Genetic analysis of Colletotrichum siamense populations from different hosts and counties in Hainan, China using microsatellite markers.

Colletotrichum siamense was demonstrated as the dominant species among Colletotrichum spp. that infected rubber tree, areca palm and coffee in Hainan, China. However, it is not known the extent of genetic differentiation within the species C. siamense in relation to geographical regions and host species. In this study, 112 C. siamense isolates were genotyped with 12 microsatellite markers. In total there were 99 multilocus genotypes (MLGs). Results from permutational multivariate analysis of variance (PERMANOVA) and analysis of molecular variance (AMOVA) indicated that there was no significant genetic differentiation between fungal populations with respect to host, location (county) and year. Discriminant analysis of principal components (DAPC) and STRUCTURE analysis showed that C. siamense isolates grouped into three clusters; further analysis confirmed that there were significant (P < 0.001) genetic differences among the three clusters. However, each cluster had isolates from different hosts, counties or years, supporting the lack of genetic differentiation with respect to host, county and year. Statistical analyses of allelic associations indicated some evidence for recombination within the populations defined on the basis of host or county. The present findings provide insights into the genetic structure of C. siamense on the three perennial host species in Hainan and suggest that the disease on these three crops can be effectively considered as one disease and hence need to be controlled simultaneously in mixed plantations.