| Soybean mosaic virus （SMV） disease is one of the main diseases in soybean production worldwide. The interaction between soybean mosaic virus and host plants in a long-term co-evolution induced the pathogenic differentiation, and produced various pathogenic types, namely strains. In China, many strains were classified based on the different soybean differentials systems, which was short of the comparability and difficult for the communication of resistant information and materials. Some soybean differentials systems produced too many strains, which was inappropriate for resistance breeding. Therefore, the objectives of this study were to inoculate the SMV isolates and strains collected by the previous reporters in the relatively consistent environment, carefully choose the soybean differentials with the stable symptoms to assign a more perfect system and adjust SMV strains in China. Effects of three methods for SMV preservation were compared to find a suitable method for SMV long term preservation. P3 sequences were determined to reveal the relationship between sequence differences of P3 gene and pathogenicity of SMV in soybean differentials. Resistant-source selection, genetic analysis and gene mapping of resistance to virulent strain in soybean were conducted. The main results were as follows:1. Differentiation of soybean mosaic virus strains in China（1） Based on the reactions of ten soybean differentials previously selected by Wang-Yang-Zhan to three hundred and ten isolates and four strains of SMV from twenty-three provinces （cities） in China,24 SMV strains were grouped. Comparing with the previous results, the reactions of 10 determined soybean differentials to 149 isolates were consistent, while that of some soybean differentials to the rests were different. Based on the symptom stablility, Nannong1138-2, Youbian30, Davis, Zaoshul8, Kwanggyo, Qihuangl and Kefengl were finally considered as a simplified differential system to adjust SMV strains. All of tested SMV accessions were classified into sixteen strains finally, designated C1～C16. The results of adjustment showed that the previous strains in the SC system could be included in the C system, except for SC17. The results from geographic distribution of strains indicated that the weak strain C1 and the virulent strain C16 covered over all six eco-regions of soybean, while strains C3, C12 and C13 only distributed in eco-regionⅡ,ⅡandⅤ, respectively.（2） Four SMV isolates were preserved in low temperature refrigerator （-40℃）, ultra low temperature freezer （-80℃） and liquid nitrogen （-196℃） for three, eight and fifteen months. Based on the incidence rate of inoculated cultivars Nannong1138-2, the results showed that the preservation effects of each isolate preserved in the three methods for three months had no significant differences, while the three methods had significant influences on the effects of each isolates preserved for eight and fifteen months. The preservation effects of isolates from different strains had significant differences. The three methods were all suitable for a long term preservation of SMV, in which the method of liquid nitrogen was the best.2. Sequence characteristics of P3 genes of soybean mosaic virus in China（3） P3 genes of 1～3 isolates from C1～C16 strains were determined. The results showed that P3 regions of all isolates encoded 347 amino acid residues. Pairwise comparisons of P3 gene of isolates were 90.5%～100% （nucleotide, nt） and 94.5%～100% （amino acid, aa） at nucleotides and amino acid levels, respectively. Phylogenetic tree and multiple sequence alignment showed that pathogenicity of strains was uncorrelated with genetic relationships of P3 gene.Comparing with the documented data of other SMV strains, the results showed that the P3 regions shared high identities （92.4%～98.9% nt and 96.0%～100% aa） with the reported Korean isolates, but a little lower identities （88.5%～97.9% nt and 91.4%～98.6% aa） with the reported American isolates. The identities betweem the isolates obtained from Pinellia ternate and that obtained from soybeans were obviously lower than that of the SMV isolates obtained from soybeans （80.5%～85.2% nt and 82.1%～84.7% aa）, resulting that whether the virus can be regarded as SMV needs further evidences.The results of pairwise comparisons and phylogenetic tree between SMV and the 16 potyviruses in P3 gene showed that SMV had a close relationship with watermelon mosaic virus （76.0%～81.9% nt and 77.5%～85.3% aa）, and a distant relationship with peanut mottle virus, beet mosaic virus and basella rugose mosaic virus with the lowest identities of 44.4%～54.3% nt and 21.4%～28.8% aa. Meanwhile, multiple sequence alignment indicated that P3 regions within a species were highly conserved, while that among species were relatively variable, especially in C terminal regions.3. Identification, inheritance and gene mapping of resistance to the virulent strain C16 in soybeans（4） The virulent strain C16 could infect all soybean differentials under the new system. Of 205 soybean accessions collected from seventeen province （or countries）, ten resistant accessions （RN-9,89-29, Dalvdou, Gandoul, Jinda53, Nannong87-23, Tongshanbopi-huangdoujia, Wan82-178, Zao16 and Aiganhuang） resistant to strain were screened out.（5） The P1, P2, F1, F2 and recombinant inbred line （RIL） of RN-9×7605 were inoculated with strain C16. The symptom reaction of F1 was resistant, the F2 populations segregated in a phenotypic ratio of 3 resistant:1 susceptible and the RIL exhibited a genotypic segregation ratio of 1 resistant:1 susceptible based on the test for goodness-of-fit. Therefore, a dominant gene was conferring to the resistance to C16, designated as Rc16.（6） 957 pairs of simple sequence repeat markers covering all over the soybean genome were screened. The linkage analysis using bulked segregant analysis method indicated that the resistance gene RC16 of RN-9 cultivar was located on the linkage group C2, and the order and genetic distance of linked genes on the the segment linkage map were Sat246-（0.9 cM）-Sat213-（8.0 cM）-RC16-（6.6 cM）-Sat286-（9.4 cM）-Satt100-（2.7 cM）-Sat238-（0.6 cM）-Satt079-（1.0 cM）-Sat263-（1.7 cM）-Staga001-（13.4 cM）-Satt433. |
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