Genetic diversity and population structure of elite cotton (Gossypium hirsutum L.) germplasm revealed by SSR markers

Abstract

Cotton (Gossypium spp.) is the world’s most important natural textile fiber crop, and Gossypium hirsutum L. has been responsible for 90 % of the annual cotton crop in the world. Few studies are conducted about the population structure and genetic diversity of elite cotton (G. hirsutum) germplasm based on a worldwide collection. In this study, we analyzed population structure and genetic diversity of 157 elite G. hirsutum cultivar accessions collected from China, American, Africa, Former Soviet Union, and Australia using 146 SSR markers randomly distributed on the 26 chromosomes of cotton. The average allele number and PIC were 2.26 and 0.2857, respectively, indicating a relatively low degree of genetic diversity. By predefining the total cotton panel as three groups according to their geographic origin, we proved that the predefined American-origin group had higher average genetic diversity than China-origin group, but the China-origin group had the widest range of genetic variation, and the highest genetic distance happened between the varieties from America and from China, implying a direction for genetic improvement. Population structure analysis revealed two groups existed in the whole cotton panel, but the two groups inferred from structure were not consistent with the predefined three groups, indicating that the exchange and domestication of germplasm all over the world. Further independent STRUCTURE run on the two inferred groups indicated that they could be subdivided into three and two subgroups. Analysis of molecular variance showed that the American-origin group had higher population substructure than China-origin group, and only a little variation between groups was explained by population structure, suggesting that our population was suitable for association mapping. Finally, the evolutionary implication of cotton population structure was discussed. These results have provided valuable information for the association mapping of important agronomic traits, as well as for the breeding and exploit of new cotton germplasms.