Comparing DNA profiles of cotton (Gossypium hirsutum L.) seeds collected from seed dealers and breeders of Punjab and Sindh

Cotton (Gossypium hirsutum) has great impact on the economy of Pakistan. Delay in the processing of candidate transgenic lines for approval along with the rapid adoption of insect resistant transgenic cotton in the country promoted selling of uncertified seed of unapproved varieties. There was no check on the seed standards in terms of expression and purity. Therefore, to assess the truth in labeling and extent of impurity seed samples from 27 tehsils of Punjab and Sindh provinces were collected. A total of 39 seed samples collected from breeders' source were compared with the 405 cotton seed samples collected from seed sellers. Germination percentage ranged from 20-74% for breeder samples and 14-76% for seed dealer samples. On the basis of reproducibility and high PIC values, 25 SSR primers were selected for DNA fingerprinting of all the collected genotypes. The amplified PCR products were run on PAGE to get high resolution and more precise results. Binary method of scoring was used for band counting and the data were subjected to NTSYS-PC software to calculate dissimilarity/ similarity index and to generate dendrograms. The Polymorphism Information Content (PIC) value of the primers was calculated to estimate the extent of informativeness. The PIC value ranged from 0.09 to 0.953 with an average of 0.526. Primer NAU-2317 was found to be most polymorphic. The dissimilarity of dealer samples ranged from 4.69 to 7.483 with their corresponding breeder variety and 4.69 to 6.481 when compared with all the breeder varieties. The comparison of DNA profiles generated on the basis of this analysis suggested narrow genetic base of the cotton germplasm in Pakistan. The dissimilarity or similarity index generated by the comparison revealed that the samples of varieties collected from seed dealers were at maximum distance with their corresponding breeder variety and at minimum distance to other breeder varieties used in this comparison. Malpractices like seed adulteration and selling varieties with fake names have also been revealed as only a few samples rematched with their corresponding breeder variety, when they were compared with all the breeder varieties.