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.

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Bacterial blight, which is one of the most common soybean diseases, is responsible for considerable yield losses. In this study, a novel Xanthomonas vasicola strain was isolated from the leaves of soybean plants infected with bacterial blight under field conditions. Sequencing the X. vasicola genome revealed type-III effector-coding genes. Moreover, the hrpG deletion mutant was constructed. To identify the soybean genes responsive to HrpG, two chromosome segment substitution lines (CSSLs) carrying the wild soybean genome, but with opposite phenotypes following Xanthomonas inoculations, were used to analyze gene expression networks based on RNA sequencing at three time points after inoculations with wild-type Xanthomonas or the hrpG deletion mutant. To further identify the hub genes underlying soybean responses to HrpG, the genes located on the substituted chromosome segments were examined. Finally, a combined analysis with the QTLs for resistance to Xanthomonas identified 35 hub genes in the substituted chromosomal segments that may help regulate soybean responses to Xanthomonas and HrpG. Furthermore, two candidate genes in the CSSLs might play pivotal roles in response to Xanthomonas.

Soybean is a pivotal protein and oil crop that utilizes atmospheric nitrogen via symbiosis with rhizobium soil bacteria. Rhizobial type III effectors (T3Es) are essential regulators during symbiosis establishment. However, how the transcription factors involved in the interaction between phytohormone synthesis and type III effectors are connected is unclear. To detect the responses of phytohormone and transcription factor genes to rhizobial type III effector NopAA and type III secretion system, the candidate genes underlying soybean symbiosis were identified using RNA sequencing (RNA‐seq) and phytohormone content analysis of soybean roots infected with wild‐type Rhizobium and its derived T3E mutant. Via RNA‐seq analysis the WRKY and ERF transcription factor families were identified as the most differentially expressed factors in the T3E mutant compared with the wild‐type. Next, qRT‐PCR was used to confirm the candidate genes Glyma.09g282900, Glyma.08g018300, Glyma.18g238200, Glyma.03g116300, Glyma.07g246600, Glyma.16g172400 induced by S. fredii HH103, S. fredii HH103ΩNopAA, and S. fredii HH103ΩRhcN. Since the WRKY and ERF families may regulate abscisic acid (ABA) content and underlying nodule formation, we performed phytohormone content analysis at 0.5 and 24 h post‐inoculation (hpi). A significant change in ABA content was found between wild Rhizobium and type III effector mutant. Our results support that NopAA can promote the establishment of symbiosis by affecting the ABA signaling pathways by regulating WRKY and ERF which regulate the phytohormone signaling pathway. Specifically, our work provides insights into a signaling interaction of prokaryotic effector‐induced phytohormone response involved in host signaling that regulates the establishment of symbiosis and increases nitrogen utilization efficiency in soybean plants.

Soybean, which originated in China, is an important oil crop. The soybean–rhizobium symbiotic relationship provides soybean plants with abundant nitrogen. The Nod factor, which is an early signalling factor, affects the establishment of this symbiosis. In this study, the generated Sinorhizobium fredii HH103ΩNodB mutant exhibited defective Nod factor synthesis. The nodulation of 30 core collections, including ‘Dongnong594’ and ‘Charleston’, by the NodB mutant differed from the nodulation by the wild‐type strain. Soybean recombinant inbred lines derived from a ‘Dongnong594’ × ‘Charleston’ cross were used for mapping soybean genes related to the Nod factor signalling pathway. Eleven QTLs related to nodule number and eight QTLs related to nodule dry weight were revealed. On the basis of a qRT‐PCR analysis, Glyma.03G120700, Glyma.08G296000 and Glyma.15G21560 were identified as candidate genes influencing the NF interaction. These genes were differentially expressed following the inoculations with the wild‐type rhizobium and the NodB mutant. This study provides important insights into the mechanism mediating soybean responses to the NF after the soybean–rhizobium symbiosis is established.