QTLs underlying the genetic interrelationship between efficient compatibility of Bradyrhizobium strains with soybean and genistein secretion by soybean roots

Functional analysis of type II chalcone isomerase (CHI) genes in regulating soybean (Glycine max L.) nodule formation

Biological nitrogen fixation (BNF) is the most cost-effective and environmentally benign method for nitrogen fertilization. Isoflavones are important signaling factors for BNF in leguminous plants. Whether chalcone isomerase (CHI), the key enzyme gene in the flavonoid synthesis pathway, contributes to soybean (Glycine max) nodulation has not yet been fully clarified. In the present study, we identified the functions of three types of GmCHI for BNF using a hairy root system. The results showed that GmCHI1A and GmCHI1B1 positively increased nodulation while GmCHI1B2 did not, with the GmCHI1A gene having a greater effect than GmCHI1B1. Meanwhile, the daidzein and genistein contents were significantly increased in composite plants overexpressing GmCHI1A and reduced in composite plants, thus interfering with GmCHI1A. However, overexpression of GmCHI1B1 significantly increased the content of glycitein but not daidzein, genistein content implied that homologous genes exhibit functional differentiation. These results provide a reference for subsequent studies on improving nitrogen fixation in soybeans and providing functional genes for the improvement of new varieties.

Identification of Novel Candidate Genes Associated With the Symbiotic Compatibility of Soybean With Rhizobia Under Natural Conditions

A robust symbiotic relationship between soybean and rhizobia can enhance the yield and quality of soybeans by reducing nitrogen fertilizer input, thereby contributing to sustainable agriculture. However, the genetic interplay between soybean cultivars and the rhizobial species colonizing their roots under natural conditions is yet to be sufficiently assessed. In this study, we build on previous observations that have revealed a significant variation in the prevalence of rhizobial species associated with the soybean cultivars "Peking" and "Tamahomare." Using recombinant inbred lines derived from a cross between Peking and Tamahomare, we performed quantitative trait loci (QTL) analysis of the proportion of Rhizobium species present in the root nodules of these cultivars and accordingly identified a major QTL on chromosome 18, accounting for 42% of the phenotypic variation, which was subsequently localized to a 240-kb region. RNA-seq analysis indicated that a single gene harboring nucleotide binding site-leucine-rich repeat domains exhibited markedly different expression within the QTL region in the parent cultivars. As this locus is distinct from the chromosomal regions containing known nodule-related genes, such as Rj and rj, we speculate that it represents a novel gene involved in the symbiosis between rhizobia and soybeans. Further research on the function and role of this new gene could potentially contribute to enhancing soybean yield, and hence sustainable agriculture, under low-nitrogen fertilization conditions.

Shoot-to-root communication via GmUVR8-GmSTF3 photosignaling and flavonoid biosynthesis fine-tunes soybean nodulation under UV-B light

Legume nodulation requires light perception by plant shoots and precise long-distance communication between shoot and root. Recent studies have revealed that TGACG-motif binding factors (GmSTFs) integrate light signals to promote root nodulation; however, the regulatory mechanisms underlying nodule formation in changing light conditions remain elusive. Here, we applied genetic engineering, metabolite measurement, and transcriptional analysis to study soybean (Glycine max) nodules. We clarify a fine-tuning mechanism in response to ultraviolet B (UV-B) irradiation and rhizobia infection, involving GmUVR8-dependent UV-B perception and GmSTF3/4-GmMYB12-GmCHS-mediated (iso)flavonoid biosynthesis for soybean nodule formation. GmUVR8 receptor-perceived UV-B signal triggered R2R3-MYB transcription factors GmMYB12-dependent flavonoid biosynthesis separately in shoot and root. In shoot, UV-B-triggered flavonoid biosynthesis relied on GmUVR8a, b, c receptor-dependent activation of GmMYB12L-GmCHS8 (chalcone synthase) module. In root, UV-B signaling distinctly promotes the accumulation of the isoflavones, daidzein, and its derivative coumestrol, via GmMYB12B2-GmCHS9 module, resulting in hypernodulation. The mobile transcription factors, GmSTF3/4, bind to cis-regulatory elements in the GmMYB12L, GmMYB12B2, and GmCHS9 promoters, to coordinate UV-B light perception in shoot and (iso)flavonoid biosynthesis in root. Our findings establish a novel shoot-to-root communication module involved in soybean nodulation and reveal an adaptive strategy employed by soybean roots in response to UV-B light.

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

Symbiotic nitrogen fixation (SNF) process makes legume crops self-sufficient in nitrogen (N) in sharp contrast to cereal crops that require an external input by N-fertilizers. Since the latter process in cereal crops results in a huge quantity of greenhouse gas emission, the legume production systems are considered efficient and important for sustainable agriculture and climate preservation. Despite benefits of SNF, and the fact that chemical N-fertilizers cause N-pollution of the ecosystems, the focus on improving SNF efficiency in legumes did not become a breeder’s priority. The size and stability of heritable effects under different environment conditions weigh significantly on any trait useful in breeding strategies. Here we review the challenges and progress made toward decoding the heritable components of SNF, which is considerably more complex than other crop allelic traits since the process involves genetic elements of both the host and the symbiotic rhizobial species. SNF-efficient rhizobial species designed based on the genetics of the host and its symbiotic partner face the test of a unique microbiome for its success and productivity. The progress made thus far in commercial legume crops with relevance to the dynamics of host–rhizobia interaction, environmental impact on rhizobial performance challenges, and what collectively determines the SNF efficiency under field conditions are also reviewed here.

Dual-luciferase assay and siRNA silencing for nodD1 to study the competitiveness of Bradyrhizobium diazoefficiens USDA110 in soybean nodulation

The symbiosis of soybean with Bradyrhizobium diazoefficiens USDA110, which always competes with other rhizobia in the field, is of great agronomic and environmental importance. Herein, a dual-luciferase reporter assay was utilized to monitor the dynamics of two dominant bradyrhizobia infecting roots of soybean. More explicitly, luciferase-tagged B. diazoefficiens USDA110 (USDA110-FLuc) and Bradyrhizobium elkanii USDA 94 (USDA94-RLuc) were designed, co-inoculated into soybean seeds, and observed for their colonization in root nodules by bioluminescence imaging. The results showed that USDA110-FLuc initiated infection earlier than USDA94-RLuc, but its occupancy in the nodules decreased as the plant grew. A nodulation test showed that nodD1 mutant USDA110 strains, including CRISPR engineered mutants, were less competitive than wild type. I constructed siRNAs to knockdown nodD1 at different target sites and transformed them into the bacteria. Surprisingly, although siRNAs - with 3' end target sites - were able to repress up to 65% of nodD1 expression, the profiling of total RNAs with a bioanalyzer revealed that 23S/16S-rRNA ratios of siRNA-transformed and wild type USDA110 strains were similar, but lower than that of nodD1 mutant. In short, the current work - while reporting the competitiveness of B. diazoefficiens USDA110 in early occupancy of soybean nodules and the gene nodD1 as a key determinant of this infection - gives an insight on siRNA silencing in microbes, and demonstrates a highly efficient imaging approach that could entail many new avenues for many biological research fields.

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

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.

The soybean rhizosphere: Metabolites, microbes, and beyond-A review

•

Rhizosphere microbial communities are important for plant health.

•

Specialized metabolites in the rhizosphere influence the microbial communities.

•

Isoflavones and saponins are major specialized metabolites secreted by soybean.

•

Secretion is regulated developmentally and nutritionally.

•

Possible links between specialized metabolites and microbial communities are highlighted.

The rhizosphere is the region close to a plant’s roots, where various interactions occur. Recent evidence indicates that plants influence rhizosphere microbial communities by secreting various metabolites and, in turn, the microbes influence the growth and health of the plants. Despite the importance of plant-derived metabolites in the rhizosphere, relatively little is known about their spatiotemporal distribution and dynamics. In addition to being an important crop, soybean (Glycine max) is a good model plant with which to study these rhizosphere interactions, because soybean plants have symbiotic relationships with rhizobia and arbuscular mycorrhizal fungi and secrete various specialized metabolites, such as isoflavones and saponins, into the soil. This review summarizes the characteristics of the soybean rhizosphere from the viewpoint of specialized metabolites and microbes and discusses future research perspectives. In sum, secretion of these metabolites is developmentally and nutritionally regulated and potentially alters the rhizosphere microbial communities.