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United States Department of Agriculture

Agricultural Research Service


Location: Sugarcane Research

Title: Use of SSR markers for DNA fingerprinting and diversity analysis of Pakistani sugarcane (Saccharum spp. hybrids) cultivars

item Pan, Yong-bao
item Hadeed, Usman
item Khushi, Mohammad
item Afghan, Shahid
item Iqbal, Javed

Submitted to: American Society of Sugar Cane Technologists
Publication Type: Abstract Only
Publication Acceptance Date: 4/12/2013
Publication Date: 6/13/2013
Citation: Pan, Y-B., Hadeed, U., Khushi, M., Afghan, S., Iqbal, J. 2013. Use of SSR markers for DNA fingerprinting and diversity analysis of Pakistani sugarcane (Saccharum spp. hybrids) cultivars. Journal of the American Society of Sugar Cane Technologists. 33:23. Also available:

Interpretive Summary:

Technical Abstract: In recent years SSR markers have been used widely for genetic analysis. The objective of this study was to use an SSR-based marker system to develop the molecular fingerprints and analyze the genetic relationship of sugarcane cultivars grown in Pakistan. Twenty-one highly polymorphic SSR markers were used for DNA fingerprinting and genetic diversity analysis of 20 Pakistani sugarcane cultivars. Using a capillary electrophoresis-based genotyping platform with fluorescently-labeled primers, the 21 SSR markers amplified through PCR a total of 144 DNA fragments (alleles) that were polymorphic. The number of alleles per SSR marker ranged from three to 11. The polymorphism information content (PIC) and resolving power (RP) values were also investigated. This study indicated that by selecting SSR markers with high PIC values, it was possible to identify sugarcane cultivars with a smaller number of markers. We also correlated PIC and RP values with marker effectiveness for sugarcane cultivar identification. Three SSR markers, namely, SMC31CUQ, mSSCIR3, and SMC597CS, were able to identify and distinguish the 20 Pakistani sugarcane cultivars. A homology tree generated by DNAMAN indicated that the 20 cultivars shared a genetic similarity greater than 58%. The SSR genotyping technology is a very useful tool for sugarcane breeders to use in the identification and genetic relationship analysis of their cultivars.

Last Modified: 10/15/2017
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