Location: Sugarcane ResearchTitle: SSR marker-based analysis of genetic relatedness among sugarcane cultivars (Saccharum spp. hybrids) from breeding programs in China and other countries Author
Submitted to: Sugar Tech
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/28/2009
Publication Date: 12/6/2009
Publication URL: http://hdl.handle.net/10113/44259
Citation: Chen, P.-H., Pan, Y.-B., Chen, R.-K., Xu, L.-P., Chen, Y.-Q. 2009. SSR marker-based analysis of genetic relatedness among sugarcane cultivars (Saccharum spp. hybrids) from breeding programs in China and other countries. Sugar Tech. 11(4):347-354. Interpretive Summary: An early study showed that 67 sugarcane simple sequence repeats (SSR or microsatellites) DNA markers from the International Sugarcane Microsatellite Consortium (ICSB) could produce DNA fragments showing a high genetic variability among U.S. sugarcane varieties. The general utility of these SSR DNA markers, however, on sugarcane cultivars grown in other geographical areas needs to be further tested to fully extend their usage in world sugarcane community. This study was set up to test 20 out of the 67 SSR markers on 35 sugarcane varieties from Bangladesh, China, Mexico, South Africa, the U.S., and Venezuela. In addition, five vegetative clones of related wild species were also included. These SSR markers produced a total of 251 DNA fragments, of which 248 distributed variably among the varieties tested with diversity indices (DI) ranging from 0.71 to 0.91 and the total number of DNA fragments (N) produced by any SSR marker varied from seven to 18. Another interesting finding was that NDI value, which is the product of N and DI, could be a good indicator of the general usefulness of a SSR marker. Ten SSR markers had NDI values of greater than 12 and provided more fingerprinting information from the 40 clones, indicating that these markers can be the better choice when fingerprinting sugarcane varieties in general. An additional finding was that SSR markers originating from sugarcane genomic DNA sequences harboring a greater number of simple sequence repeats may produce less non-specific fragments. Finally, based on the SSR data, the 35 varieties could be grouped into five clusters and the order of contributing species in modern sugarcane varieties is S. officinarum, S. spontaneum, S. robustum Brandes et. Jesw.ex., S. sinense Roxb., and S. barberi Jesweit. The inclusion of CP67-412, CP72-1210, and N27 into the Chinese varietal groups is due to the fact that these varieties have been used extensively as parental material in Chinese sugarcane breeding programs.
Technical Abstract: Capillary electrophoresis-based molecular genotyping was conducted on 35 sugarcane cultivars (Saccharum spp. hybrids) and five clones of related wild species with 20 polymorphic SSR DNA markers. A total of 251 alleles were identified with 248 alleles displaying varying degrees of polymorphism and the remaining three alleles being monomorphic. The total number of alleles by any SSR marker varied from as few as 7 to as many as 18, with an average of 12.5 alleles per marker. Diversity index for these SSR markers ranged from 0.71 to 0.91, with a mean of 0.83. A composite parameter NDI, representing a product of the number of alleles (N) and DI, is an indicator on the general usefulness of a DNA marker. Ten SSR markers, namely, mSSCIR43, mSSCIR66, SMC119CG, SMC24DUQ, SMC278CS, SMC31CUQ, SMC336BS, SMC597CS, SMC703BS, and SMC851MS, have NDI values of greater than 12 in comparison to less than 10 from the rest markers, indicating that these 10 SSR markers provide much information for genotyping the 40 clones. A finding to minimize stutters and minus-Adenine peaks gave a guideline for the selection of best SSR markers for other SSR research. The 35 cultivars were clustered into five groups based on pairwise similarity coefficient values and their relationships to the wild species were demonstrated. Inclusion of CP67-412, CP72-1210, N21, N27, and S. officinarum clone Badila into the cultivar groups is due to the fact that these clones have been extensively used as parental material in sugarcane breeding programs. The results are in general agreement with the evolutionary course of the sugarcane cultivars that the order of contributing species in modern sugarcane cultivars is S. officinarum, S. spontaneum, S. robustum Brandes et. Jesw.ex., S. sinense Roxb., and S. barberi Jesweit. The accordance of molecular results with recorded evolution of sugarcane verified the fidelity and usefulness of these 20 SSR markers in progeny selection and allele transmission study in this aneu-polyploidy crop.