Abstract: 【Objective】The objectives of this study are to obtain the sequences of ITS, EF-1α and β-tubulin gene regions from plant pathogen, Fusarium spp., compare the suitable gene sequences for species identification, and to analyze the population distribution and genetic variation of Fusarium spp. in Shanxi province by using the suitable gene sequences. 【Method】 A total of 625 Fusarium strains were collected from 28 counties and 11 cities in Shanxi Province from 2013 to 2015. The ITS, EF-1α and β-tubulin gene fragments of the morphology of clear strains from 625 strains were sequenced and analyzed. The sequences were assembled and edited using Sequencher software, then blasted in Genbank in NCBI and FUSARIUM-ID databases. The sequences from the clearly documented and reference species were downloaded. All the sequences were aligned and edited manually using ClustalX and GelDoc. The inter- and intra-specific variations of Fusarium spp. were analyzed with MEGA, Excel, DNAstar and TaxonGap. All the three gene sequences consisting of ITS, EF-1α and β-tubulin were selected for the taxonomy of the Fusarium species and then the best optimal fragment genes were used in the analysis of the population distributions of Fusarium spp. in Shanxi Province. 【Result】EF-1α was the best gene fragment for identifying Fusarium species among the three candidate gene fragments. Intra-specific pairwise distances was 24 times higher than that of the inter-specific pairwise distances. The intra-specific variation was smaller than those of the inter-specific variation by 73% of the tested species. The accuracy rate for identification was the highest, reached 87%. The phylogenetic relationships derived from the EF-1α sequences showed that different strains in 22 of 27 Fusarium species were monophyly, clustering in a same clade with high supporting values. Among the 27 species of Fusarium, F. oxysporum was the dominant species with 22.1% frequency and covered the largest geographical distribution in the 23 counties or regions in Shanxi province. Followed by F. solani with 13.8% in 14 counties or regions. The results of population distribution of Fusarium in different geographical regions in Shanxi province showed that F. oxysporum was the dominant species in Yuncheng, Linfen, Xinzhou, Changzhi, Lüliang, Jinzhong and Taiyuan city; F. lateritium was the dominant species in Shuozhou, F. solani in Datong, F. verticillioides in Jincheng and F. incarnatum in Yangquan. Among the different regions in Shanxi province, the most abundant Fusarium species was in Jinzhong and Xinzhou, followed by Linfen, and the least distribution was in Shuozhou. The results of the population distribution of Fusarium from different hosts showed that the 15 Fusarium species extracted from Lycopersicon esculentum, 13 species from Solanum tuberosum and 12 from Glycine max. In these hosts, F. oxysporum was the dominant species in Lycopersicon esculentum, Cucumis sativus, Citrullus lanatus, Solanum tuberosum, Solanum melongena, Cucurbita pepo and Brassica oleracea. F. verticillioides was the dominant species in Glycine max and Zea mays. F. avenaceum and F. graminearum were the dominant species in Triticum aestivum. 【Conclusion】There are abundant genetic variation between inter- and intra-specific of Fusarium. Of the three gene regions, EF-1α is the most suitable region for Fusarium species identification. Fusarium morphological taxonomy results are not fully agreed with the molecular phylogenetic results using EF-1α sequences. F. oxysporum is the dominant Fusarium species in Shanxi province. There are obvious genetic variations of Fusarium populations in different districts and hosts. The research results will provide a theoretic and scientific basis for Fusarium taxonomy, DNA barcode screening, quarantine and integrated control.

Key words: Fusarium, population distribution, intra- and inter-specific variation, genetic variation, phylogenetic analysis