Genetic Diversity within Bt cotton in Pakistan

For many developing countries cotton production is an essential part of their economic standing. In Pakistan cotton comprises more than half of the total exports (GOP, 2010). Unfortunately due to pests, specifically the bollworm, the cotton yield in these countries has decreased substantially. In response many countries, including Pakistan, have begun to rely on genetically modified insect resistant crop cultivars in order to lower the chances of bollworms. The component that makes it insect resistant is expressed in the Cry1Ac d-endotoxin from the bacter Bacillus thuringiensis (Bt). Since 2010 more than 21 million hectares have been planted with GM cottons in six major cotton-growing countries. Though Bt cotton has exponentially helped with cotton harvest, there is still hesitation with GM crops due to the fear of crop homogeneity. In a study conducted by Ullah et al. (2012) the researchers evaluated genetic divergence among 19 Bt cotton genotypes using simple sequence repeat (SSR) markers. The researchers took 119 surveyed primers and thirty-seven were found informative. Overall the results proved a lack of diversity within the Bt cotton, both from private and public sectors.¾Rachel Warburton
Ullah,A., Iram, M.Z.,Iqbal, M., Hasni., S.M., Jamil, S., 2012, Genetic diversity analysis of Bt Cotton genotypes in Pakistan using simples sequence repeat markers, Genetics and Molecular Research, Volume 2,597—605
GOP, 2010, Economic Survey of Pakistan: Finance Division. Government of Pakistan, Pakistan
James C., 2010 Global Status of Commercialized Biotech/GM Crops ISAAA, Ithica, 42
Ford, E.B 1940 “Polymorphism and Taxonomy” The New Systematic, Oxford, Volume 1, 493-513

            Bt cotton makes up for the majority of the cotton grown there. One reason for this is that exotic Bt cotton varieties have entered cultivation through informal channels. Breeders from public and private sectors then developed Bt varieties with familiar genetic backgrounds by backcrossing cottonseeds with the exotic Bt cotton, which contains the Cry1Ac gene. Approximately 60,000 farmers in Pakistan have planted Bt cotton as of 2010. (James 2010). Most of the first and second generation Bt and GM cottons in general were developed by incorporating transgenes into regeneration-responsive genotypes and then transferred to the desirable genetic makeup through conventional means. The use of selective varieties such as recurrent parts has brought up the suspicion of genetic homogeneity along with the promotion of large-scale monoculture. Eventually these factors may contribute to increased vulnerability to environmental stresses, both biotic and abiotic.
            Research on genetic variability has improved greatly with the introduction of DNA markers. Within the different types of DNA markers micro satellite markers or SSRs have become the best fit for conducting research on genetic analysis. SSR markers are essentially repeating sequences of 2-6 base pairs of DNA. They usually present high levels inter-polymorphism that help in detecting genetic diversity. Currently, approximately 17,448 cotton SSR primer pair sequences are available in the public domain, which allows for intense genetic and genomic studies in cotton, including hybrid cotton identification. In the study conducted by Ullah et al. (2012), the researchers aim to use SSR markers to explore the genetic diversity among the 19 Bt cotton genotypes—of which eight are normal commercial cultivars, two are hybrids and nine are advanced breeding lines. The tested insect-resistant transgenic cotton material contained the Cry1Ac gene, except for the two hybrid primer pairs. For the sampling, 104 cotton SSR primer pairs that represented at least two markers from each chromosome were selected. Within the 104 SSR primer pairs, 52 were tested because of a reported intra-hirsutum polymorphism. Polymorphism occurs when two or more different phenotypes exist within the same population of a species; it functions to retain variety of form in a population living in a varied environment. The researchers considered each genetic band  single locus or allele. An allele is one member of a pair or series of genes that occupies a specific position on a chromosome.  Over the 104 surveyed primers, 37 were found  to be informative. Among 52 supposed polymorphic primers selected, 30 were found informative with a polymorphism rate of 56%.
            Data from the SSR analysis were used to create a similarity matrix. The matrix showed a mean genetic similarity of 0.947 among all of the genotypes. This reveals a very high level of genetic relatedness.
            Among the public-sector organization genotypes, those from one organization, the Cotton Research Station in Multan, were relatively diverse with 0.929, specifically in comparison with the National Institute from Biotechnology and Genetic Engineering, where the mean similarity was lower with 0.919. The results also revealed that hybrids were more genetically distinct than commercial cultivars and advanced breeding lines.
            Overall, genetic diversity is important for dealing with environmental changes and Bt cotton has proven to decrease genetic diversity. The SSR markers show that the reported percentage of polymorphic SSR primers is low in cotton. Low genetic diversity estimates have also been reported in cotton using different DNA marking systems in locations such as Australia. The study conducted by Ullah et al. (2012) was the first study to analyze genetic diversity in Pakistani-bred Bt cotton, previous research which compared Pakistani bred non-Bt cotton have also revealed low estimates for genetic distances. Other results found were that genotypes developed in public-sector organizations were fairly similar to those produced in private sector. Most of the  Pakistani cotton material bred before the early 1990s was produced from local varieties with American cotton germplasms and were relatively diverse. After the first Bt variety was informally introduced in 1998 to Pakistan the amount of genetic diversity has decreased substantially, which may eventually make it more susceptible to potential epidemics or environmental change. 

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