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Symbiosis between soybean and rhizobia contributes to soybean yield and quality. Although secreted rhizobial type III effectors are known to regulate infection and promote nitrogen fixation, much about them remains unknown. Mutation of NopC, a type III effector from Sinorhizobium frediiHH103, reduced nodule numbers and dry weights in 310 soybean accessions, and expression of NopC in soybean hairy roots promoted symbiosis. Based on observed differences in nodule traits between Suinong 14 and Zyd 00,006 inoculated with HH103 and the NopC mutant, 11 QTL associated with rhizobia were identified in chromosome segment substitution lines (CSSLs) derived from Suinong 14 and Zyd 00006. Using chromosome fragment insertion, whole-genome sequencing of Suinong 14 and Zyd 00006, and qRT-PCR, Glyma.19G176300(GmCRP) was identified as a candidate gene associated with NopC, and GmCRPwas found to be induced by NopC to positively regulate nodulation. SNPs located in the regulatory regions of GmCRPinfluenced its expression response to NopC, with SNPs contributing to nodulation having been selected during domestication. Our findings reveal the function of a soybean gene encoding a rhizobial type III effector that contributes to symbiosis, and will facilitate the practical application of symbiotic nitrogen fixation in molecular breeding.

Phytophthora sojaeinfection severely impairs soybean production. We previously identified a dirigent protein, GmDRR1 (Glycine maxDisease Resistant Response 1), that increases soybean resistance to P. sojae. However, the molecular basis of GmDRR1 function remained largely uncharacterized. In the present study, analysis of GmDRR1-RNAi, GmDRR1-overexpressing, and CRISPR/Cas9-derived Gmdrr1mutant lines revealed that GmDRR1expression significantly restricted P. sojaegrowth.Combining co-immunoprecipitation with liquid chromatography–tandem mass spectrometry revealed a GmDRR1-interacting protein, GmDRR2, which is homologous to GmDRR1. An E-coniferyl alcohol coupling assay indicated that GmDRR1 promotes the synthesis of (+)-pinoresinol, which helps to protect plants from P. sojae. The GmNAC1 (Glyma.05G025500) transcription factor bound to the GmDRR1promoter both in vitroand in vivoto upregulate GmDRR1expression. Soybean resistance to P. sojaewas increased by overexpression of GmNAC1. Our findings suggest a novel signaling pathway involving a NAC transcription factor that mediates soybean resistance to P. sojae. Specifically, GmNAC1 directly induces GmDRR1expression to increase resistance of soybean plants to P. sojae.

Mature soybean phenotyping is an important process in soybean breeding; however, the manual process is time-consuming and labor-intensive. Therefore, a novel approach that is rapid, accurate and highly precise is required to obtain the phenotypic data of soybean stems, pods and seeds. In this research, we propose a mature soybean phenotype measurement algorithm called Soybean Phenotype Measure-instance Segmentation (SPM-IS). SPM-IS is based on a feature pyramid network, Principal Component Analysis (PCA) and instance segmentation. We also propose a new method that uses PCA to locate and measure the length and width of a target object via image instance segmentation. After 60,000 iterations, the maximum mean Average Precision (mAP) of the mask and box was able to reach 95.7%. The correlation coefficients R2of the manual measurement and SPM-IS measurement of the pod length, pod width, stem length, complete main stem length, seed length and seed width were 0.9755, 0.9872, 0.9692, 0.9803, 0.9656, and 0.9716, respectively. The correlation coefficients R2of the manual counting and SPM-IS counting of pods, stems and seeds were 0.9733, 0.9872, and 0.9851, respectively. The above results show that SPM-IS is a robust measurement and counting algorithm that can reduce labor intensity, improve efficiency and speed up the soybean breeding process.