Genetic diversity analysis of Corynespora cassiicola isolates on the rubber tree (Hevea brasiliensis) in Vietnam using ribosomal DNA internal transcribed spacer (rDNA-ITS) sequences and sequence-related amplified polymorphism (SRAP)

Abstract

A total of 76 Corynespora cassiicola isolates collected from 16 rubber clones in several geographic regions of Vietnam, were studied for genetic diversity by ribosomal DNA internal transcribed spacer (rDNA-ITS) sequences and sequence-related amplified polymorphism (SRAP) techniques. Results of rDNA-ITS sequence analysis indicated 2 nucleotide polymorphisms at the 135th (cytosine/thymine) and 474th (guanine/adenine) base pair positions of rDNA-ITS region, which differentiated the 76 studied isolates into 3 clusters. All isolates could be uniquely distinguished by 208 polymorphism bands which generated 93.3% polymorphic ratio with SRAP markers. A dendrogram produced from UPGMA analysis based on Nei and Li’s coefficient divided the 76 C. cassiicola isolates into 2 main clusters. Cluster one included 54 fungal isolates of which 51 and 3 were observed in subgroup 1A and 1B, respectively. There were 22 C. cassiicola isolates belonging to cluster 2 with subgroups 2A and 2B consisted of 20 and 2 fungal isolates, respectively. Bootstrap values for groups one and two were 61% and 100%, respectively and the grouping was reliable, with similarity coefficient between the two main groups at 67%. rDNA-ITS sequence analysis revealed a new genetic group, signifying at least three C. cassiicola genetic groups that infect rubber trees in Vietnam. SRAP markers divided the studied isolates into two distinct groups, which correlated with geographical location rather than host source. To the best of our knowledge, this is the first demonstration using SRAP markers on the systematics of C. cassiicola isolates which cause the Corynespora leaf fall disease on various rubber (Hevea brasiliensis) clones in Vietnam.