Population Structure And Genetic Variation Of Phytophthora Capsici In China

Phytophthora capsici is an oomycete pathogen, it can infect multiple hosts, and has a worldwide distribution. The main objective of this study is to investigate the population structure and analyze the genetic variation of P. capsici in China. The results are as follows:During 2007 and 2011,279 isolates of P. capsici isolated from pepper at 24 locations in Gansu were used to characterize their phenotypic and genotypic diversity. The number of isolates with A1 and A2 mating types was 153 and 126, respectively. Those with metalaxyl sensitive, intermediate resistance, and resistance were 155,88 and 36, respectively and metalaxyl resistant isolates were recovered only from three locations. A total of 104 isolates tested on the AVRDC panel resolved five physiological races, and race 3 was dominant in Gansu province. None of 42 isolates tested on the NMRIL panel caused visible infection. SSR genotyping of 127 isolates revealed 59 multi-locus genotypes (MLGs) with 42 present as singletons and 17 having between 2 and 13 isolates. Isolates with identical genotypes were recovered from multiple sites across multiple years and in many cases had different race types and/or metalaxyl sensitivities. Isolates were clustered into three groups with each group having almost exclusively the Al or A2 mating type. Overall it appears long-lived genetically diverse clonal lineages are dispersed across Gansu, and functionally important variation exists within a clonal framework.We combined Crude DNA extraction from infected tissue samples, PCR pre-amplification and high resolution DNA melting analysis, which was able to genotype 172 SNP loci with more than 200 infected tissue samples and cultures from P. capsici,86 cultures from P. infestans and 8 infected tissue samples from Peronospora farinosa f. sp. spinaciae. Overall, the cost of recovering genomic DNA from individual strains or from infected tissue was greatly reduced by crude DNA extraction, and the pre-amplification provided sufficient template from a single tissue sample to genotype at least 10,000 SNPs. Other than the SNP loci, there is nothing in this approach specific to Phytophthora or Peronospora and it should be useful for many other organisms.18 isolates from locations worldwide were re-sequenced to develop liable SNP markers for genetic diversity research. Candidate SNPs were selected from the 20568 sites used for the genetic map of Phytophthora capsici construction. All SNP markers were known to have simple Mendelian inheritance and included only those loci which were suitable for HR-DMA, genic, predicted to be silent and at least 22% heterozygous SNP loci in the 18 re-sequenced isolates. Finally,437 SNPs were able to be developed for genetic diversity analysis of P. capsici populations all over the world.From 2006 to 2012,276 isolates of P. capsici were recovered from 136 locations in 27 provinces and genotyped using 45 nuclear and 2 mitochondrial SNPs. There were two main mitochondrial haplotypes and 95 multi-locus genotypes (MLGs) identified. Genetic diversity was geographically structured with a high level of genotypic diversity in the north and on Hainan Island in the south, suggesting outcrossing contributes to diversity in these areas. The remaining areas of China are dominated by four clonal lineages that share mitochondrial haplotypes, are almost exclusively the A1 or A2 mating type and appear to exhibit extensive diversity based on loss of heterozygosity (LOH). Analysis of SNPs directly from infected peppers confirmed LOH in field populations.Single zoospore progeny (SZP) of P. capsici and P. infestans were investigated for the phenotypic and genotypic variations. The results showed that SZP from intermediate resistant parental isolates have different levels of sensitivity to mefenoxam. Zoospore isolates of all the three A2 parental isolates can have three different mating types (A1, A2 and A1/A2), and all zoospore isolates of the three A1 parental isolates have the same Al mating type. Of the four parental isolates of P. capsici and one parental isolate of P. infestans investigated, LOH at some SNP loci occurred in some SZP of two P. capsici and one P. infestans parental isolates. Further analysis on SNP loci with LOH indicated that the LOH events on genome sequence maybe driven by different machanisms.