The question about the impact that GM crops have had on crop genetic diversity is one that gets asked quite a bit. Genetic diversity within a given crop is an issue distinct from the potential impact that GM crops may have on biodiversity at an ecosystem or more global level. Another question on impacts on biodiversity has been previously answered by Martina Newell-McGloughlin.
It is important to recall that GE crops differ from conventional varieties at only the one location in the genome where the transgene has been inserted. As breeders develop new varieties containing the GM trait (using all of the same tools and assessments used in conventional breeding), the rest of the genome continues to be as diverse as would be found in the range of conventional varieties in the marketplace. So, in a very simple sense, genetic diversity is increased by the inclusion of the transgene into a breeding population. Looking more broadly, we have found some good papers out there that have specifically looked at the genetic diversity in the commercially available germplasm following the introduction of GM soybean (glyphosate-tolerant) and cotton (insect-protected) in the late 1990s.
Articles such as those by Sneller (2003) and Mikel et al. (2010) have shown that the advent of GM cultivars has had little impact on genetic diversity in soybean because of the wide use of this technology by many programs and its incorporation into many lines. In cotton, the analysis that was conducted looked at the genetic uniformity of the commercial cultivars that were planted. The work showed that in the years following the introduction of GE cotton, genetic uniformity decreased because of a range of factors.
A broader meta-analysis that was done a few years ago by Van de Wouw et al. (2010) might also be useful to address your question. The authors of this study completed an analysis to assess the claim that modern breeding has resulted in a dramatic drop in genetic diversity since the beginning of the 20th century. In looking at diversity across several crops from 1900 to 2000, they concluded that overall, in the long run, no substantial reduction in the regional diversity of crop varieties released by plant breeders has taken place over the time period assessed.
- Sneller, C.H. 2003. Impact of Transgenic Genotypes and Subdivision on Diversity within Elite North American Soybean Germplasm. Crop Sci. 43:409-414. [link]
- Mikel, MA, Dier, BW, Nelson, RL, Smith, HH. 2010. Genetic Diversity and Agronomic Improvement of North American Soybean Germplasm. Crop Sci. 50(4):1219-1229. [link]
- D.T. Bowman, et al.. Genetic uniformity of the US upland cotton crop since the introduction of transgenic cottons Crop Sci., 43 (2003), pp. 515–518 [link]
- Van de Wouw, M., van Hintum, T., Kirk, C., van Treuren, R., Visser, B. 2010. Genetic diversity trends in twentieth century crop cultivars: a meta analysis. Theor. Appl. Genet. 120(6):1241-1252. [link]