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Population genetic structure of plant pathogens directly affect the strategies of deploying resistant genes and agrochemicals and molecular genetic markers play an important role for the recent success in population genetic analysis of many destructive pathogens.Compared to other molecular markers,simple sequence repeats (SSRs) have several advantages including high reliability, less demand for sample DNA, easy to operate and co-dominant.In this study, we used genomic library approach to develop a set of SSR markers for the population genetic study of Alternaria Solani, a pathogenic fungi causing early blight disease of potato and tomato worldwide.Population genetic analysis of 270 A.solani sampled from four locations each representing one of four potato production systems in China indicates that these SSR markers are moderately diverse, selectively neutral and possibly unlinked.Population genetic analysis also indicates that genetic variation of A.solani in China is high.2/3 of genotypes was detected only once and genotype diversity measured by standardized Shannon index reaches 0.91 in some population.Though clones were detected in multiple populations separated by thousands kilometers geographically, random association among SSR loci was found in the half of these populations.On average, nearly six copies of genetic materials were exchanged among these populations each generation and no isolation by distance was detected.We hypothesize that joint effects of cryptic sexual reproduction and human-mediated gene flow may account for the observed population genetic structure of A.solani in China.