Genetic relationships of D-genome species based on two types of EST-SSR markers derived from G. arboreum and G. raimondii in Gossypium

The tetraploid cotton species, which includes two commercially important species, Gossypium hirsutum L. and Gossypium barbadense L., were synthesized by A and D compound genomes. There are two A-genome species and 13 D-genome species in Gossypium. The A-genome species are distributed throughout Africa and Asia, and the D-genome species occur primarily in Mexico, but also in Peru, the Galapagos Islands and Arizona in the United States. There is a clear genetic relationship between the two A-genome species; however, genetic relationships among the D-genome species remain unclear. We randomly chose 324 expressed sequence tag-simple sequence repeat (EST-SSR) primer pairs to analyze the genetic relationships of the D-genome diploid cotton (Gossypium L.), using the A-genome species as the out-group. The primer pairs were developed from 7 to 10 day post-anthesis (dpa) fiber cDNA library of diploid A-genome G. arboreum, and from −3 to 3 dpa cDNA library and the first-true-leaves library in G. raimondii, for the A-genome and D-genome species, respectively. Both independent and combined analyses of the two types of EST-SSRs resolved that A- and D-genome species could be easily grouped. Further, each type of EST-SSR was effective in distinguishing the respective in-group species. Following the combined analyses, 12 D-genome species were clustered into six groups in complete agreement with current subsection taxonomy. However, there was an intersecting relationship among D-genome species at the section level, indicating that cotton species belonging to the different sections likely had close genetic relationships and, therefore, no distinctive boundaries exist between the two sections. Based on the larger sampling of combined EST-SSR markers, molecular data supplied new proof that there was modest genetic affinity between G. raimondii belonging to subsection Austroamericana and G. gossypioides belonging to subsection Selera (Ulbrich) Fryxell at the genomic level. The relationships between G. raimondii, G. davidsonii and G. klotzschianum belonging to different sections are also discussed in the paper.