N6-methyladenosine (m6A) sequencing reveals Heterodera glycines-induced dynamic methylation promoting soybean defense.

Unraveling the intricacies of soybean cyst nematode (Heterodera glycines) race 4 resistance and susceptibility in soybean breeding lines-11-452 (highly resistant) and Dongsheng1 (DS1, highly susceptible)-was the focal point of this study. Employing cutting-edge N6-methyladenosine (m6A)-seq and RNA-seq techniques, we delved into the impact of m6A modification on gene expression and plant defense responses. Through the evaluation of nematode development in both resistant and susceptible roots, a pivotal time point (3 days post inoculation) for m6A methylation sequencing was identified. Our sequencing data exhibited robust statistics, successful soybean genome mapping, and prevalent m6A peak distributions, primarily in 3'UTR (Untranslated region) and stop codon regions. Analysis of differentially expressed m6A peaks (DMPs) and expressed genes (DEGs) revealed distinctive patterns between resistant and susceptible genotypes. In the highly resistant line (11-452), key resistance and defense-associated genes displayed increased expression coupled with inhibited methylation, encompassing crucial players like R genes, receptor kinases, and transcription factors. Conversely, the highly susceptible DS1 line exhibited heightened expression correlated with decreased methylation in genes linked to susceptibility pathways, including Mildew Locus O (MLO)-like proteins and regulatory elements affecting defense mechanisms. Genome-wide assessments, GO/KEGG analyses, and DMP/DEG overlap emphasized the intricate interplay of m6A modifications, alternative splicing, microRNA and gene regulation in plant defense. Protein-protein interaction networks illuminated defense-pivotal genes, delineating divergent mechanisms in resistant and susceptible responses. This study sheds light on the dynamic correlation between methylation, splicing, and gene expression, providing profound insights into plant responses to nematode infection.

Protective effects of polymer amendment on specific metabolites in soil and cotton leaves under cadmium contamination.

Polymer materials have great potential for soil heavy metal contamination remediation, but the metabolic mechanism by which polymer amendments regulate the responses of soil-plant systems to cadmium (Cd) stress is still unclear. To clarify the metabolic mechanism by which a self-developed soluble polymer amendment (PA) remediates Cd contamination in cotton fields, the common and differential metabolites in soil and cotton leaves were analyzed during the critical period of cotton growth (flowering and bolling stage) in a field experiment. The results showed that Cd stress increased Cd concentration in the soil-cotton system, and reduced enzyme activity in soil and cotton leaves. Besides, Cd stress also reduced the abundance of α-linolenic acid in soil and the abundance of 2-Oxoarginine and S-Adenosylmethionine in cotton leaves. These ultimately led to reductions in weight, boll number, yield, and fiber elongation. However, the application of PA to the Cd-contaminated soil significantly reduced the soil exchangeable Cd (Ex-Cd) concentration by 41.43%, and increased the boll number, yield, and fiber strength by 14.17%, 21.04%, and 19.89%, respectively compared with the Cd treatment. The results of metabolomic analysis showed that PA application mainly affected the Nicotinate and nicotinamide metabolism pathway, Lysine degradation pathway, and Arginine and proline metabolism pathway in cotton leaves and soil. Besides, in these metabolic pathways, succinic acid semialdehyde of cotton leaves, saccharopine of soil, and S-Adenosylmethionine of soil and cotton had the most significant response to PA application. Therefore, the application of PA to Cd-contaminated soil can increase soil and cotton leaf enzyme activity and cotton yield (boll number and seed cotton yield) and quality (fiber strength), and maintain soil-plant material balance by regulating the distribution of Cd ions and key metabolites in the soil-cotton system. This study will deepen our understanding of the metabolic mechanism of PA remediating Cd-contaminated cotton fields, and provide a technical reference for the remediation of heavy metal contamination in drip-irrigated cotton fields in arid areas.

Full-Length Transcriptome Analysis of Soybean Cyst Nematode (Heterodera glycines) Reveals an Association of Behaviors in Response to Attractive pH and Salt Solutions with Activation of Transmembrane Receptors, Ion Channels, and Ca2+ Transporters.

Soybean cyst nematode (Heterodera glycines Ichinohe), a devastating pathogen in soybean, was chosen as a model system to investigate nematode behavior and gene expression changes in response to acidic and basic pH and salt signals (pH 4.5, 5.25, 8.6, and 10 and NaCl) through full-length transcriptome sequencing of 18 samples. An average of 4.36 Gbp of clean reads per sample were generated, and 3972 novel genes and 29,529 novel transcripts were identified. Sequence structural variation during or after transcription may be associated with the nematode's behavioral response. The functional analysis of 1817/4962 differentially expressed genes/transcripts showed that signal transduction pathways, including transmembrane receptors, ion channels, and Ca2+ transporters, were activated, but pathways involved in nematode development (e.g., ribosome) and energy production (e.g., oxidative phosphorylation) were inhibited. A corresponding model was established. Our findings suggest that these receptors and ion channels might be potential targets for nematicides or drug discovery.

Full-Length Transcriptional Analysis of the Same Soybean Genotype With Compatible and Incompatible Reactions to Heterodera glycines Reveals Nematode Infection Activating Plant Defense Response.

Full-length transcriptome sequencing with long reads is a powerful tool to analyze transcriptional and post-transcriptional events; however, it has not been applied on soybean (Glycine max). Here, a comparative full-length transcriptome analysis was performed on soybean genotype 09-138 infected with soybean cyst nematode (SCN, Heterodera glycines) race 4 (SCN4, incompatible reaction) and race 5 (SCN5, compatible reaction) using Oxford Nanopore Technology. Each of 9 full-length samples collected 8 days post inoculation with/without nematodes generated an average of 6.1 GB of clean data and a total of 65,038 transcript sequences. After redundant transcripts were removed, 1,117 novel genes and 41,096 novel transcripts were identified. By analyzing the sequence structure of the novel transcripts, a total of 28,759 complete open reading frame (ORF) sequences, 5,337 transcription factors, 288 long non-coding RNAs, and 40,090 novel transcripts with function annotation were predicted. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of differentially expressed genes (DEGs) revealed that growth hormone, auxin-activated signaling pathway and multidimensional cell growth, and phenylpropanoid biosynthesis pathway were enriched by infection with both nematode races. More DEGs associated with stress response elements, plant-hormone signaling transduction pathway, and plant-pathogen interaction pathway with more upregulation were found in the incompatible reaction with SCN4 infection, and more DEGs with more upregulation involved in cell wall modification and carbohydrate bioprocess were detected in the compatible reaction with SCN5 infection when compared with each other. Among them, overlapping DEGs with a quantitative difference was triggered. The combination of protein-protein interaction with DEGs for the first time indicated that nematode infection activated the interactions between transcription factor WRKY and VQ (valine-glutamine motif) to contribute to soybean defense. The knowledge of the SCN-soybean interaction mechanism as a model will present more understanding of other plant-nematode interactions.

Polymer amendment regulates cadmium migration in cadmium contaminated cotton field: Insights from genetic adaptation and phenotypic plasticity.

Polymer materials have been widely used in the remediation of soil heavy metal contamination for their good performance in the absorption of metal ions. To reveal the effect of polymer amendment (PA) on the remediation of cadmium-contaminated cotton fields, the cadmium (Cd) fractions in soil, Cd concentration in cotton organs, bioconcentration factor (BCF) of Cd, translocation factor (TF) of Cd, and the antioxidant capacity and photosynthesis of functional leaves were evaluated combining with the transcriptomic and metabolomic analyses, in barrel experiments in the field at the flowering and boll-forming stage of cotton. The results showed that, cotton improved the tolerance to Cd through self-regulation in Cd-contaminated soil. The expression of oxoglutaric acid and jasmonic acid were down-regulated by the application of PA to improve the photosynthetic rate (7.71%-46.20%), chlorophyll content (17.59%-63.18%), chlorophyll fluorescence (7.66%-32.25%), and antioxidant enzyme activity (15.49%-45.50%) of functional leaves, and the down-regulation of the expression of jasmonic acid and up-regulation of the expression of stearic acid reduced the exchangeable Cd concentration in the soil, which reduced the transport of Cd from the root to the bolls (54.39%). Thereby, the balance of the genetic adaptation and phenotypic plasticity of cotton was achieved, and the cell structure of leaves was restored. This study deepens our understanding of the molecular mechanism of PA in the remediation of Cd contamination in cotton fields, and provides guidance for the remediation of heavy metal contamination in farmland soil and agricultural safety under drip irrigation.

Metabolic regulation in soil microbial succession and niche differentiation by the polymer amendment under cadmium stress.

Cadmium (Cd) contamination seriously threatens the agricultural production, so exploring the response of soil microenvironment to amendments in Cd-contaminated soils is of importance. In this study, the mechanism of remediation of Cd-contaminated soil using the polymer amendment was studied in cotton flowering stage. The results showed that the concentration of Cd in cotton root and various Cd forms in Cd-contaminated soils were obviously high. High concentration of Cd, especially exchangeable Cd, could seriously affect the soil microenvironment. The root growth of cotton could be promoted, the carbon and nitrogen concentration and storage in soil were increased by 21.72-50.00%, while the exchangeable Cd concentration in soil were decreased by 41.43%, after applying the polymer amendment. In addition, the polymer amendment affected the soil microbial niche, increased the relative abundance of soil bacteria (Flaviaesturariibacter, Rubellimicrobium, and Cnuella), fungi (Verticillium and Tricharina), actinomycetes (Blastococcus and Nocardioides), and fungivores nematodes (Aphelenchus), and improved soil microbial metabolic functions (metabolism of nucleotides and carbohydrates). Therefore, this polymer amendment could be used to remediate severe Cd-contaminated soils, and the changes in the microbial and nematode communities help us understand the detoxification mechanism of the polymer amendment in Cd-contaminated soils.

Transgressive resistance to Heterodera glycines in chromosome segment substitution lines derived from susceptible soybean parents.

Chromosome segment substitution lines (CSSLs) are valuable genetic resources for quantitative trait loci (QTL) mapping of complex agronomic traits especially suitable for minor effect QTL. Here, 162 BC3 F7 -BC7 F3 CSSLs derived from crossing two susceptible parent lines, soybean [Glycine max (L.) Merr.] 'Suinong14' (recurrent parent) × wild soybean (G. soja Siebold & Zucc.) ZYD00006, were used for QTL mapping of soybean cyst nematode (SCN, Heterodera glycine Ichinohe) resistance based on female index (FI) and cysts per gram root (CGR) through phenotypic screening and whole-genome resequencing of CSSLs. Phenotypic results displayed a wide range of distribution and transgressive lines in both HG Type 2.5.7 FI and CGR and demonstrated a higher correlation between CGR and root weight (R2 = .5424) compared with than between FI and CGR (R2 = .0018). Using the single-marker analysis nonparametric mapping test, 33 significant QTL were detected on 18 chromosomes contributing resistance to FI and CGR. Fourteen QTL contributing 5.6-15.5% phenotypic variance (PVE) to FI were revealed on 11 chromosomes, and 16 QTL accounting for 6.1-36.2% PVE in CGR were detected on 14 chromosomes with strong additive effect by multiple-QTL model (MQM) mapping. Twenty-five and 13 out of all 38 QTL identified for FI and CGR on 20 chromosomes were from ZYD00006 and Suinong14, respectively. The CSSLs with the combination of positive alleles for FI, CGR, and root weight exhibited low nematode reproduction. For the first time, QTL associated with CGR have been detected, and both FI and CGR should be considered for breeding purposes in the absence of strong resistance genes such as rhg1 and Rhg4.