NOTE: One of the lead scientists involved in this research is Prof. BM Khadi. Khadi is no minor figure. He is Principal Scientist at India's University of Agricultural Sciences, and at one time headed India's Central Institute for Cotton Research (CICR). 

BM Khadi is also a GM regulator. As well as sitting on India's apex GM regulatory body, the GEAC, Khadi is an advisor to the Indian Government's Dept of Biotechnology. In fact, Khadi was serving as a regulator during the period when his university and the CICR were seeking regulatory approval for his allegedly fraudulent GM cotton varieties. This would seem to mean Khadi was one of the regulators who failed to identify the actual gene construct used in these GM varieties! Khadi also headed up a regulatory subcommittee which recommended the streamlining of Bt cotton approvals.
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Another Bt-cotton variant falls to fraud charges
Zia Haq
Hindustan Times, December 30 2011
http://www.hindustantimes.com/India-news/NewDelhi/Another-Bt-cotton-variant-falls-to-fraud-charges/Article1-788888.aspx

New Delhi – In what could be a significant fraud in India's publicly funded biotech research, a second Bt cotton variant NHH 44 – claimed by government scientists as indigenous technology has been found to be sourced from US firm Monsanto's original patented product, sources have confirmed to Hindustan Times.

While Bikaneri, a Bt cotton technology developed by University of Agricultural Sciences (UAS), Dharwad, has already been traced to Monsanto's genes, NHH 44 is a hybrid variant, but both essentially are based on a "proprietary technology" created by Monsanto.

The first fraud came to light on the basis of disclosures made under the Right to Information (RTI) Act. 

Together, "Bikaneri" and "NHH 44" were the only genetically-modified varieties of the Bt cotton developed through government-funded research to provide cheaper alternatives to poor farmers, while numerous other privately-developed varieties crowd India's royalty-driven Rs 2,000-crore cotton seed market.

Much of the flak is being heaped on UAS scientist BM Khadi, one of the lead scientists involved in the research. He headed the Central Institute for Cotton Research, Nagpur, until May 2008 and it was during his tenure that NHH 44 was initiated. He is also part of India's biotech regulator, pointing to a potential conflict of interest. Khadi could not reached for comments.

However, what were deemed to be original products, involving heavy government investment, have turned out to be not entirely indigenous. Relying on Monsanto's technology could have possible because its intellectual property rights protection of 15 years had ended, freeing violators from legal tangles, sources said.

The Indian Council of Agricultural Research's "network programme on transgenics" had a budgetary provision of R100 crore in the XI Plan.

The revelations have led critics opposed to GM crops to question government funding for technologies that are suspect. "This puts a question mark on whether capabilities to produce 'indigenous' GM crops exist, not that we want these," Kavitha Kuruganti, who represents the Alliance for Sustainable & Holistic Agriculture, said.