Usefulness of SSR Derived from Tetraploid Gossypium spp. for Analyses of Diploid Gossypium spp.

Abstract

This investigation is the first attempt to utilize tetraploid species-derived primers to generate markers for mapping in diploid cotton species. About 113 individual F2 plants, developed from the cross between Gossypium nelsoni and G. australe, were used to construct a linkage map. One allotetraploid (ADj) G. hirsutum (TM-1) plant and its putative diploid ancestors, G. arboreum (A2) and G. raimondii (D5), were also included for comparative analysis. We developed a high-throughput multi-mix PCR assay for simple sequence repeat (SSR) marker separation using fluorescent-labeled capillary electrophoresis. Of a total of 205 tetraploid-derived SSR primers, 83% amplified in all four diploid species, indicating that flanking primer sequences are conserved in the diploid and tetraploid ADj genome of cotton. DNA sequence information of 18 randomly selected clones revealed that all of the clones contained SSR repeat motifs in the diploid species, suggesting that SSR markers including the flanking primer sequences have been conserved at the inter-specific level in genomic DNA across years of evolution. About 85% of the amplified primers showed polymorphism among the diploid genome species. Forty percent of SSRs in the diploid G. nelsoni and 35% in G. australe amplified the same size DNA fragment as in the tetraploid, (TM-1). This is further evidence that many of the tetraploid SSRs are conserved across diploid and tetraploid species. G. nelsoni compared with G. australe had more conserved genomic regions in common with G. hirsutum. From 73 markers scored in the F2 population, 50 exhibited codominance and 23 dominance. There were 47 markers linked across 10 linkage groups covering a total map distance of 754 cM with an average of 16 cM per marker. One linkage group (lg-3) with six loci has been assigned to chromosome 20. Comparative analysis of DNA sequences between G. hirsutum and its two putative parental diploid species indicated that changes within a few selected clones have occurred during evolution as follows: (1) by increasing or decreasing the number of the repeat motif, (2) by single nucleotide mutations occurring within or outside of the repeat motif, (3) by inter conversion of a simple to a compound SSR motif, and (4) by inversion of the repeat regions. Tetraploid-derived microsatellites should be useful in comparative genetic mapping of both tetraploid and diploid Gossypium species for evolutionary studies and introgression of agriculturally important traits from exotic diploid and tetraploid germplasm sources.