Genetic Diversity Of The Potato Late Blight Pathogen Phytophthora Infestans In Northwestern China

Late blight, caused by the oomycete plant pathogen Phytophthora infestans(Mont.) de Bary, is an agriculturally important and devastating disease of potato worldwide. The pathogen infects potato at all development stages, causing diseases on leaves, stems and tubers. In serious cases, there were no production. The losses in potato production and increased fungicide costs caused by late blight are estimated in the billions of US dollars annually worldwide and one billion in China. The ecology of P. infestans has been investigated intensively because of the direct importance of this topic to disease management, with particular importance to disease epidemiology and disease forecasting. The low temperature and high humidity are two essential conditions to the late blight disease development. In northwestern China, the rainy season is mainly concentrated in late July to August. Understanding the genetic structure and dynamics of P. infestans populations is important for development of effective disease control strategies.In this study, an intensive sampling and analysis of P. infestans populations were carried out for the commercial potato fields and a potato germplasm nursery in northwestern and southern China for three consecutive years. A set of nine recently developed SSR markers were employed. A total of 1815 isolates were analyzed, including 306 isolates from southern regions, for genetic diversity, genetic differentiation, analysis of molecular variance, principle coordinate analysis and phylogenetic relationship analysis. The results are as follows:1. Low level of genetic diversity with a few SSR genotypes being dominant in P. infestans populations and no sexual reproduction was detected in commercial potato fields in northwestern China. A total of 959 single-lesion P. infestans isolates were purified in three consecutive years(2009-2011), including 418, 293, and 248 isolates for 2009, 2010, and 2011, respectively. Genotyping using nine SSR markers distinguished 959 isolates into 151 genotypes, and association analysis indicated that P. infestans populations in 2010 and 2011 were strictly asexual while in 2009 showed sign of sexual reproduction. AMOVA analysis of SSR genotype data revealed that the majority of the genetic variation was distributed within P. infestans populations. Isolates sharing identical SSR genotypes were detected in distant regions, indicating that migration could have occurred between regions and is likely the dominant driving factor for the population dynamics of P. infestans. Based on the above analyses, we conclude that migration and asexual reproduction were the predominant mechanisms influencing the P. infestans population structure in northwestern China. The results have implications for the trade of healthy seed tubers as a means of managing late blight.2. Analysis of P. infestans populations in a potato germplasm nursery in Ningxia showed low level of population genetic diversity. A total of 279 isolates were recovered from 63 potato varieties or lines in 2010 and 2011. Nine SSR markers distinguished the whole isolates into 26 SSR genotypes. The overall P. infestans population was characterized as having a low level of genetic diversity. The majority of the local potato varieties and a series of potato lines were susceptible to the contemporary predominant P. infestans population. Both A1 and A2 mating types, as well as self-fertile isolates were present, but there was no evidence of sexual reproduction. The low level of genetic differentiation in P. infestans populations is probably due to the action of relatively high levels of migration, as supported by AMOVA analysis and detection of the same SSR genotypes shared between the two years. The results further confirmed that migration and asexual reproduction were the predominant mechanisms influencing the P. infestans population structure in the germplasm nursery. It is therefore important to ensure the production of pathogen-free potato seed tubers to aid sustainable production of potato in northwestern China.3. To determine population structures of P. infestans in a potato seed production area in China, a total of 146 isolates were collected from six sites in Qinghai and were analyzed using SSR markers. The P. infestans populations showed a relatively high levels of genetic diversity in northwest high altitude areas, but there was no obvious predominant genotypes. In all populations, the observed heterozygosity was higher than the expected heterozygosity and gave a negative fixation index which indicates a significant excess in heterozygotes. The multilocus linkage disequilibrium tests for P. infestans rejected the null hypothesis of recombination and supported a clonally reproducing population. Additionaly, we detected for the first time the presence of A2 and Ia isolates that represent an exotic “new” population in Qinghai. It revealed that populations of P. infestans in the high altitude area Qinghai has undergone genetic changes and have become more and more complicated.4. To understand the P. infestans population structure in northern Shaanxi, an emerging potato production region in China, 125 single-lesion isolates were randomly collected from commercial fields in 2009 and were phenotypically and genotypically characterized. Mating type assay showed that 94 isolates were A1. Virulence determination of selected isolates on a set of differential near-isogenic potato lines containing R1 to R11, respectively, showed the presence of two pathotypes, of which the pathotype lacking Avr3, 4, and 10 was dominant. A total of seven SSR genotypes were distinguished among 125 isolates as determined with seven polymorphic SSR markers. The genotype SG-1 was dominant in the population with a frequency of 75.2% and was present throughout the region. Analysis of the phenotypic and genotypic structures of P. infestans populations indicated that migration and strict clonal reproduction were the predominant mechanisms influencing the P. infestans population structure in northern Shaanxi of China.5. Analysis of genetic relationship between P. infestans populations showed low level of gene flow and significant genetic differentiation in northwestern and southern China. A total of 1265 isolates were examined using eight SSR markers. The results showed that the overall low level of genetic diversity and significant genetic differentiation between P. infestans populations in northwestern and southern China, suggesting that migration of P. infestans populations is likely limited between northwestern and southern China. AMOVA analysis showed that the majority of genetic variation was distributed within populations. The results indicated that geographical isolation might play an important role in the population genetic differentiation. Phylogenetic analysis indicated that P. infestans populations in northwestern and southern China were isolated, being genetically distant from overseas reference isolates. The results have implications for the trade of healthy seed tubers as a means of managing late blight.