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ARS Home » Southeast Area » Houma, Louisiana » Sugarcane Research » Research » Publications at this Location » Publication #329945
Title: Genotype-specific microsatellite (SSR) markers for the sugarcane germplasm in the Karst region of Guizhou, China

Author
item FU, YU-HUA - Guizhou Academy Of Agricultural Sciences
item Pan, Yong-Bao
item LEI, CHAO-YUN - Guizhou Academy Of Agricultural Sciences
item Grisham, Michael
item YANG, CHENG - Guizhou Academy Of Agricultural Sciences
item MENG, QIU - Guizhou Academy Of Agricultural Sciences

Submitted to: American Journal of Plant Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/6/2016
Publication Date: 11/9/2016
Publication URL: https://handle.nal.usda.gov/10113/5695367
Citation: Fu, Y., Pan, Y., Lei, C., Grisham, M.P., Yang, C.L., Meng, Q.Y. 2016. Genotype-specific microsatellite (SSR) markers for the sugarcane germplasm in the Karst region of Guizhou, China. American Journal of Plant Sciences. 7:2209-2220. doi:10.4236/ajps.2016.715195.

Interpretive Summary: Every year, sugarcane breeders make crosses between different varieties to create new progenies for field evaluation and selection. To make the best cross combinations, breeders need to know the extent of the genetic diversity among the available germplasm collection. In this cooperative study, 21 pairs of microsatellite (SSR) primers were used to amplify through PCR DNA fingerprints from 18 sugarcane varieties using a fluorescence- and capillary electrophoresis-based detection system. The 18 varieties included 13 Chinese active cultivars and five QT-series clones that were recently developed in the Karst region in Guizhou. A total of 167 DNA fragments were amplified with an average of eight fragments per primer pair. Genetic analysis of the molecular data categorized the 18 varieties into three major groups, each group containing 3, 10, and 5 varieties. There was no geographical affinity among varieties from each group. Eight SSR primer pairs produced variety-specific DNA fingerprints, of which, five were unique to the QT-series clones. DNA fingerprints SMC334BS-165 and SMC851MS-145 were unique for the variety QT 08-558, DNA fingerprint mSSCIR43-229 was unique for variety QT 4, DNA fingerprint SM597CS-182 was specific to variety QT 08-536, and DNA fingerprint SMC7CUQ-168 was observed only in QT 06-212. These clone-specific SSR alleles will be useful in identifying and utilizing of these elite QT-series clones in sugarcane breeding programs in China.

Technical Abstract: It is the first report on SSR-based molecular evaluation of genetic variability among sugarcane genotypes from the Karst region of China that provides useful information for local sugarcane improvement. Eighteen sugarcane genotypes including 13 active cultivars and five elite QT-series clones bred locally were screened for genetic variability with 21 highly polymorphic SSR markers. All these markers were polymorphic and amplified a total of 167 alleles with an average of eight alleles per marker. The average PIC value was 0.86 with a range of 0.68 and 0.92. A UPGMA dendrogram categorized the 18 sugarcane genotypes into three major groups containing three, 10 and five genotypes, respectively. There is no geographical affinity observed among genotypes within the same group. Eight SSR markers produced cultivar-specific alleles, of which five alleles were unique to the QT-series clones, namely, SMC334BS-165 and SMC851MS-145 in QT 08-558, mSSCIR43-229 in QT 4, SM597CS-182 in QT 08-536 and SMC7CUQ-168 in QT 06-212, respectively. These clone-specific SSR alleles will be useful in identification and utilization of elite QT-series clones involved in the sugarcane crossing programs in China.