EST-SSR based analysis revealed narrow genetic base of in-use cotton varieties of Pakistan

Genetic improvement of cotton relies on extent of variation in germplasm. The in-use cultivars of Pakistan have been selected to assess genetic dissimilarities. A total of 44 cotton varieties/cultivars were selected for molecular analysis. These varieties were screened by 100 EST-SSR primers, selected on the basis of wider genome coverage. Analysis showed that the range of bands per primer varied from one to six. The average number of bands was 2.23 per primer. The range of PIC value varied from 0.28 to 0.94. The maximum PIC value of 0.95 was recorded for NAU-2503, considered as highly informative marker. A large number of markers, 73.07%, showed PIC value higher than 0.60 and considered highly informative. The results of dendogram showed that the in-use cotton varieties of Pakistan had very narrow genetic base. High similarity index existed among BT varieties as well. We observed very low genetic diversity in the selected varieties which are commonly grown in the country. There is need to include wide range of variation for genetic improvement in cotton. There is need to Introduce exotic varieties, Inter-specific hybridization, mutation breeding etc. may be used to avoid genetic bottle neck.