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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC IMPROVEMENT OF SUGARCANE BY CONVENTIONAL AND MOLECULAR APPROACHES Title: Use of Simple Sequence Repeat (SSR) markers for DNA fingerprinting and diversity analysis of sugarcane (Saccharum spp.) cultivars resistant and susceptible to red rot

Authors
item Hameed, U -
item Pan, Yong-Bao
item Muhammad, K -
item Afghan, S -
item Iqbal, J -

Submitted to: Genetics and Molecular Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 16, 2012
Publication Date: May 8, 2012
Citation: Hameed, U., Pan, Y-B., Muhammad, K., Afghan, S., Iqbal, J. 2012. Use of simple sequence repeat (SSR) markers for DNA fingerprinting and diversity analysis of sugarcane (Saccharum spp) cultivars resistant and susceptible to red rot. Genetics and Molecular Research. 11(2):1195-1204.

Interpretive Summary: Mislabeling of clones may occur from time to time during exchange of sugarcane clones in the form of stalk cuttings (setts) between different breeding stations. A SSR marker-based DNA fingerprinting technique employing fluorescence and capillary electrophoresis was developed in recent years to enable the early detection of mislabeled sugarcane clones. As part of a U.S.-Pakistan Technology Transfer Program, twenty sugarcane cultivars grown in Pakistan were fingerprinted with twenty-one highly polymorphic SSR markers in this study using this technique. The number of DNA fingerprints produced by each SSR marker varied from three to eleven. In total, 144 DNA fingerprints were observed. The distribution of these 144 DNA fingerprints among the twenty cultivars allowed the construction of Molecular identities for these cultivars, the computation of polymorphism information content and resolving power values for each SSR marker, and the genetic relatedness among the twenty cultivars. A combination of three SSR markers, namely, SMC31CUQ, mSSCIR3, and SMC597CS, was sufficient to allow the distinction between all twenty cultivars. The results will help the Pakistani cane breeders identify these cultivars if needed and enable them to make crosses between cultivars that are less related.

Technical Abstract: In recent years SSR markers have been used widely for the genetic analysis. The objective of present research was to use SSR markers to develop DNA-based genetic identification and analyze genetic relationship of sugarcane cultivars grown in Pakistan either resistant or susceptible to red rot. Twenty-one highly polymorphic SSR markers were used for DNA fingerprinting and genetic diversity analysis of twenty sugarcane cultivars. These SSR markers were highly robust, identified 144 alleles, with three to eleven alleles per marker and with an average of 6.8. The polymorphism information content (PIC) and resolving power (RP) values were also worked out. Three SSR markers used in this study were sufficient to identify all twenty cultivars. According to the homology tree, the cultivars presented at least 58% of similarity among them. We correlated PIC and RP values with marker effectiveness in sugarcane cultivar identification. This study indicated that with selection of small number of SSR derived DNA markers, information very useful for breeder can be obtained for correct identification of red rot resistant and susceptible cultivars.

Last Modified: 10/20/2014