Soybean (Glycine max (L.) Merr.) is an important nutritional crop with high seed protein content. Production of high protein concentrations relies on sufficient nutrient supplies, especially of nitrogen (N) and phosphorus (P). Although the genetic basis for seed quality traits has been well studied, little information exists on any genetic connections between seed quality and nutrient supplies in soybean. Here, a recombinant inbred line (RIL) population of 179 progeny was generated using HC6 and JD17 as parents contrasting in seed quality and N and P translocation efficiencies. Seed protein and N and P translocation efficiencies were higher in HC6 than in JD17. Meanwhile, positive correlations were observed between seed protein content and translocation efficiency of N and P in RILs, implying that high N and P translocation efficiencies might facilitate seed protein accumulation. A genetic map was constructed using 5250 SNP markers covering a genetic distance of 3154.83 cM. A total of 6 loci for quality and 13 loci for N and P translocation efficiency were detected. Among them, two fragments on chromosome 6 and chromosome 20 contained multiple significant markers for both quality and N and P translocation efficiencies, with the respective observed LOD values ranging from 2.98 to 5.61, and 3.01 to 11.91, while the respective PVE values ranged from 8.2% to 13.9%, and 8.3% to 28.0%. Interestingly, one significant locus on chromosome 20 appears to be the product of a transposable element (TE) InDel in Glyma.20G085100, with progeny lacking the TE also exhibiting higher N and P translocation efficiencies, along with higher seed protein contents. Taken together, these results provide genetic evidence that increasing N and P translocation efficiencies may lead to increasing protein contents in soybean seeds. Furthermore, a TE InDel may be used as a genetic marker for breeding elite soybean cultivars with high protein content and N and P translocation efficiencies.

Symbiotic nitrogen fixation (SNF) provides sufficient nitrogen (N) to meet most legume nutrition demands. In return, host plants feed symbionts carbohydrates produced in shoots. However, the molecular dialogue between shoots and symbionts remains largely mysterious. Here, we report the map-based cloning and characterization of a natural variation in GmNN1, the ortholog of Arabidopsis thaliana FLOWERING LOCUS T (FT2a) that simultaneously triggers nodulation in soybean and modulates leaf N nutrition. A 43-bp insertion in the promoter region of GmNN1/FT2a significantly decreased its transcription level and yielded N deficiency phenotypes. Manipulating GmNN1/GmFT2a significantly enhanced soybean nodulation, plant growth, and N nutrition. The near-isogenic lines (NILs) carrying low mRNA abundance alleles of GmNN1/FT2a, along with stable transgenic soybeans with CRISPR/Cas9 knockouts of GmNN1/FT2a, had yellower leaves, lower N concentrations, and fewer nodules than wild-type control plants. Grafting together with split-root experiments demonstrated that only shoot GmNN1/FT2a was responsible for regulating nodulation and thereby N nutrition through shoot-to-root translocation, and this process depends on rhizobial infection. After translocating into roots, shoot-derived GmNN1/FT2a was found to interact with GmNFYA-C (nuclear factor-Y subunit A-C) to activate symbiotic signaling through the previously reported GmNFYA-C-ENOD40 module. In short, the description of the critical soybean nodulation regulatory pathway outlined herein sheds novel insights into the shoot-to-root signaling required for communications between host plants and root nodulating symbionts.

MYB-CC transcription factors (TFs) are essential for plant growth and development. Members of the MYB-CC subfamily with long N terminal domains, such as phosphate starvation response 1 (PHR1) or PHR1-like TFs, have well documented functions, while those with short N terminal domains remain less understood. In this study, we identified a nodule specific MYB-CC transcription factor 1 (GmPHR1) in soybean that is different from other canonical PHR family genes in that GmPHR1 harbors a short N terminal ahead of its MYB-CC domain and was highly induced by rhizobium infection. The overexpression of GmPHR1 dramatically increased the ratio of deformed root hairs, enhanced subsequent soybean nodulation, and promoted soybean growth in pot experiments. The growth promotion effects of GmPHR1 overexpression were further demonstrated in field trails in which two GmPHR1-OE lines yielded 10.78% and 8.19% more than the wild type line. Transcriptome analysis suggested that GmPHR1 overexpression led to global reprogramming, with 749 genes upregulated and 279 genes downregulated, especially for genes involved in MYB transcription factor activities, root growth, and nutrient acquisition. Taken together, we conclude that GmPHR1 is a key gene involved in the global regulation of nodulation, root growth, and nutrient acquisition in soybeans, and is thus a promising candidate gene to target for soybean yield enhancement.

Soybean (Glycine max (L.) Merr.) is an important nutritional crop, not only as a rich source of protein and oil, but also for the production of isoflavones. There is a demand to breed soybean cultivars bearing consistently high protein, oil and isoflavone yields, yet this requires a clear heritable genetic relationship among isoflavone, protein and oil production. Here, two soybean genotypes contrasting in terms of protein, oil and isoflavone contents and their 185 F8:10 recombinant inbred lines (RILs) were employed to characterize seed protein, oil and isoflavone contents over two years of field trials. In this population, protein, but not oil, was significantly correlated with isoflavone content. A high-density genetic linkage map containing 3943 SNP markers identified through genotyping-by-sequencing (GBS) technology was constructed for further genetic analysis, whereby a total of 25 integrated isoflavone loci were identified, including qISO1, qISO 6.1, qISO 6.3 and qISO 6.4, which are newly identified QTLs. Two major QTLs identified in this study, qISO5 and qISO6.2, were fine-mapped for production of daidzein and genistein derivatives, as well as for glycitein derivatives, in the sequences between nucleotide positions 41042159 and 42098680 on chromosome 5 and between 18449510 and 19395795 on chromosome 6, which, respectively, explain 9.3–20.4% and 7.8–24.8% of the phenotypic variation in these traits. Further combination of qISO5 and qISO6.2 resulted in additive impacts on isoflavone production. Among the 13 QTLs linked with seed protein content in this study, three also colocated with QTLs for isoflavone content, indicating that seed isoflavone and protein content may be coordinately inherited. These results contribute to understanding the relationships between isoflavone and protein or oil content in soybean seeds. This knowledge could be valuable for soybean breeding programs aiming to combine consistently high isoflavone production with high protein or oil content.