| Rice false smut, caused by fungal pathogen Ustilaginoidea virens,is a word-wide disease. The symptom usually occurs on a few grains of a panicle leaving the rest healthy. In recent years, rice false smut has become one of the most important diseases throughout major rice-growing countries resulting from increasing use of nitrogen fertilize and large-scale planting of hybrid rice. The occurrence of rice false smut not only reduces the yield and quality but also directly threaten the health of human and animals by toxins produced by the pathogen.Previous studies and reports on rice false smut focused on its incidence in fields, pathogen life cycle and disease control. Although previous investigations indicate the genetic variation is subtle in U. virens based on the small size of samples from limited locations using RAPD and AFLP, the genetic structure of U. virens throughout China was still unknown.On the basis of genome sequences of Uv7, 37 primers were designed to amplify the sequences with potentially enriched SNPs from 4 isolates collected from 4 geographically distant locations. Sequencing of the PCR products revealed the a XX bp DNA fragment contains multiple SNPs. By phylogenically analyzing the sequences of of this fragment among 99 strains isolated from different regions, the genetic structure of U. virens in China was preliminarily determined.The results indicated that U. virens in China mainly consists of three groups and no obvious geographical isolation was observed. In order to get more SNPs enriched fragments, the genomic DNA of another stain Uv86 which was located at a clade different from Uv7 was sequenced. By comparative analysis of the genome sequences between these two strains, 216,968 SNPs were identified and 320 fragments containing SNPs above 100 within 2 KB sequence length were found. These results indicated U.virens in China has daramatic genetic variation among strains. |
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