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

Abstract

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.

Rhizobial–Host Interactions and Symbiotic Nitrogen Fixation in Legume Crops Toward Agriculture Sustainability

“…A QTL mapping study in soybean recombinant inbred lines (RILs) involving a symbiosis with Sinorhizobium fredii HH103 rhcJ mutant, which resulted in a reduced nodule number, identified three host genes that might be participating in the reduction process (Zhu et al, 2019). Another protein, NopD, which is one of the type III effectors of S. fredii, influences the expression of two genes associated with two QTLs (Wang et al, 2020b). These interactions resulted in nodule phenotypic differences in soybean RILs.…”

Mapping quantitative trait loci related to nodule number in soybean (Glycine max (L.) Merr.) in response to the Sinorhizobium (Ensifer) fredii HH103 NopT type III effector

“…The QTL and candidate genes underlying the symbiosis-related traits were identified in recombinant inbred lines (RILs) based on a linkage map with SNP markers. The responses of QTL to NopL, NopP, and NopD have been studied (Wang et al 2018;Zhang et al 2018;Wang et al 2020). Although previous research has identified several QTL associated with symbiosis-related traits in soybean, more work is needed to identify the genes involved in QTL responses to different T3Es.…”

The New Putative Type III Effector SkP48 in Bradyrhizobium sp. DOA9 is Involved in Legume Nodulation

“…These results suggest that among the cocktail of T3Es secreted, SkP48 is most probably recognised by Rproteins, thereby inhibiting infection and/or nodulation to a greater or lesser extent. As previously mentioned, some SUMO proteases and SKs have been reported to act as negative T3Es in plant hosts 9,[26][27][28] , raising the possibility that DOA9 SkP48 responsible for this incompatibility can be either one or both protein domains (SUMO protease and/or SK domain).…”