh was categorized at Bt, non-Bt, or inconclusive based on the combination of data from strip test and ELISA results.
These results allow for the construction of an alternative classification of varieties as Bt or non-Bt that uses a combination of the strip test and the ELISA test results. To construct this classification, we first establish a lower bound for Bt protein expression that accounts for values set by the bioassays. These values fall between 0.598 μg/g and 1.590 μg/g for LD50, LD95, respectively. Second, we establish a conservative although subjective lower bound at 0.09 μg/g for "ineffective" protein expression, as it is unlikely that the targeted insect population can be effectively controlled at such lower levels.
Third, we determine that a farmer is planting Bt cotton if (1) all leaves collected from his main cotton plot at 70 DAS tested positive for Cry1Ac based on the strip test, and (2) the ELISA test results are greater than 0.09 ug/g. Similarly, we determine that a farmer is not planting Bt cotton if (1) all leaves collected from his main plot tested negative for Cry1Ac based on the strip tests, and (2) ELISA test results are less than 0.09 ug/g. Finally, anything that falls between these two strict classifications are reported as "inconclusive." Using the criteria specified in Table S2A below for the classification of Bt, non-Bt or inconclusive, the results for Punjab and Sindh are summarized in Table S2B below.
The results indicate that 50 percent of plots tested were planted with "effective" Bt cotton, and just 7 percent were planted with non-Bt cotton. This suggests that adoption rates based on strip test results alone may over-estimate adoption by more than 30 percentage points, while adoption rates based on farmer self-reporting may over-estimate adoption by 35 percentage points.
Next, we return to the question of farmers' beliefs about whether they were planting Bt cotton (Table  S2C below). We do this by revising lower threshold for lethal concentration at 0.589 ug/g and apply it to results from ELISA results from leaf tissue samples taken at 70 DAS. First, findings indicate that 52 percent of the cases in which farmers believed that they did plant Bt cotton were consistent with the detailed classification indicating the presence of effective Bt gene expression. Type 1 errors occurred in just 3 percent of cases where farmers reported that they had planted Bt cotton, while 46 percent of these cases were inconclusive. Second, 7 percent of the cases in which farmers believed that they did not plant Bt cotton were consistent with the detailed classification indicating the presence of effective Bt gene expression. Type 2 errors occurred in 43 percent of cases where farmers reported that they had not planted Bt cotton, while 51 percent were inconclusive. Across the entire sample, Type 1 and Type 2 errors accounted for 9 percent of all cases.