EST-SSR and SSR analyses of genetic diversity in diploid cotton genotypes from Iran

Abstract

There are 21 diploid species/genotypes of the cotton genus Gossypium L. that are cultivated in many regions of Iran. Due to continuous artificial selection and cultivation practice there is a decrease in its genetic diversity causing genetic erosion. Therefore, cotton breeders continue to make various cross combinations among available cultivars. Genetic diversity analysis was considered in 21 cotton genotypes by using SSR and EST-derived SSR markers. Amplification of the EST-SSR and SSR markers produced 19 reproducible alleles in the cotton plants studied. The mean number of effective alleles was 1.12, and the mean value of Shannon’s information index was 0.10. The mean value for genetic polymorphism was 20 % in cotton plants studied. AMOVA test showed that only 2 % of total genetic variation is accounted in 3 populations groups, of which 98 % is due to genetic variations among accessions in each population group. Neighbor Joining tree and PCoA plot showed genetic affinity between plants from different populations. STRUCTURE result confirmed AMOVA test and showed presence of genetic diversity within each presumed population groups. Reticulogram showed gene exchange among some of the cotton plants. Gene exchange/allelic similarity were observed between VTDL (G. arboreum) and Semnan (G. herbaceum) genotypes and between some interspecific hybrids.