Abstract: SSR(simple sequence repeats) and AFLP(amplified fragment length polymorphism) were used to assess the genetic divergence of 54 Chinese cottons with Verticillium and Fusarium wilt resistance. 446 DNA polymorphic markers were scored from amplifications of 22 SSR primers and 20 AFLP primer pairs, with 8.26 markers for each variety in average. Euclidean distances were calculated using the software of SPSS version 11.5 and dendrograms were constructed. The Euclidean distances were 5.568-11.790, with the mean Euclidean distance 8.906. Average genetic distances for every single variety were 8.530-10.011, and those of 10 varieties, accounted for 18.52% of the total, were above the total mean Euclidean distance. The genetic distances of 85.55% of the varieties ranged from 7.000 to 10.000. All of above results showed a narrow genetic base in the tested cotton population. Four foreign cultivars were used as control and their Euclidean distances varied from 6.481 to 12.490. The Euclidean distances between Chinese- and foreign- cultivars were 6.481-12.490. Euclidean distances of 82.02% of the varieties distributed from 8.000 to11.000. These indicated that the genetic divergence between the Chinese cottons and foreign cultivars was more abundant. All the determined materials could be classified into five SAGs (SSR&AFLP-based groups) . The SAGs, to some extent, could reflect the pedigrees of the cultivars.

Key words: Cotton, Fusarium and Verticillium wilt resistance, Genetic divergence, SSR, AFLP