Soybean mosaic virus （SMV）, a member of the genus Potyvirus, is a major pathogen of soybean plants in China, and 16 SMV strains have been identified nationwide based on a former detailed SMV classification system. As the P3 gene is thought to be involved in viral replication, systemic infection, pathogenicity, and overcoming resistance, knowledge of the P3 gene sequences of SMV and other potyviruses would be useful in efforts to know the genetic relationships among them and control the disease. P3 gene sequences were obtained from representative isolates of the above-mentioned 16 SMV strains and were compared with other SMV strains and 16 Potyvirus species from the National Center for Biotechnology GenBank database. The P3 genes from the 16 SMV isolates are composed of 1041 nucleotides, encoding 347 amino acids, and share 90.7-100% nucleotide （NT） sequence identities and 95.1-100% amino acid （AA） sequence identities. The P3 coding regions of the 16 SMV isolates share high identities （92.4-98.9% NT and 96.0-100% AA） with the reported Korean isolates, followed by the USA isolates （88.5-97.9% NT and 91.4-98.6% AA）, and share low identities （80.5-85.2% NT and 82.1-84.7% AA） with the reported HZ 1 and P isolates from Pinellia ternata. The sequence identities of the P3 genes between SMV and the 16 potyviruses varied from 44.4 to 81.9% in the NT sequences and from 21.4 to 85.3% in the AA sequences, respectively. Among them, SMV was closely related to Watermelon mosaic virus （WMV）, with 76.0-81.9% NT and 77.5-85.3% AA identities. In addition, the SMV isolates and potyvirus species were clustered into six distinct groups. All the SMV strains isolated from soybean were clustered in Group I, and the remaining species were clustered in other groups. A multiple sequence alignment analysis of the C-terminal regions indicated that the P3 genes within a species were highly conserved, whereas those among species were relatively variable.
To investigate the genetic mechanism of AI-tolerance in soybean, a recombinant inbred line population （RIL） with 184 F2：7：11 lines derived from the cross of Kefen9 No.1×Nannong 1138-2 （AI-tolerant×AI-sensitive） were tested in pot experiment with sand culture medium in net room in Nanjing. Four traits, i.e. plant height, number of leaves, shoot dry weight and root dry weight at seedling stage, were evaluated and used to calculate the average membership index （FAi） as the indicator of AI-tolerance. The composite interval mapping （CIM） under WinQTL Cartographer v. 2.5 detected five QTLs （i.e. qFAi-1, qFAi- 2, qFAi-3, qFAi-4 and qFAi-5）, explaining 5.20%-9.07% of the total phenotypic variation individually. While with the multiple interval mapping （MIM） of the same software, five QTLs （qFAi-1, qFAi.5, qFAi.6, qFAi-7, and qFAi-8） explaining 5.7%-24.60% of the total phenotypic variation individually were mapped. Here qFAi-1 and qFAi-5 were detected by both CIM and MIM with the locations in a same flanking marker region, GMKF046-GMKF080 on B1 and satt278-sat_95 on L, respectively. While qFAi-2 under CIM and qFAi-6 under MIM both on Dlb2 were located in neighboring regions with their confidence intervals overlapped and might be the same locus. Segregation analysis under major gene plus polygene inheritance model showed that AI-tolerance was controlled by two major genes （h^2mg=33.05%） plus polygenes （h^2pg=52.73%）. Both QTL mapping and segregation analysis confirmed two QTLs responsible for AI-tolerance with relatively low heritability, and there might be a third QTL, confounded with the polygenes in segregation analysis.
Bo QiPaul KorirTuanjie ZhaoDeyue YuShouyi ChenJunyi Gai
