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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetic Improvement of Sugarcane for Temperate Climates

Location: Sugarcane Research Unit

Title: Genetic analysis of diversity within a Chinese local sugarcane germplasm based on start codon targeted polymorphism

Authors
item Que, Youxiong -
item PAN, YONG-BAO
item Lu, Yunhai -
item Yang, Cui -
item Yang, Yuting -
item Huang, Ning -
item Xu, Liping -

Submitted to: BioMed Research International
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 3, 2014
Publication Date: March 24, 2014
Repository URL: http://handle.nal.usda.gov/10113/58974
Citation: Que, Y., Pan, Y.-B., Lu, Y., Yang, C., Yang, Y., Huang, N., Xu, L. 2014. Genetic analysis of diversity within a Chinese local sugarcane germplasm based on start codon targeted polymorphism. BioMed Research International. 2014:1-10. Article ID 468375. DOI: 10.1155/2014/468375.

Interpretive Summary: Almost all sugarcane breeding programs worldwide have local sugarcane germplasm collection to maintain cultivars, breeding lines, and foreign introductions. How to choose accessions from the local germplasm collection remains the most critical step, especially when breeders have limited research funds and field space. Therefore, genetic diversity analysis is essential to help understand the genetic relatedness among accessions. In this study, the potential utility of a new DNA marker system called SCoT was investigated for the first time in sugarcane. Twenty PCR primers were used to amplify DNA products from 107 accessions from a local sugarcane germplasm collection. The resulting PCR products were separated through agarose gel electrophoresis and the electrophoregrams taken under UV lights. Only distinguishable PCR products were scored manually followed by statistical analysis. In total, 176 amplified PCR products were scored, of which 163 were variably produced across all accessions. Several genetic reference values were obtained, including polymorphism information content, percentage of polymorphic bands, genetic diversity indexes, etc. Cluster analysis divided the 107 accessions into six clusters at the genetic similarity coefficient 0.674, while principal component analysis partitioned the 107 accessions into two major groups, one domestic group and the other foreign introduction group. The results indicated that it would be beneficial for breeders to use accessions originated from different breeding institutions as crossing parents due to their higher genetic diversity. The highest genetic diversity values were found among the accessions belonging to the “ROC”-series from Taiwan, the ”CP”-series from the U.S., and “other”-series from different breeding institutes, indicating these accessions being the best parents to cross for the improvement of sugarcane genetic diversity in China.

Technical Abstract: In-depth information on sugarcane germplasm is the basis for its conservation and utilization. Data on sugarcane molecular markers are limited for the Chinese sugarcane germplasm collections. In the present study, 20 start codon targeted (SCoT) marker primers were designed to assess the genetic diversity among 107 sugarcane accessions within a local sugarcane germplasm collection. These primers amplified 176 DNA fragments, of which 163 were polymorphic (92.85%). Polymorphic information content (PIC) values ranged from 0.783 to 0.907 with a mean of 0.861. Un-weighted pair group method of arithmetic averages (UPGMA) cluster analysis of the SCoT marker data divided the 107 sugarcane accessions into six clusters at 0.674 genetic similarity coefficient level. Relatively abundant genetic diversity was observed among ROC22, ROC16 and ROC10, which occupied about 80% of the total sugarcane acreage in China, indicating their potential breeding value on Mainland China. Principal component analysis (PCA) partitioned the 107 sugarcane accessions into two major groups, the Domestic Group and the Foreign Introduction Group. Each group was further divided based on institutions, where the sugarcane accessions were originally developed. The knowledge of genetic diversity among the local sugarcane germplasm provided foundation data for managing sugarcane germplasm, including construction of a core collection and regional variety distribution and subrogation.

Last Modified: 9/10/2014
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