Location: Sugarcane ResearchTitle: Biogeographical variation and population genetic structure of sporisorium scitamineum in mainland China: Insights from ISSR and SP-SRAP markers Author
Submitted to: The Scientific World
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/4/2014
Publication Date: 3/17/2014
Publication URL: http://handle.nal.usda.gov/10113/59504
Citation: Xu, L., Lu, Y., You, Q., Liu, X., Grisham, M.P., Pan, Y.-B., Que, Y. 2014. Biogeographical variation and population genetic structure of sporisorium scitamineum in mainland China: Insights from ISSR and SP-SRAP markers. The Scientific World. 2014:1-13. Article ID 296020. DOI: 10.1155/2014/296020. Interpretive Summary: Sugarcane smut, caused by the fungus Sporisorium scitamineum, is the most important fungal disease in sugarcane growing areas in Mainland China. One hundred isolates of this fungus were collected from 20 sugarcane growing districts of seven provinces of China and from 38 sugarcane cultivars. Two types of genetic markers were used to analyze how closely related each isolate was to the others. The 100 isolates were clearly assorted into three distinct clusters regardless of method used. Our study showed considerable genetic variation among the 100 isolates, and the different environmental characteristics found at the different locations has played an important role in the high degree of variation observed among the three groups. The genetic differentiation of sugarcane smut fungus appears to be the result of long-term adaptations of the pathogens to their ecological environments.
Technical Abstract: Sugarcane smut caused by Sporisorium scitamineum is the most important fungal disease in sugarcane growing in Mainland China. A total of 100 pathogen isolates collected from 20 sugarcane growing districts of 7 provinces of China and from 38 sugarcane cultivars, were investigated by inter simple sequence repeat (ISSR) and single primer-sequence related amplified polymorphism (SP-SRAP) markers. In ISSR analysis, seven primers produced a total of 121 differently sized bands of which 105 (86.78%) were identified as polymorphic among the 100 pathogen isolates, while the seven SP-SRAP primers amplified a total of 153 bands of which 152 (99.34%) were polymorphic among the same set of isolates. The 100 isolates were clearly assorted into three distinct clusters regardless of method used: either cluster analysis or by principal component analysis (PCA) of the ISSR, SP-SRAP or ISSR+SP-SRAP data set. Among the pathogen isolates collected for the study, those from the same geographical region tend to be grouped into the same cluster. The total gene diversity (Ht) and gene diversity between subpopulations (Hs) were estimated to be 0.34 to 0.38 and 0.22 to 0.29, respectively, by analyzing separately the ISSR and SP-SRAP data sets, and to be 0.26-0.36 by analyzing ISSR+SP-SRAP data set. The gene diversity attributable to differentiation among populations (Gst) was estimated to be 0.35 and 0.22, and the gene flow (Nm) was 0.94 and 1.78, respectively, when analyzing separately ISSR and SP-SRAP data set, and was 0.27 and 1.33, respectively, when analyzing ISSR+SP-SRAP data set. In each case, the estimated values of Ht and Nm are relatively higher for SP-SRAP than for ISSR and ISSR+SP-SRAP, and the highest values of Hs (0.36) and Gst (0.35) were found in ISSR+SP-SRAP and in ISSR. Our study showed that there is considerable genetic variation in the analyzed 100 isolates, and the environmental heterogeneity has played an important role for this observed high degree of variation. The genetic differentiation of sugarcane smut fungus depends to a large extent on the heterogeneity of the habitats of pathogens, and is the result of long-term adaptations of pathogens to their ecological environments.