Agrobacterium rhizogenes-induced soybean hairy roots versus Soybean mosaic virus (ARISHR-SMV) is an efficient pathosystem for studying soybean-virus interactions

MdPHR2 and MdARF6-4 synergistically regulate arbuscular mycorrhizal symbiosis and the transcription of MdPHT1;13, enhancing phosphorus uptake in apple rootstocks

Phosphorus in the soil is easily chelated into forms that are unavailable to plants, leading to phosphorus deficiency, which severely affects the growth, development, and fruit quality of apple trees. To address phosphorus deficiency, we used four different arbuscular mycorrhizal fungi (AMF) to investigate their effects on the growth and development of apple rootstocks and phosphorus uptake in the soil. We identified Glomus mosseae (Gm) fungi as the most effective AMF for promoting growth and found that under phosphorus-deficient conditions, inoculating with Gm fungi promoted the growth of the above-ground parts of the plants and phosphorus absorption, while it inhibited root growth. After inoculating with Gm fungi, we found phosphorus starvation response factors (PHRs) and auxin response factors (ARFs) were upregulated. Knockdown of MdPHR2 or MdARF6-4 resulted in decreased root arbuscular structures, total mycorrhizal colonization rate, and root phosphorus content, indicating that MdPHR2 and MdARF6-4 positively regulate the symbiosis of Gm fungi and phosphorus absorption. In contrast, overexpressing MdARF6-4 led to reduced root development but increased root phosphorus content under Gm fungi inoculation, suggesting that MdARF6-4 is involved in Gm-mediated phosphorus absorption and root development. Moreover, both MdPHR2 and MdARF6-4 directly bound to the promoter area of the downstream phosphorus transporter MdPHT1;13, and these two transcription factors interacted with each other in vivo and in vitro. In summary, our study demonstrates that the interaction between MdPHR2 and MdARF6-4 synergistically regulates the Gm symbiosis and the transcription of MdPHT1;13, thereby promoting phosphorus absorption in apple rootstocks.

Characterization and Genomic Analysis of Affinirhizobium gouqiense sp. nov. Isolated from Seawater of Gouqi Island Located in the East China Sea and Reclassification of Rhizobium lemnae to the Genus Affinirhizobium as Affinirhizobium lemnae comb. nov

A novel bacterium designated as SSA5.23T was isolated from seawater. Cells of SSA5.23T are Gram-stain-negative, short, rod-shaped, and exhibit motility via numerous peritrichous flagella. The strain could grow at temperatures ranging from 15 to 35 °C (optimum at 25 °C), in a salinity range of 0-5.0% (w/v) NaCl, and within a pH range of 6.0-9.0 (optimum at pH 7.0). The predominant cellular fatty acid of SSA5.23T was C18:1 ω7c/C18:1 ω6c, and the major respiratory quinones were Q-9 and Q-10. Diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol were identified as the primary polar lipids. The complete genome (5.47 Mb) of SSA5.23T comprises of a circular chromosome of 3.64 Mb and three plasmids, specifically sized at 59.73 kb, 227.82 kb, and 1.54 Mb, respectively. Certain genes located on the plasmids play roles in denitrification, oxidative stress resistance, and osmotic tolerance, which likely contribute to the adaptability of this strain in marine conditions. Core-proteome average amino acid identity analysis effectively identified the strain's affiliation with the genus Affinirhizobium, showing the highest value (89.9%) with Affinirhizobium pseudoryzae DSM 19479T. This classification was further supported by the phylogenetic analysis of concatenated alignment of 170 single-copy orthologous proteins. When compared to related reference strains, SSA5.23T displayed an average nucleotide identity ranging from 74.9 to 80.3% and digital DNA-DNA hybridization values ranging from 19.9 to 23.9%. Our findings confirmed that strain SSA5.23T represents a novel species of the genus Affinirhizobium, for which the name Affinirhizobium gouqiense sp. nov. (type strain SSA5.23T = LMG 32560T = MCCC 1K07165T) was suggested.

WGCNA Reveals Hub Genes and Key Gene Regulatory Pathways of the Response of Soybean to Infection by Soybean mosaic virus

Soybean mosaic virus (SMV) is one of the main pathogens that can negatively affect soybean production and quality. To study the gene regulatory network of soybeans in response to SMV SC15, the resistant line X149 and susceptible line X97 were subjected to transcriptome analysis at 0, 2, 8, 12, 24, and 48 h post-inoculation (hpi). Differential expression analysis revealed that 10,190 differentially expressed genes (DEGs) responded to SC15 infection. Weighted gene co-expression network analysis (WGCNA) was performed to identify highly related resistance gene modules; in total, eight modules, including 2256 DEGs, were identified. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of 2256 DEGs revealed that the genes significantly clustered into resistance-related pathways, such as the plant-pathogen interaction pathway, mitogen-activated protein kinases (MAPK) signaling pathway, and plant hormone signal transduction pathway. Among these pathways, we found that the flg22, Ca2+, hydrogen peroxide (H2O2), and abscisic acid (ABA) regulatory pathways were fully covered by 36 DEGs. Among the 36 DEGs, the gene Glyma.01G225100 (protein phosphatase 2C, PP2C) in the ABA regulatory pathway, the gene Glyma.16G031900 (WRKY transcription factor 22, WRKY22) in Ca2+ and H2O2 regulatory pathways, and the gene Glyma.04G175300 (calcium-dependent protein kinase, CDPK) in Ca2+ regulatory pathways were highly connected hub genes. These results indicate that the resistance of X149 to SC15 may depend on the positive regulation of flg22, Ca2+, H2O2, and ABA regulatory pathways. Our study further showed that superoxide dismutase (SOD) activity, H2O2 content, and catalase (CAT) and peroxidase (POD) activities were significantly up-regulated in the resistant line X149 compared with those in 0 hpi. This finding indicates that the H2O2 regulatory pathway might be dependent on flg22- and Ca2+-pathway-induced ROS generation. In addition, two hub genes, Glyma.07G190100 (encoding F-box protein) and Glyma.12G185400 (encoding calmodulin-like proteins, CMLs), were also identified and they could positively regulate X149 resistance. This study provides pathways for further investigation of SMV resistance mechanisms in soybean.

Phylogenomic reappraisal of the family Rhizobiaceae at the genus and species levels, including the description of Ectorhizobium quercum gen. nov., sp. nov

The family Rhizobiaceae contains 19 validly described genera including the rhizobia groups, many of which are important nitrogen-fixing bacteria. Early classification of Rhizobiaceae relied heavily on the poorly resolved 16S rRNA genes and resulted in several taxonomic conflicts. Although several recent studies illustrated the taxonomic status of many members in the family Rhizobiaceae, several para- and polyphyletic genera still needed to be elucidated. The rapidly increasing number of genomes in Rhizobiaceae has allowed for a revision of the taxonomic identities of members in Rhizobiaceae. In this study, we performed analyses of genome-based phylogeny and phylogenomic metrics to review the relationships of 155-type strains within the family Rhizobiaceae. The UBCG and concatenated protein phylogenetic trees, constructed based on 92 core genes and concatenated alignment of 170 single-copy orthologous proteins, demonstrated that the taxonomic inconsistencies should be assigned to eight novel genera, and 22 species should be recombined. All these reclassifications were also confirmed by pairwise cpAAI values, which separated genera within the family Rhizobiaceae with a demarcation threshold of ~86%. In addition, along with the phenotypic and chemotaxonomic analyses, a novel strain BDR2-2T belonging to a novel genus of the family Rhizobiaceae was also confirmed, for which the name Ectorhizobium quercum gen. nov., sp. nov. was proposed. The type strain is BDR2-2T (=CFCC 16492T = LMG 31717T).

Genome resequencing reveals genetic loci and genes conferring resistance to SMV-SC8 in soybean

KEY MESSAGE

A soybean natural population genotyped by resequencing and another RIL population genotyped by SoySNP6K were used to explore consistent genetic loci and genes under greenhouse- and field-conditions for SMV-SC8 resistance. Soybean mosaic virus (SMV) is a member of the genus Potyvirus that occurs in all soybean-growing areas of the world and causes serious losses of yield and seed quality. In this study, a natural population composed of 209 accessions resequenced at an average depth of 18.44 × and another RIL population containing 193 lines were used to explore genetic loci and genes conferring resistance to SMV-SC8. There were 3030 SNPs significantly associated with resistance to SC8 on chromosome 13 in the natural population, among which 327 SNPs were located within an ~ 0.14 Mb region (from 28.46 to 28.60 Mb) of the major QTL qRsc8F in the RIL population. Two genes among 21 candidate genes, GmMACPF1 and GmRad60, were identified in the region of consistent linkage and association. Compared to the mock control, the changes in the expression of these two genes after inoculation with SC8 differed between resistant and susceptible accessions. More importantly, GmMACPF1 was shown to confer resistance to SC8 by significantly decreasing virus content in soybean hairy roots overexpressing this gene. A functional marker, FMSC8, was developed based on the allelic variation of GmMACPF1, and a high coincidence rate of 80.19% between the disease index and marker genotype was identified in the 419 soybean accessions. The results provide valuable resources for studies on the molecular mechanism of SMV resistance and genetic improvement in soybean.

Fluorescent Soybean Hairy Root Construction and Its Application in the Soybean-Nematode Interaction: An Investigation

Simple Summary

The soybean cyst nematode is a pathogen that is parasitic on soybean roots and causes high yield losses. To control it, it is necessary to study resistance genes and their mechanisms. The existing means take half a year but our new method can accelerate the process. We built new tools and integrated the advantages of current technologies to develop an FHR-SCN system. This method shortens the experimental period from half a year to six weeks. Researchers can differentiate between the roots that are transgenic and those that are not with a blue light flashlight and filter. Using this method, we verified a gene that could provide an additional contribution to resistance against the nematode. In addition, we used a transgenic soybean to verify and further indicate that this resistance was caused by an increase of jasmonic acid. The FHR-SCN pathosystem will accelerate the study of the soybean resistant gene.

Abstract

Background: The yield of soybean is limited by the soybean cyst nematode (SCN, Heterodera glycines). Soybean transformation plays a key role in gene function research but the stable genetic transformation of soybean usually takes half a year. Methods: Here, we constructed a vector, pNI-GmUbi, in an Agrobacterium rhizogenes-mediated soybean hypocotyl transformation to induce fluorescent hairy roots (FHRs). Results: We describe the operation of FHR-SCN, a fast, efficient and visual operation pathosystem to study the gene functions in the soybean-SCN interaction. With this method, FHRs were detected after 25 days in 4 cultivars (Williams 82, Zhonghuang 13, Huipizhiheidou and Peking) and at least 66.67% of the composite plants could be used to inoculate SCNs. The demographics of the SCN could be started 12 days post-SCN inoculation. Further, GmHS1^pro-1 was overexpressed in the FHRs and GmHS1^pro-1 provided an additional resistance in Williams 82. In addition, we found that jasmonic acid and JA-Ile increased in the transgenic soybean, implying that the resistance was mainly caused by affecting the content of JA and JA-Ile. Conclusions: In this study, we established a pathosystem, FHR-SCN, to verify the functional genes in soybeans and the SCN interaction. We also verified that GmHS1^pro-1 provides additional resistance in both FHRs and transgenic soybeans, and the resistance may be caused by an increase in JA and JA-Ile contents.

Optimizing RNAi-Target by Nicotiana benthamiana-Soybean Mosaic Virus System Drives Broad Resistance to Soybean Mosaic Virus in Soybean

Soybean mosaic virus (SMV) is a prevalent pathogen of soybean (Glycine max). Pyramiding multiple SMV-resistance genes into one individual is tedious and difficult, and even if successful, the obtained multiple resistance might be broken by pathogen mutation, while targeting viral genome via host-induced gene silencing (HIGS) has potential to explore broad-spectrum resistance (BSR) to SMV. We identified five conserved target fragments (CTFs) from S1 to S5 using multiple sequence alignment of 30 SMV genome sequences and assembled the corresponding target-inverted-repeat constructs (TIRs) from S1-TIR to S5-TIR. Since the inefficiency of soybean genetic transformation hinders the function verification of batch TIRs in SMV-resistance, the Nicotiana benthamiana-chimeric-SMV and N. benthamiana-pSMV-GUS pathosystems combined with Agrobacterium-mediated transient expression assays were invented and used to test the efficacy of these TIRs. From that, S1-TIR assembled from 462 bp CTF-S1 with 92% conservation rate performed its best on inhibiting SMV multiplication. Accordingly, S1-TIR was transformed into SMV-susceptible soybean NN1138-2, the resistant-healthy transgenic T₁-plants were then picked out via detached-leaf inoculation assay with the stock-plants continued for progeny reproduction (T₁ dual-utilization). All the four T₃ transgenic progenies showed immunity to all the inoculated 11 SMV strains under individual or mixed inoculation, achieving a strong BSR. Thus, optimizing target for HIGS via transient N. benthamiana-chimeric-SMV and N. benthamiana-pSMV-GUS assays is crucial to drive robust resistance to SMV in soybean and the transgenic S1-TIR-lines will be a potential breeding source for SMV control in field.

Highly efficient Agrobacterium rhizogenes-mediated hairy root transformation for gene functional and gene editing analysis in soybean

BACKGROUND

Agrobacterium-mediated genetic transformation is a widely used and efficient technique for gene functional research in crop breeding and plant biology. While in some plant species, including soybean, genetic transformation is still recalcitrant and time-consuming, hampering the high-throughput functional analysis of soybean genes. Thus we pursue to develop a rapid, simple, and highly efficient hairy root system induced by Agrobacterium rhizogenes (A. rhizogenes) to analyze soybean gene function.

RESULTS

In this report, a rapid, simple, and highly efficient hairy root transformation system for soybean was described. Only sixteen days were required for the whole workflow and the system was suitable for various soybean genotypes, with an average transformation frequency of 58-64%. Higher transformation frequency was observed when wounded cotyledons from 1-day-germination seeds were inoculated and co-cultivated with A. rhizogenes in 1/2 B5 (Gamborg' B-5) medium. The addition of herbicide selection to root production medium increased the transformation frequency to 69%. To test the applicability of the hairy root system for gene functional analysis, we evaluated the protein expression and subcellular localization in transformed hairy roots. Transgenic hairy roots exhibited significantly increased GFP fluorescence and appropriate protein subcellular localization. Protein-protein interactions by BiFC (Bimolecular Fluorescent Complimentary) were also explored using the hairy root system. Fluorescence observations showed that protein interactions could be observed in the root cells. Additionally, hairy root transformation allowed soybean target sgRNA screening for CRISPR/Cas9 gene editing. Therefore, the protocol here enables high-throughput functional characterization of candidate genes in soybean.

CONCLUSION

A rapid, simple, and highly efficient A. rhizogenes-mediated hairy root transformation system was established for soybean gene functional analysis, including protein expression, subcellular localization, protein-protein interactions and gene editing system evaluation.