Genetic diversity and population structure of Rhizoctonia solani AG-1 IA, the causal agent of rice sheath blight, in South China

Abstract The genetic diversity and population structure among 72 rice-infecting isolates of Rhizoctonia solani AG-1 IA, collected from 12 counties (subpopulations) of Guangdong, Guangxi and Hainan provinces (populations) in south China, were investigated using nine inter-simple sequence repeat (ISSR) markers. A total of 116 bands were amplified, with a majority of amplified fragments ranging from 500 bp to 2500 bp in size, of which 110 (94.8%) were polymorphic. Seventy-two isolates were grouped into six major clusters at 73% genetic similarity coefficient by the unweighted pair group method with arithmetic mean (UPGMA) with Dice’s distance matrices. The genetic diversity was high [percentage of polymorphic bands (P %) = 94.83%; Shannon’s diversity index (I) = 0.3175; Nei’s diversity (h) = 0.2034] at the population level, but low within populations [P % = 53.38%; Shannon’s diversity index (I) = 0.2734; Nei’s diversity (h) = 0.1811]. The mean coefficient of gene differentiation (Gst) was 0.165, indicating that 83.5% of the genetic diversity resided within the population. The genetic similarity values among 12 subpopulations ranged from 0.9672 to a minimum of 0.8641, and genetic distance values ranged from 0.1461 to 0.0333. Total gene flow (Nm) of 5.5810 indicated that there was significant gene flow among the sampled populations. Analysis of molecular variance (AMOVA) demonstrated that there was a relatively high level (81.93%) of genetic variation within subpopulations, with the gene differentiation coefficient (ΦST) being 0.181. A Mantel test suggested that there was no significant correlation between genetic differentiation and geographical distance.