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ARS Home » Southeast Area » Houma, Louisiana » Sugarcane Research » Research » Publications at this Location » Publication #351502

Research Project: Genetic Improvement of Sugarcane for Temperate Climates

Location: Sugarcane Research

Title: Genetic diversity analysis of nine chewing cane varieties (lines) and construction of their DNA fingerprints

Author
item He, Er-qi - Collaborator
item Pan, Yong-bao
item Fu, Yu-hua - Collaborator
item Lei, Shi-fu - Collaborator
item Li, Xiang-yong - Collaborator
item Lu, Jia-ju - Collaborator
item Zhang, Zheng-xue - Collaborator

Submitted to: Journal of Southern Agriculture
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/12/2016
Publication Date: 12/27/2016
Citation: He, E.-Q., Pan, Y.-B., Fu, Y.-H., Lei, S.-F., Li, X.-Y., Lu, J.-J., Zhang, Z.-X. 2016. Genetic diversity analysis of nine chewing cane varieties (lines) and construction of their DNA fingerprints. Journal of Southern Agriculture. 47(11):1815-1821. https://doi.org/10.3969/j:issn.2095-1191.2016.11.1815.
DOI: https://doi.org/10.3969/j:issn.2095-1191.2016.11.1815

Interpretive Summary: The study was conducted to construct the DNA fingerprints of nine chewing cane varieties from four provinces and analyze the genetic diversity among these varieties. DNA fingerprints were amplified through PCR with 21 pairs of fluorescence-labeled sugarcane microsatellite (SSR) primers and were separated via capillary electrophoresis. A total of 204 bands were amplified with every pair of SSR primers amplifying 4 to 31 fingerprints. Seventeen pairs of primers amplified 44 variety-specific fingerprints, while five primer pairs were able to discriminate among the nine chewing cane varieties. Three pairs of primers, namely, SMC36BUQ, SMC597CS, and SMC851MS, were chosen to construct the DNA fingerprints for the nine chewing cane varieties. Genetic similarity coefficients among these DNA fingerprints varied from 0.62 to 0.90, with an average of 0.77, and the Unweighted Pair-Group Method with Arithmetic Averaging (UPGMA) analysis clustered the nine chewing cane varieties into three groups, irrespective of their provincial origins. Based on the results, it is recommended that the genetic background of crossing parents involving in the breeding process needs to be expanded.

Technical Abstract: In order to provide theoretical basis for variety identification and parental selection during sugarcane breeding process, the present study was conducted to analyze genetic diversity of nine chewing cane varieties (lines) and construct their DNA fingerprints. Combining twenty-one SSR molecular markers with capillary electrophoresis technique, genetic diversities of nine chewing cane varieties(lines) from four provinces were analyzed, and genetic similarity coefficient between tested materials was calculated using NTSYS-pc 2.11. Then nine chewing cane varieties (lines) were clustered for analysis using UPGMA, and their DNA fingerprints were constructed. Results showed that, a total of 204 bands were amplified from nine chewing cane varieties (lines) using twenty-one pairs of SSR primers, with polymorphic rate of 75.99%. So every pair of SSR primers could amplify 4-31 bands, with an average of 9.71 bands. Seventeen pairs of primers contained 44 cultivar-specific loci of nine chewing cane varieties (lines). Only five pairs of primers had the strongest ability to discriminate nine chewing cane varieties (lines), and each pair of primers was able to discriminate each chewing cane varieties (lines). However, only three pairs of primers (SMC36BUQ, SMC597CS and SMC851MS), which were characterized by high polymorphism and discriminability and contained cultivar-specific loci , were chosen to construct DNA fingerprints of nine chewing cane varieties (lines). Furethermore, genetic similarity coefficients among nine chewing cane varieties(lines) varied from 0.62 to 0.90, with an average of 0.77. UPGMA clustering result showed that, nine chewing cane materials were clustered into three groups, this result was not related to origins of materials. There are little differences in genetic basis, close genetic relationship and poor genetic diversity among nine chewing cane varieties (lines), so genetic background of parents should be increased in breeding process of new varieties.