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In some legume–rhizobium symbioses, host specificity is influenced by rhizobial type III effectors-nodulation outer proteins (Nops). However, the genes encoding host proteins that interact with Nops remain unknown. In this study, we aimed to identify candidate soybean genes associated with NopD, one of the type III effectors of  Sinorhizobium fredii  HH103. The results showed that the expression pattern of NopD was analyzed in rhizobia induced by genistein. We also found NopD can be induced by TtsI, and NopD as a toxic effector can induce tobacco leaf death. In 10 soybean germplasms, NopD played a positively effect on nodule number (NN) and nodule dry weight (NDW) in nine germplasms, but not in Kenjian28. Significant phenotype of NN and NDW were identified between Dongnong594 and Charleston, Suinong14 and ZYD00006, respectively. To map the quantitative trait locus (QTL) associated with NopD, a recombinant inbred line (RIL) population derived from the cross between Dongnong594 and Charleston, and chromosome segment substitution lines (CSSLs) derived from Suinong14 and ZYD00006 were used. Two overlapping conditional QTL associated with NopD on chromosome 19 were identified. Two candidate genes were identified in the confident region of QTL, we found that NopD could influence the expression of  Glyma.19g068600  (FBD/LRR) and expression of  Glyma.19g069200  (PP2C) after HH103 infection. Haplotype analysis showed that different types of  Glyma.19g069200  haplotypes could cause significant nodule phenotypic differences, but  Glyma.19g068600  (FBD/LRR) was not. These results suggest that NopD promotes  S. fredii  HH103 infection  via  directly or indirectly regulating  Glyma.19g068600  and  Glyma.19g069200  expression during the establishment of symbiosis between rhizobia and soybean plants.

QTL Mapping and Data Mining to Identify Genes Associated With the Sinorhizobium fredii HH103 T3SS Effector NopD in Soybean