SCN Resistance Research Articles

GmSABP2-1 encodes methyl salicylate esterase and functions in soybean defense against soybean cyst nematode.

The soybean gene GmSABP2-1 encodes methyl salicylate esterase and its overexpression led to significant reduction in development of pathogenic soybean cyst nematode. Soybean cyst nematode (SCN, Heterodera glycines) is one of the most devastating pests of soybean (Glycine max L. Merr.). In searching for SCN-defense genes, a soybean gene of the methylesterase (MES) family was found to be upregulated in an SCN-resistant soybean line and downregulated in an SCN-susceptible line upon SCN infection. This gene was designated as GmSABP2-1. Here, we report on biochemical and overexpression studies of GmSABP2-1 to examine its possible function in SCN resistance. The protein encoded by GmSABP2-1 is closely related to known methyl salicylate esterases. To determine the biochemical function of GmSABP2-1, a full-length cDNA of GmSABP2-1 was cloned into a protein expression vector and expressed in Escherichia coli. The resulting recombinant GmSABP2-1 was demonstrated to catalyze the demethylation of methyl salicylate. The biochemical properties of GmSABP2-1 were determined. Its apparent Km value was 46.2 ± 2.2μM for methyl salicylate, comparable to those of the known methyl salicylate esterases. To explore the biological significance of GmSABP2-1 in soybean defense against SCN, we first overexpressed GmSABP2-1 in transgenic hairy roots of an SCN-susceptible soybean line. When infected with SCN, GmSABP2-1-overexpressing hairy roots showed 84.5% reduction in the development of SCN beyond J2 stage. To provide further genetic evidence for the role of GmSABP2-1 in SCN resistance, stable transgenic soybean plants overexpressing GmSABP2-1 were produced. Analysis of the GmSABP2-1-overexpressing lines showed a significant reduction in SCN development compared to non-transgenic plants. In conclusion, we demonstrated that GmSABP2-1 encodes methyl salicylate esterase and functions as a resistance-related gene against SCN.

Soybean MKK2 establishes intricate signalling pathways to regulate soybean response to cyst nematode infection.

Mitogen-activated protein kinase (MPK) cascades play central signalling roles in plant immunity and stress response. The soybean orthologue of MPK kinase2 (GmMKK2) was recently identified as a potential signalling node whose expression is upregulated in the feeding site induced by soybean cyst nematode (SCN, Heterodera glycines). To investigate the role of GmMKK2 in soybean-SCN interactions, we overexpressed a catabolically inactive variant referred to as kinase-dead variant (KD-GmMKK2) using transgenic hairy roots. KD-GmMKK2 overexpression caused significant reduction in soybean susceptibility to SCN, while overexpression of the wild-type variant (WT-GmMKK2) exhibited no effect on susceptibility. Transcriptome analysis indicated that KD-GmMKK2 overexpressing plants are primed for SCN resistance via constitutive activation of defence signalling, particularly those related to chitin, respiratory burst, hydrogen peroxide and salicylic acid. Phosphoproteomic profiling of the WT-GmMKK2 and KD-GmMKK2 root samples upon SCN infection resulted in the identification of 391 potential targets of GmMKK2. These targets are involved in a broad range of biological processes, including defence signalling, vesicle fusion, chromatin remodelling and nuclear organization among others. Furthermore, GmMKK2 mediates phosphorylation of numerous transcriptional and translational regulators, pointing to the presence of signalling shortcuts besides the canonical MAPK cascades to initiate downstream signalling that eventually regulates gene expression and translation initiation. Finally, the functional requirement of specific phosphorylation sites for soybean response to SCN infection was validated by overexpressing phospho-mimic and phospho-dead variants of two differentially phosphorylated proteins SUN1 and IDD4. Together, our analyses identify GmMKK2 impacts on signalling modules that regulate soybean response to SCN infection.

Mitogen-activated protein kinases MPK3 and MPK6 phosphorylate receptor-like cytoplasmic kinase CDL1 to regulate soybean basal immunity.

Soybean cyst nematode (SCN; Heterodera glycines Ichinohe), one of the most devastating soybean (Glycine max) pathogens, causes significant yield loss in soybean production. Nematode infection triggers plant defense responses; however, the components involved in the upstream signaling cascade remain largely unknown. In this study, we established that a mitogen-activated protein kinase (MAPK) signaling module, activated by nematode infection or wounding, is crucial for soybeans to establish SCN resistance. GmMPK3 and GmMPK6 directly interact with CDG1-LIKE1 (GmCDL1), a member of the receptor-like cytoplasmic kinase (RLCK) subfamily VII. These kinases phosphorylate GmCDL1 at Thr-372 to prevent its proteasome-mediated degradation. Functional analysis demonstrated that GmCDL1 positively regulates immune responses and promotes SCN resistance in soybeans. GmMPK3-mediated and GmMPK6-mediated phosphorylation of GmCDL1 enhances GmMPK3 and GmMPK6 activation and soybean disease resistance, representing a positive feedback mechanism. Additionally, 2 L-type lectin receptor kinases, GmLecRK02g and GmLecRK08g, associate with GmCDL1 to initiate downstream immune signaling. Notably, our study also unveils the potential involvement of GmLecRKs and GmCDL1 in countering other soybean pathogens beyond nematodes. Taken together, our findings reveal the pivotal role of the GmLecRKs-GmCDL1-MAPK regulatory module in triggering soybean basal immune responses.

Transcriptome-wide N6-methyladenosine (m6A) profiling of compatible and incompatible responses reveals a nonhost resistance–specific m6A modification involved in soybean–soybean cyst nematode interaction

Soybean cyst nematode (SCN, Heterodera glycines) is a devastating pathogen that infects soybean (Glycine max L. Merrill) and disrupts soybean production worldwide. SCN infection upregulates or downregulates the expression of multiple genes in soybean. However, the regulatory mechanisms that underlie these changes in gene expression remain largely unexplored. N6-methyladenosine (m6A) methylation, one of the most prevalent mRNA modifications, contributes to transcriptional reprogramming during plant responses to pathogen infection. Nevertheless, the role of m6A methylation in establishing compatible and incompatible soybean responses to SCN has not previously been studied. Here, we performed transcriptome-wide m6A profiling of soybean roots infected with virulent and avirulent populations of SCN. Compared with the compatible response, the incompatible response was associated with higher global m6A methylation levels, as well as more differentially modified m6A peaks (DMPs) and differentially expressed genes (DEGs). A total of 133 and 194 genes showed significant differences in both expression and m6A methylation levels in compatible and incompatible interactions; the most significantly enriched gene ontology terms associated with these genes were plant–pathogen interaction (compatible) and folate biosynthesis (incompatible). Our findings demonstrate that the m6A methylation profiles of compatible and incompatible soybean responses are distinct and provide new insights into the regulatory mechanism underlying soybean response to SCN at the post-transcriptional modification level, which will be valuable for improving the SCN resistance breeding.

Identification of QTL, QTL-by-environment interactions, and their candidate genes for resistance HG Type 0 and HG Type 1.2.3.5.7 in soybean using 3VmrMLM.

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is an important disease affecting soybean yield in the world. Potential SCN-related QTLs and QTL-by-environment interactions (QEIs) have been used in SCN-resistant breeding. In this study, a compressed variance component mixed model, 3VmrMLM, in genome-wide association studies was used to detect QTLs and QEIs for resistance to SCN HG Type 0 and HG Type 1.2.3.5.7 in 156 different soybean cultivars materials. The results showed that 53 QTLs were detected in single environment analysis; 36 QTLs and 9 QEIs were detected in multi-environment analysis. Based on the statistical screening of the obtained QTLs, we obtained 10 novel QTLs and one QEI which were different from the previous studies. Based on previous studies, we identified 101 known genes around the significant/suggested QTLs and QEIs. Furthermore, used the transcriptome data of SCN-resistant (Dongnong L-10) and SCN-susceptible (Suinong 14) cultivars, 10 candidate genes related to SCN resistance were identified and verified by Quantitative real time polymerase chain reaction (qRT-PCR) analysis. Haplotype difference analysis showed that Glyma.03G005600 was associated with SCN HG Type 0 and HG Type 1.2.3.5.7 resistance and had a haplotype beneficial to multi-SCN-race resistance. These results provide a new idea for accelerating SCN disease resistance breeding.

Identification of resistant sources from Glycine max against soybean cyst nematode.

Soybean cyst nematode (SCN, Heterodera glycines, HG) is one of the severe pests in plant-parasitic nematodes, which impairs root development and causes severe losses in soybean production worldwide. Breeding SCN-resistant cultivars is an important measure for securing harvests without affecting the environment, as can be done with pesticides. The majority of genetic resources for plant pest resistances are found in wild or closely related species which are often difficult to use in breeding due to crossing barriers or close linkage with unfavorable agronomic traits. In this study, 12 soybean cultivars were evaluated for their marker haplotype at the rhg1 and Rhg4 SCN resistance loci and their SCN resistance tested against multiple races in environmentally controlled bioassays. The results showed that all 12 cultivars displayed Peking-type resistance marker haplotypes and all of them proved to be resistant to multiple SCN races. These cultivars provide potential for improving H. glycines resistance of soybean as donor parent in breeding and can contribute to reduce SCN field populations as part of a sustainable agriculture management.

Deciphering the genetic basis of resistance to soybean cyst nematode combining IBD and association mapping

Key messageIBD analysis clarified the dynamics of chromosomal recombination during the ZP pedigree breeding process and identified ten genomic regions resistant to SCN race3 combining association mapping.Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most devastating pathogens for soybean production worldwide. The cultivar Zhongpin03-5373 (ZP), derived from SCN-resistant progenitor parents, Peking, PI 437654 and Huipizhi Heidou, is an elite line with high resistance to SCN race3. In the current study, a pedigree variation map was generated for ZP and its ten progenitors using 3,025,264 high-quality SNPs identified from an average of 16.2 × re-sequencing for each genome. Through identity by decent (IBD) tracking, we showed the dynamic change of genome and detected important IBD fragments, which revealed the comprehensively artificial selection of important traits during ZP breeding process. A total of 2,353 IBD fragments related to SCN resistance including SCN-resistant genes rhg1, rhg4 and NSFRAN07 were identified based on the resistant-related genetic paths. Moreover, 23 genomic regions underlying resistance to SCN race3 were identified by genome-wide association study (GWAS) in 481 re-sequenced cultivated soybeans. Ten common loci were found by both IBD tracking and GWAS analysis. Haplotype analysis of 16 potential candidate genes suggested a causative SNP (C/T, − 1065) located in the promoter of Glyma.08G096500 and encoding a predicted TIFY5b-related protein on chr8 was highly correlated with SCN race3 resistance. Our results more thoroughly elucidated the dynamics of genomic fragments during ZP pedigree breeding and the genetic basis of SCN resistance, which will provide useful information for gene cloning and the development of resistant soybean cultivars using a marker-assisted selection approach.

Soybean transporter AAT Rhg1 abundance increases along the nematode migration path and impacts vesiculation and ROS.

Rhg1 (Resistance to Heterodera glycines 1) mediates soybean (Glycine max) resistance to soybean cyst nematode (SCN; H. glycines). Rhg1 is a 4-gene, ∼30-kb block that exhibits copy number variation, and the common PI 88788-type rhg1-b haplotype carries 9 to 10 tandem Rhg1 repeats. Glyma.18G022400 (Rhg1-GmAAT), 1 of 3 resistance-conferring genes at the complex Rhg1 locus, encodes the putative amino acid transporter AATRhg1 whose mode of action is largely unknown. We discovered that AATRhg1 protein abundance increases 7- to 15-fold throughout root cells along the migration path of SCN. These root cells develop an increased abundance of vesicles and large vesicle-like bodies (VLB) as well as multivesicular and paramural bodies. AATRhg1 protein is often present in these structures. AATRhg1 abundance remained low in syncytia (plant cells reprogrammed by SCN for feeding), unlike the Rhg1 α-SNAP protein, whose abundance has previously been shown to increase in syncytia. In Nicotiana benthamiana, if soybean AATRhg1 was present, oxidative stress promoted the formation of large VLB, many of which contained AATRhg1. AATRhg1 interacted with the soybean NADPH oxidase GmRBOHG, the ortholog of Arabidopsis thaliana RBOHD previously found to exhibit upregulated expression upon SCN infection. AATRhg1 stimulated reactive oxygen species (ROS) generation when AATRhg1 and GmRBOHG were co-expressed. These findings suggest that AATRhg1 contributes to SCN resistance along the migration path as SCN invades the plant and does so, at least in part, by increasing ROS production. In light of previous findings about α-SNAPRhg1, this study also shows that different Rhg1 resistance proteins function via at least 2 spatially and temporally separate modes of action.

A Survey of Soybean Cyst Nematode Population Densities and Phenotypes in Illinois: 2018 and 2020

In Illinois, soybean cyst nematode (SCN; Heterodera glycines) has been estimated to cause over $15 million in losses as recently as 2021. In addition, populations of SCN insensitive to PI 88788-derived resistance, the most commonly used SCN resistance source in commercially available soybeans, continues to increase in soybean production areas in the United States. Despite this, awareness of this pathogen and its current status in the state is relatively lacking. A survey was conducted in 2018 and 2020 to assess the presence, population level, and virulence phenotypes in Illinois soybean fields. Soil samples were collected and processed for SCN eggs after harvest each year, and samples with sufficient numbers of SCN eggs were virulence tested using the Hg type test. A total of 95 samples were collected, representing 46 counties. Eighty-seven percent of fields sampled contained SCN eggs, with 38% containing population densities over 2,000 eggs/100 cm3. All samples included in the Hg type test had a female index > 10 on indicator line PI 88788, indicating insensitivity to this resistance source. Extrapolated across soybean production acres, these data indicate that approximately 4.4 million acres of soybeans contain levels of SCN requiring SCN management, and over 54% of acres using cultivars derived from PI 88788 are not fully protected from this pathogen.

Comparative genomics of dairy-associated Staphylococcus aureus from selected sub-Saharan African regions reveals milk as reservoir for human-and animal-derived strains and identifies a putative animal-related clade with presumptive novel siderophore.

Staphylococcus aureus infection is considered to be a neglected tropical disease with huge impact on human and animal health alike. Dairy production in sub-Saharan Africa (SSA) relies heavily on various animals such as cows, goats, and camels, depending on the region. S. aureus causes mastitis and exhibits high prevalence in raw milk. The population structure including genotypic and phenotypic traits of dairy S. aureus in relation to animal and human isolates is, however, unknown for SSA. In this work, 20 S. aureus dairy isolates from East and West Africa were selected for comparative genomics and phenotypic analysis. Comparing their population structure revealed a large diversity of different origins suggesting milk to be a reservoir for human and animal strains alike. Furthermore, a novel putative siderophore was detected in multiple strains in a distinct animal-clade with strains of global origin. This putative siderophore shares a high genetic identity with that from Streptococcus equi suggesting possible horizontal gene transfer. These findings combined with the virulence genes harbored by these dairy-derived strains such as pvl, human evasion factor scn, various enterotoxin, leucocidin and antibiotic resistance genes, stresses the need for an integrative One Health approach to tackle the problem of S. aureus infections in animals and humans in sub-Saharan Africa.

Generation and Identification of the Number of Copies of Exogenous Genes and the T-DNA Insertion Site in SCN-Resistance Transformation Event ZHs1-2.

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) causes an estimated economic loss of about USD 3 billion each year in soybean (Glycine max L.) production worldwide. Overexpression of resistance genes against SCN provides a powerful approach to develop SCN resistance cultivars in soybean. The clarification of molecular characterization in transformation events is a prerequisite for ecological risk assessment, food safety, and commercial release of genetically modified crops. Here, we generated transgenic events harboring the BCN (beet cyst nematode) resistance Hs1pro−1 gene using the Agrobacterium-mediated method in soybean, evaluated their resistance to SCN infection, and clarified the molecular characterization of one of the transformation events. Five independent and stable inheritable transformation events were generated by an Agrobacterium-mediated transformation method. SCN resistance tests showed the average number of developed females per plant and female index (FI) in T4 ZHs1-1, ZHs1-2, ZHs1-3, ZHs1-4, and ZHs1-5 transformation events were significantly lower than that in the nontransgenic control. Among these, the ZHs1-2 transformation event had the lowest number of developed females per plant and FI. Southern hybridization showed the exogenous target Hs1pro−1 gene was inserted in one copy and the Bar gene was inserted two copies in the ZHs1-2 transformation event. The exogenous T-DNA fragment was integrated in the reverse position of Chr02: 5351566–5231578 (mainly the Bar gene expression cassette) and in the forward position of Chr03: 17083358–17083400 (intact T-DNA, including Hs1pro−1 and Bar gene expression cassette) using a whole genome sequencing method (WGS). The results of WGS method and Southern hybridization were consistent. All the functional elements of exogenous T-DNA fragments were verified by PCR using specific primer pairs in the T5 and T6 ZHs1-2 transformation events. These results demonstrated that the overexpression of Hs1pro−1 gene enhanced SCN resistance, and provide an important reference for the biosafety assessment and the labeling detection in transformation event ZHs1-2.

Essential Roles of Cupredoxin Family Proteins in Soybean Cyst Nematode Resistance.

Soybean cyst nematode (SCN, Heterodera glycines), one of the most devastating soybean pathogens, causes a significant yield loss in soybean production. One of the most effective ways to manage SCN is to grow resistant cultivars. Therefore, comparative study using resistant and susceptible soybean cultivars provides a powerful tool to identify new genes involved in soybean SCN resistance. In the present study, a transcriptome analysis was carried out using both the resistant (PI88788) and susceptible (Williams 82) soybean cultivars to characterize the responses to nematode infection. Various defense-related genes and different pathways involved in nematode resistance were recognized as being highly expressed in resistant cultivar. Promoter-GUS analysis was conducted to monitor the spatial expression pattern of the genes highly induced by nematode infection. Two nematode-inducible promoters for Glyma.05g147000 (encoding caffeoyl-CoA O-methyltransferase) and Glyma.06g036700 (encoding cupredoxin superfamily protein) were characterized, and the promoters could efficiently drive the expression of known nematode resistance genes (α-SNAPRhg1HC or GmSHMT) to affect soybean SCN resistance. Interestingly, expression of the cupredoxin family genes was upregulated not only by SCN, but also by jasmonic acid treatment. DNA sequence analysis identified that a conserved motif (GGTGCATG) with high similarity to SCNbox1 and GC-rich element is enriched in their promoter regions, suggesting its potential to serve as a nematode-responsive regulatory element. Overexpression of Glyma.06g036700 significantly enhanced soybean resistance to cyst nematode. Overall, our findings not only highlight the essential role of cupredoxin family genes in SCN resistance, but also offer potential functional tools to develop nematode resistance in crops.

Identification of Candidate Genes Controlling Soybean Cyst Nematode Resistance in “Handou 10” Based on Genome and Transcriptome Analyzes

Soybean cyst nematode (SCN; Heterodera glycines Ichinohe) is a highly destructive pathogen for soybean production worldwide. The use of resistant varieties is the most effective way of preventing yield loss. Handou 10 is a commercial soybean variety with desirable agronomic traits and SCN resistance, however genes underlying the SCN resistance in the variety are unknown. An F2:8 recombinant inbred line (RIL) population derived from a cross between Zheng 9525 (susceptible) and Handou 10 was developed and its resistance to SCN HG type 2.5.7 (race 1) and 1.2.5.7 (race 2) was identified. We identified seven quantitative trait loci (QTLs) with additive effects. Among these, three QTLs on Chromosomes 7, 8, and 18 were resistant to both races. These QTLs could explain 1.91–7.73% of the phenotypic variation of SCN’s female index. The QTLs on chromosomes 8 and 18 have already been reported and were most likely overlapped with rhg1 and Rhg4 loci, respectively. However, the QTL on chromosome 7 was novel. Candidate genes for the three QTLs were predicted through genes functional analysis and transcriptome analysis of infected roots of Handou 10 vs. Zheng 9525. Transcriptome analysis performed also indicated that the plant–pathogen interaction played an important role in the SCN resistance for Handou 10. The information will facilitate SCN–resistant gene cloning, and the novel resistant gene will be a source for improving soybeans’ resistance to SCN.

Enhanced resistance to soybean cyst nematode in transgenic soybean via host-induced silencing of vital Heterodera glycines genes.

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is the most economically damaging pathogen affecting soybean production worldwide. Host-induced gene silencing provides a promising approach to confer resistance to plant parasitic nematodes. In the present study, we produced stable transgenic soybean plants individually harboring the inverted repeats of three essential H. glycines genes, Hg-rps23, Hg-snb1, and Hg-cpn1, and evaluated their resistance to SCN infection. Molecular characterization confirmed the stable integration of the hairpin double stranded (ds) RNA in host plants. Inoculation assays with SCN race 3 showed significant reduction of female index (FI, 11.84 ~ 17.47%) on the roots of T4 transgenic plants, with 73.29 ~ 81.90% reduction for the three RNA interference (RNAi) constructs, compared to non-transformed plants (NT, 65.43%). Enhanced resistance to SCN race 3 was further confirmed in subsequent generations (T5) of transgenic soybean. Moreover, when inoculated with SCN race 4 which was considered highly virulent to most of soybean germplasms and varieties, transgenic soybean plants also exhibited reduced FIs (9.96 ~ 23.67%) and increased resistance, relative to the NT plants (46.46%). Consistently, significant down-regulation in transcript levels of the Hg-rps23, Hg-snb1, Hg-cpn1 genes were observed in the nematodes feeding on the transgenic roots, suggesting a broad-spectrum resistance mediated by the host-mediated silencing of vital H. glycines genes. There were no significant differences in morphological traits between transgenic and NT soybean plants under conditions with negligible SCN infection. In summary, our results demonstrate the effectiveness of host-induced silencing of essential H. glycines genes to enhance broad-spectrum SCN resistance in stable transgenic soybean plants, without negative consequences on the agronomic performance.

Classification Methods and Identification of Reniform Nematode Resistance in Known Soybean Cyst Nematode-Resistant Soybean Genotypes.

Plant parasitic nematodes are a major yield-limiting factor of soybean in the United States and Canada. It has been indicated that soybean cyst nematode (SCN; Heterodera glycines Ichinohe) and reniform nematode (RN; Rotylenchulus reniformis Linford and Oliveira) resistance could be genetically related. For many years, fragmentary data have shown this relationship. This report evaluates RN reproduction on 418 plant introductions (PIs) selected from the U.S. Department of Agriculture Soybean Germplasm Collection with reported SCN resistance. The germplasm was divided into two tests of 214 PIs reported as resistant and 204 PIs reported as moderately resistant to SCN. The defining and reporting of RN resistance changed several times in the last 30 years, causing inconsistencies in RN resistance classification among multiple experiments. Comparison of four RN resistance classification methods was performed: (i) ≤10% as compared with the susceptible check, (ii) using normalized reproduction index (RI) values, and using (iii) transformed data log10(x), and (iv) transformed data log10(x + 1) in an optimal univariate k-means clustering analysis. The method of transformed data log10(x) was selected as the most accurate for classification of RN resistance. Among 418 PIs with reported SCN resistance, the log10(x) method grouped 59 PIs (15%) as resistant and 130 PIs (31%) as moderately resistant to RN. Genotyping of a subset of the most resistant PIs to both nematode species revealed their strong correlation with rhg1-a allele. This research identified genotypes with resistance to two nematode species and potential new sources of RN resistance that could be valuable to breeders in developing resistant cultivars.

Host-induced silencing of a nematode chitin synthase gene decreases abundance of rhizosphere fungal community while enhancing

Context A transgenic variety of soybean (Glycine max (L.) Merr.), H57, has been developed from wild-type variety Jack, with host-induced gene silencing of a chitin synthase gene (CHS) in soybean cyst nematode (SCN, Heterodera glycines Ichinohe), a devastating pathogen in soybean. H57 needs to be characterised for suitability to manage SCN, especially because rhizosphere microbial communities may be sensitive to genetically modified crops. Aims We aimed to evaluate the SCN resistance of H57 at the T7 generation, and analyse the impact on the rhizosphere microbial community of planting H57 into SCN-infected soil. Methods Infection with SCN was assessed at 60 days after planting of H57 and Jack into SCN-infected soil by examining recovered cysts from rhizosphere soil and comparing with an infected bulk soil control. For analysis of rhizosphere microbial communities (bacterial and fungal), 16S and ITS amplicons were identified by high-throughput sequencing, and bioinformatic analysis was used to define operational taxonomic units. Alpha diversity, using five indexes, and relative abundance were determined. Key results Soybean H57 showed significantly enhanced and heritable resistance to SCN compared with Jack. The diversity and richness (abundance) of the bacterial community of H57 and Jack were significantly and similarly increased relative to the bulk soil. The fungal community of H57 had considerably lower abundance than both other treatments, and lower diversity than the bulk soil. The relative abundance of only two bacterial phyla (Acidobacteria and Actinobacteria) and one fungal phylum (Glomeromycota), and three bacterial genera (Candidatus_Solibacter, Candidatus_Udaeobacter and Bryobacter) and one fungal genus (Aspergillus), differed significantly between rhizosphere soils of H57 and Jack. Conclusions Host-induced gene silencing of SCN-CHS substantially and heritably enhanced SCN resistance in soybean, did not significantly alter the rhizosphere bacterial community, but greatly suppressed the abundance of the rhizosphere fungal community, which was likely associated with boosted SCN resistance. Implications This study established a basis for interaction research between soybean with SCN-CHS host-induced gene silencing and the rhizosphere microbial community, and for potentially planting soybean H57 to manage SCN.

Genome-wide identification and expression profile analysis of the

Context Soybean cyst nematode is the most important pest of soybean (Glycine max (L.) Merr.) worldwide, causing serious yield losses. Lignin is a vital component of the cell wall that can provide resistance to cyst nematode. O-Methyltransferase (OMT) is a key enzyme involved in lignin metabolism in the phenylalanine pathway. Aims In this study, the soybean OMT gene family was systematically identified, and the expression response of GmOMT to abiotic and cyst nematode stresses was investigated. Methods In total, 67 OMT genes were obtained from the soybean genome through conserved structural domain alignment. GmOMT expression under abiotic stress of soybean was examined based on next-generation RNA sequencing (RNA-Seq). Comprehensive analysis of the genes was conducted, including gene structure, conserved structure, affinity, chromosomal localisation, functional prediction, Gene Ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis, promoter analysis, and expression pattern analysis. Key results The 67 GmOMT genes were identified and distributed among the 19 chromosomes. The GmOMT genes were classified into two categories: CCOMT subfamily and COMT subfamily. GmOMT genes from the same family shared similar gene structures and conserved structural domains, which have undergone strong purifying selection during evolution. The presence of multiple cis-responsive elements in the promoters of GmOMT genes suggested that members of the soybean OMT family may be involved in growth and developmental activities and resistance to stress in soybean. Conclusions GmOMT expression under abiotic stress showed that some of the genes may play a role in abiotic stress. Of them, GmCCOMT3 and GmCCOMT7 were closely associated with lignin synthesis based on both RNA-Seq and quantitative real-time PCR analysis. Implications These findings are valuable for elucidating the function of GmOMT in lignin metabolism and the relationship with SCN resistance.

Detection of rare nematode resistance Rhg1 haplotypes in Glycine soja and a novel Rhg1 α-SNAP.

This study pursued the hypothesis that wild plant germplasm accessions carrying alleles of interest can be identified using available single nucleotide polymorphism (SNP) genotypes for particular alleles of other (unlinked) genes that contribute to the trait of interest. The soybean cyst nematode (SCN, Heterodera glycines [HG]) resistance locus Rhg1 is widely used in farmed soybean [Glycine max (L.) Merr.]. The two known resistance-conferring haplotypes, rhg1-a and rhg1-b, typically contain three or seven to 10 tandemly duplicated Rhg1 segments, respectively. Each Rhg1 repeat carries four genes, including Glyma.18G022500, which encodes unusual isoforms of the vesicle-trafficking chaperone α-SNAP. Using SoySNP50K data for NSFRAN07 allele presence, we discovered a new Rhg1 haplotype, rhg1-ds, in six accessions of wild soybean, Glycine soja Siebold & Zucc. (0.5% of the ∼1,100 G. soja accessions in the USDA collection). The α-SNAP encoded by rhg1-ds is unique at an important site of amino acid variation and shares with the rhg1-a and rhg1-b α-SNAP proteins the traits of cytotoxicity and altered N-ethylmaleimide sensitive factor (NSF) protein interaction. Copy number assays indicate three repeats of rhg1-ds. G. soja PI 507613 and PI 507623 exhibit resistance to HG type 2.5.7 SCN populations, in part because of contributions from other loci. In a segregating F2 population, rhg1-b and rhg1-ds made statistically indistinguishable contributions to resistance to a partially virulent HG type 2.5.7 SCN population. Hence, the unusual multigene copy number variation Rhg1 haplotype was present but rare in ancestral G. soja and was present in accessions that offer multiple traits for SCN resistance breeding. The accessions were initially identified for study based on an unlinked SNP.

Response of soybean genotypes from Northeast China to Heterodera glycines races 4 and 5, and characterisation of rhg1 and Rhg4 genes for soybean resistance

Summary Soybean cyst nematode (SCN, Heterodera glycines) is a devastating plant-parasitic nematode worldwide. Two SCN races, race 4 (HG Type 1.2.3.5.6.7) and race 5 (HG Type 2.5.7), with increased virulence were previously identified in Northeast China. To obtain new resistance sources to these SCN populations, the response of 62 genotypes, including 51 local varieties and breeding lines, and 11 indicator lines for SCN race and HG Type identification, were evaluated. Four new primers in the regions of two loci of GmSHMT08 (Rhg4) and GmSNAP18 (rhg1) were designed for PCR amplification and subsequent sequencing to characterise haplotypes instead of genome resequencing. Results indicated three haplotypes among 51 local genotypes; there were 26 lines in Haplotype I carrying both the rhg1-a and Rhg4-a resistant loci as in ‘Peking’, 13 lines in Haplotype II containing only the resistant rhg1-a locus but Rhg4-b susceptible loci, and 12 lines in Haplotype III with rhg1-c and Rhg4-b susceptible loci. Interestingly, there was no ‘PI 88788’-type resistance identified in Northeast China, although it accounts for 90% of sources in the USA. Two local breeding lines in Haplotype I displayed resistance to both SCN races. The resistance lines carried higher copy number (>1) of the tandem duplication at the rhg1 locus compared with susceptible lines (⩽1). The combination of the two microsatellite markers, Sat_162 on Chr 8 and 590 on Chr 18, distinguished the three haplotypes and predicted the resistance/susceptibility for SCN race 5. The knowledge of the phenotypes and molecular characteristics of 51 local breeding lines in Northeast China will accelerate the utilisation of sources for broad-based SCN resistance and marker-assisted selection.

Registration of three soybean germplasms with novel cyst nematode resistance from PI 567516C

AbstractSoybean [Glycine max (L.) Merr.] germplasm lines JTN‐5316 (Reg. no. GP‐443, PI 691524), JTN‐5416 (Reg. no. GP‐444, PI 691525), and JTN‐5516 (Reg. no. GP‐445, PI 691526) were released by the USDA‐ARS in 2019 and trace 25% of their pedigree to PI 567516C. These F6–derived sister lines are the first releases derived from this accession. The new lines were developed to provide broad genetic resistance to the predominant damaging pest of soybean in the United States, soybean cyst nematode (SCN; Heterodera glycines Ichinohe), by combining the novel genetic resistance of PI 567516C with the established resistance of ‘Hartwig’. Development of these lines was characterized by intensive selection of F3 plants based on agronomic characteristics and simple sequence repeat markers associated with SCN resistance quantitative trait loci (QTL) in PI 567516C and Hartwig. The new lines have inherited resistance alleles at five QTL: two originating from PI 567516C and three originating from Hartwig, across four chromosomes. The lines were evaluated for and exhibit varying levels of resistance to other economically important pathogens of soybean, including: reniform nematode (Rotylenchulus reniformis Linford & Oliveira), frogeye leaf spot (caused by Cercospora sojina Hara), and southern stem canker (caused by Diaporthe phaseolorum var. meridionalis F. A. Fernández). JTN‐5316, JTN‐5416, and JTN‐5516 were field tested for multiple years in Jackson and Milan, TN, and produce moderate seed yield. These determinate maturity group (MG) V germplasm lines are excellent parent material for breeding programs with an interest in incorporating broad genetic resistance to SCN.