Abstract

The primary gene pool for tetraploid cotton species includes Gossypium hirsutum L., as well as the other four 2n = 52 species of Gossypium (G. barbadense, G. mustellinum, G. tomentosum and G. darwinii). To help overcome barriers to effective introgression, we have developed a number of alien chromosome substitution (CS) lines from G. barbadense, G. mustellinum and G. tomentosum, most of which are nearly isogenic to the inbred ‘Texas Marker-1’, a genetic standard. At the time CS line develop- ment was initiated, molecular markers did not exist for some CS lines, and most of these lines were developed based on cytological analysis without using any marker-based testing. Here we report on tests with SSR markers from one ore more linkage maps specific to the substituted chromosome or chromosome segment from one or more linkage maps to assess the constitution and genetic identity of the CS lines. The specific objective of this paper is to report on the genetic identity of the CS lines using SSR markers and some special characteristics associated with some of the CS lines. We used chromosome-specific SSR markers following standard methods of DNA extraction, PCR and according to manufacturer’s protocol on ABI Genetic Analyzer 3130xl to confirm the identity of the introgressed alien chromosome or chromosome segments in the CS lines. For most CS lines and most mapped markers, the observed SSR profiles were concordant with expectations as per the results of cytological analysis. For a minority of markers and lines, however, the results were discordant; these markers, linkage groups, and CS lines will be further investigated to understand and define their genetic identity for use as breeding resources. Interspecific germplasm introgression can be useful for genetic improvement of Upland cotton. However, such efforts are constrained by genetic incompatibilities between the species. Our results document for the first time the development of CS lines from G. tomentosum and G. mustelinum. These CS lines will open a new paradigm in cotton breeding program by providing a tool for introgression of useful genes from wild and unadapted species in the genetic improvement of Upland cotton.