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ARS Home » Southeast Area » Houma, Louisiana » Sugarcane Research » Research » Publications at this Location » Publication #246422

Title: Assessment of genetic diversity in Saccharum using SSR markers and capillary electrophoresis

item LIANG, J - Guangxi Academy Of Agricultural Sciences
item Pan, Yong-Bao
item LI, Y - Guangxi Academy Of Agricultural Sciences
item FANG, F - Guangxi Academy Of Agricultural Sciences

Submitted to: Guihaia
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/22/2009
Publication Date: 1/20/2010
Citation: Liang, J., Pan, Y.-B., Li, Y.-R., Fang, F.-X. 2010. Assessment of genetic diversity in Saccharum using SSR markers and capillary electrophoresis. Guihaia. 30(1):106-111.

Interpretive Summary: An early study showed that 67 International Sugarcane Microsatellite Consortium-developed sugarcane microsatellite (SSR) DNA markers were highly usable on U.S. sugarcane varieties. However, the general utility of these SSR markers, on sugarcane varieties grown in other geographical areas needs to be further tested to fully extend their utilization. This study was set up to test 19 out of the 67 SSR markers on four Chinese and two U.S. sugarcane varieties and six vegetative clones of related wild species from Guangxi, China and India using capillary electrophoresis (CE). The two U.S. varieties have been used extensively in the Chinese sugarcane crossing programs. These SSR markers produced a total of 229 DNA fragments with sizes ranging from 100 to 260 base pairs. The SSR data revealed that the pairwise genetic similarity indices varied from 0.09 between commercial variety and S. spontaneum to 0.65 between two S. spontaneum clones. The 12 sugarcane clones were clustered into two main groups; one group included the six varieties and three clones of S. officinarum and the other included all three S. spontaneum clones. This study proves the concept that S. officinarum is more closely related to sugarcane cultivars than S. spontaneum and that CE-based SSR genotyping is simpler, more accurate, and easier to automate than other molecular markers or slab-gel electrophoresis systems.

Technical Abstract: This study was conducted to assess the genetic diversity amongst 12 Saccharum clones from 3 species using SSR markers and CE (capillary electrophoresis). Genomic DNA of 12 sugarcane cultivars was amplified with 19 SSR primer pairs. A total of 229 bands generated with a size range between 100 and 260 bp. Using the SSR data, the Jaccard's genetic similarity coefficients ranged from a minimum of 0.09 between CP 72-1210 (cultivar) and In 81-142 (S. spontaneum) to a maximum of 0.65 between GX87 (S. Spontaneum) to GX86 (S. spontaneum). The dendrogram using UPGMA method among 12 Saccharum clones were cluster into two groups. Three S. spontaneum clones formed a single group, while 3 S. officinarum clones clustered with 6 cultivar clones, which demonstrated that officinarum had closer genetic relation with cultivars than spontaneum. The SSR markers based on capillary electrophoresis is more accurate, simpler, automatic than other molecular markers or electrophoresis.