Population Genetic Diversity Of Puccinia Striiformis F.sp. Tritici In China

Long-distance dispersal of Puccinia striiformis f.sp.tritici(Pst)urediniospores causes the epidemic of wheat strip rust,which severely threatens the wheat production in China.Conducting genetic diversity study on the Pst populations is an effective approach in speculating the dispersal routes in China,which can provide the valuable information for monitoring and development control strategies of stipe rust.In the present study,we analysed the population genetic diversity,origin,and dispersal routes of Pst in China by conducting whole genome sequencing.The main results show as following:1.We collected 6381 strip rust samples from 41 cities in 11 provinces which covered the main stripe rust epidemic regions in China.After purification and multiplication for each sample,we extracted the DNA of urediniospores of 154 representative Pst strains and conducted whole genome sequencing for each strain.2.A total of 893.54 Gb high-quality reads were acquired through examining and filtering raw sequenced data.After variations detection and quality control,around 840,000 high quality SNP were used in downstream analyses.The average depth of each isolate was 55×and the average mapping rate was 88.95%.After mapping with reference genome,the average coverage 1× was found to be 91.83%.3.Pst populations in China had complex population structure and high genetic diversity.Additionally,there were frequently exchange between different Pst populations.Population structure analysis conducted by phylogenic analysis,principal component,and genetic structure analysis uncovered that Pst in China were mainly divided into two clusters,Cluster1 and Cluster 2.Cluster 1 was further separated into Cluster 1.1,Cluster 1.2,and Cluster 1.3,which represented the Pst populations in Gansu,Tibet,and Guizhou,respectively.The isolates in Cluster 2 were divided into four clusters.Cluster 2.1 mainly contained the isolates from Henan,Hubei,Shaanxi,Ningxia,Guizhou,and Sichuan.Cluster 2.2 represented the Pst population in Sichuan and Yunnan region.Cluster 2.3 and Cluster 2.4 represented the Pst population in Qinghai,Xinjiang,and Tibet.The genetic diversity indices and population heterozygosity analyses illustrated that the nucleotide diversity of sub-clusters in Cluster 1were significantly higher than sub-clusters in Cluster 2.These results uncovered that western Qinling Mountains,Himalayan region,and Guizhou Plateau of which Pst populations were represented by Cluster 1.1,Cluster 1.2,and Cluster 1.3 were recognized as three origin centres of Pst in China.The results of genetic different index,genetic introgression,and migration events estimation indicated that the Pst populations in three origins were exchanged frequently with Cluster 2.2 representing Sichuan-Yunnan region.Additionally,Cluster 2.2 were exchanged frequently with Cluster 2.1 representing other wheat growing region in China.These results showed that one of the important dissemination routes of Pst in China is Pst in origin centres firstly gathered in Sichuan-Yunnan region,then disseminated to other region in China.