Soybean Nematode Research Articles

Identification of candidate genes associating with soybean cyst nematode in soybean (Glycine max L.) using BSA-seq.

Soybean cyst nematode disease represents the major soil-borne disease of soybean. Identifying disease-resistant genes in soybean has a substantial impact on breeding of disease-resistant crops and genetic improvement. The present work created the F2 population with the disease-resistant line H-10 and disease-susceptible line Chidou4. 30 respective F2disease-resistant and disease-susceptible individuals for forming two DNA pools for whole-genome re-sequencing were selected. As a result, a total of 11,522,230 single nucleotide polymorphism (SNPs) markers from these two parental lines and two mixed pools were obtained. Accordng to SNP-index based association analysis, there were altogether 741 genes out of 99% confidence interval, which were mainly enriched into regions of 38,524,128∼39,849,988 bp with a total length of 1.33 Mb contain 111 genes on chromosome 2, 27,821,012∼29,612,574 bp with a total length of 1.79 Mb contain 92 genes on chromosome 3, 308∼348,214 bp with a total of length 0.35 Mb contain 34 genes on chromosome 10, and 53,867,581∼58,017, 852 bp with a total length of 4.15 Mb contain 504 genes on chromosome 18. Bulk segregant analysis in F2 generations (BSA-seq) was correlated with a disease resistance interval containing 15 genes. Then, using bioinformatics analysis and differential expression analysis, five candidate genes were identified: Glyma.02G211400, Glyma.18G252800, Glyma.18G285800, Glyma.18G287400 and Glyma.18G298200. Our results provides a key basis for analyzing the soybean resistance mechanism against soybean cyst nematode and cloning soybean resistance genes.

Efficiency of Vinasse Application on Root-Knot Nematodes in Soybean

Vinasse is not only effectively used in pest control but also creates a conducive environment for the growth of antagonistic microorganisms. Thus, this study aimed to evaluate the potential of vinasse applied via soil for the management of root-knot nematodes in soybean culture. The experimental design was entirely random, in a factorial scheme (2 × 6), consisting of two species of nematodes, Meloidogyne incognita and M. javanica, under vinasse application at five concentrations (20, 40, 60, 80, and 100%) and one control (water), with five repetitions. Soybean plants Intacta cv. M-Soy 8644 IPRO were inoculated with 4000 eggs/juveniles of each species separately. At 60 days after the first application of vinasse, evaluations of parasitism and agronomic characteristics in soybean were performed. Stillage resulted in the highest average values for root volume and root fresh mass in plants inoculated with M. incognita, showing respective increases of 24.33% and 14.92% compared to plants inoculated with M. javanica. However, concentrations exceeding 60% had a detrimental effect on all agronomic variables of soybean. For parasitism, an interaction among the factors was observed, with a significant effect (p < 0.01) for most of the evaluated variables, except for the number of eggs in the soil. The concentration equivalent to 60% vinasse promoted a sharp reduction in parasitism for the two nematode species, making reproduction on plant roots unfeasible.

Plant-parasitic nematode community and enzyme activities in soils under no-till soybean crops in Brazil

Soybean is Brazil's largest agricultural crop, grown across a variety of climates and soil conditions, and it is subjected to a large number of pests, including plant-parasitic nematodes. In general, the occurrence of plant-parasitic nematodes in soybean is influenced by various soil physicochemical properties, such as the pH, texture, and nutrient content. These soil properties may determine the nematodes community composition and affect soil quality and functioning, which can be monitored by analysing of soil enzyme activity. In this sense, the analysis of β-glucosidase and acid phosphatase enzymes can provide valuable information to assist decisions in the sustainable management of soybean cultivated soils in Brazil. In this study, we used 216 samples collected from no-till soybean fields across Brazil. The samples were used to investigate the influence of soil physical and chemical properties on the plant-parasitic nematode community and enzymatic activity. We identified seven genera of plant-parasitic nematodes including Meloidogyne, Pratylenchus, Heterodera, Rotylenchulus, Helicotylenchus, Scutellonema, and Xiphinema. Our results indicate that clay content and soil pH were the main properties modulating the plant-parasitic nematode community. We observed a higher abundance of plant-parasitic nematodes in highly acidic soils when compared to slightly acidic. In addition, soil organic matter content, available P, and pH were the main properties modulating microbial activity in the soil. No significant correlations were observed between enzymatic activity and nematode population density. This is the first study to provide insights into plant-parasitic nematode community composition and soil enzymes activity in soybean cultivated soils on a national scale in Brazil.

Plantas de cobertura e agentes de biocontrole no manejo de nematoides na cultura da soja

ABSTRACT In the Brazilian Cerrado, phytonematodes, phytonematodes are a challenge for agriculture, and the association of forms of control is the best strategy to be used in coexistence with this pathogen. Faced with this problem, this study aimed to evaluate the efficiency of cover crops and biocontrol agents in the management of nematodes in soybean. For each nematode species under study (Meloidogyne incognita and Pratylenchus brachyurus), two experiments were carried out under greenhouse conditions in a completely randomized design arranged in a 6 × 2 factorial scheme with eight replications. Six cover crops (millet ADRG 9050, millet ADR 300, Urochloa ruziziensis, Crotalaria ochroleuca, C. spectabilis, and corn hybrid DKB 290) and two treatments (treated or not with Bacillus subtilis and B. methylotrophicus - 1×106 CFU per seed) were evaluated. The cover crops were sown in soil infested with nematodes and then soybeans were sown under the straw, and cultivated for 45 and 60 days, for M. incognita and P. brachyurus, respectively. Fresh root mass, total nematode population, and the number of nematodes per gram of root were evaluated. The association of microorganisms with C. spectabilis, U. ruziziensis, and millet ADR 300 conferred an additional effect in reducing the population of P. brachyurus. For M. incognita, the association was successful only for combining C. spectabilis with B. methylotrophicus. DKB 290 corn, when treated with B. methylotrophicus, had the nematode population per gram of soybean root reduced by 90% compared to plants that did not receive biological treatment.

Nematodes Associated with Terrestrial Slugs in Mid-Atlantic (Delaware, USA) Soybean

Slugs are cryptic terrestrial pests that target a wide range of crops and are especially damaging to seedlings. Management of these invertebrates mostly relies on synthetic chemistry. These molecules can be efficient against slugs and snails but can be toxic to other organisms (e.g., dogs) and harmful to the environment (e.g., leaching into surface and groundwater). The usage of pathogenic nematodes has been effective in several crops and European countries. A survey was conducted to investigate the presence of natural populations of malacopathogenic nematodes in soybean in the mid-Atlantic region. Slugs were sampled in nine fields across Delaware at various distances from the field edges (0 m, 5 m, 10 m, 15 m). Soil cover and soil type were also recorded. Invertebrates were brought back to the laboratory. Slugs were monitored for four weeks, and mortality was classified into one of three categories: (1) death with the presence of nematodes; (2) death with the presence of fungi; (3) death without the presence of nematodes or fungi. Nematodes associated with slugs were identified based on 18S rRNA sequencing. The distance from the field edge did not impact the number of trapped slugs and the incidence of slug death associated with the presence of nematodes. Overall, nematodes were collected from ca. 20% of the slug cadavers, and most have previously been associated with slugs (ca. 35% of deaths associated with fungi and ca. 45% not associated with nematodes or fungi). The number of captured slugs and slug death associated with the presence of nematodes were positively correlated with ground cover. Soil type impacted both the number of captured slugs and the presence of pathogenic nematodes. This survey provides a first insight into the natural populations of mollusk-associated nematodes in the mid-Atlantic region. This knowledge may contribute to implementing cultural practices favoring these natural enemies of slug pests.

Development of SNP molecular markers associated with resistance to reniform nematode in soybean using KASP genotyping

Reniform nematode (Rotylenchulus reniformis, Linford and Oliveira) is a sedentary, semi-endoparasite that infects a wide range of plant hosts and is one of the top three nematode pathogens affecting soybean in the southeastern United States. Previous studies have linked resistance to reniform nematode in soybean to two quantitative trait loci on chromosomes 11 and 18. A Kompetitive Allele-Specific PCR (KASP) assay was designed using SNP markers within these two regions to distinguish reniform nematode-resistant soybean based on genotype. A collection of 44 soybean plant introductions with resistant phenotype to reniform nematode and 40 susceptible soybean lines were genotyped at the two target loci to validate the KASP assay design. Of the 44 observed resistant lines, two carried the susceptible genotype; PI 438489B at the locus on chromosome 18 and PI 495017C on chromosome 11. Of the 40 observed susceptible soybean lines, only 25 had the expected susceptible genotype at the loci on chromosome 18 and 13 on chromosome 11. Our KASP assay was 68% accurate in predicting the phenotype of 84 soybean accessions based on their genotype at the SNP marker on chromosome 18 and 83% accurate at chromosome 11. These results indicate a moderate correlation of soybean SNP markers GlyREN18_46 and GlyREN11_190 with reniform nematode resistance. Further research is required to improve the accuracy of KASP assays to predict soybean response to reniform nematode, particularly host susceptibility.

Abstracts of Presentations at the 2022 National Soybean Nematode Conference.

Abstracts of Presentations at the 2022 National Soybean Nematode Conference.

Biocontrol of plant-parasitic nematodes by soil in soybean cultivation

Soybean is a commodity widely cultivated in Brazil and represents one of the main export products. Several biotic and abiotic factors have limited the productivity growth of this oilseed, one of them are the nematodes associated with the monoculture. Therefore, the objective of this study was to evaluate the effect of different bioagents in control of plant-parasitic nematodes in soybean, via soil. The experiment was carried in Gurupi-TO in a randomized complete block design, with four repetitions and 14 treatments, including the witness. The treatments consisted of biocontrol agents: Paecilomyces sp., Trichoderma asperirellum, Bacillus subtilis and Pochonia sp., evaluated singly and in combinations. The treatments with Paecilomyces sp. + Bacillus subtilis and the combination of all the microorganisms results in higher averages for most traits when compared to the control treatment. The treatments Paecilomyces spp. + Bacillus subtilis and Paecilomyces sp. + Trichoderma asperellum + Bacillus subtilis + Pochonia sp., were also the most efficient in reduction of the population of nematodes evaluated. For this reason, the combination of biological control agents can reduce the population of phytonematodes.

Comparisons of constitutive resistances to soybean cyst nematode between PI 88788- and Peking-type sources of resistance in soybean by transcriptomic and metabolomic profilings.

Soybean cyst nematode (SCN) is a serious damaging disease in soybean worldwide. Peking- and PI 88788-type sources of resistance are two most important germplasm used in breeding resistant soybean cultivars against this disease. However, until now, no comparisons of constitutive resistances to soybean cyst nematode between these two types of sources had been conducted, probably due to the influences of different backgrounds. In this study, we used pooled-sample analysis strategy to minimize the influence of different backgrounds and directly compared the molecular mechanisms underlying constitutive resistance to soybean cyst nematode between these two types of sources via transcriptomic and metabolomic profilings. Six resistant soybean accessions that have identical haplotypes as Peking at Rgh1 and Rhg4 loci were pooled to represent Peking-type sources. The PI88788-type and control pools were also constructed in a same way. Through transcriptomic and metabolomics anaylses, differentially expressed genes and metabolites were identified. The molecular pathways involved in the metabolism of toxic metabolites were predicted to play important roles in conferring soybean cyst nematode resistance to soybean. Functions of two resistant candidate genes were confirmed by hairy roots transformation methods in soybean. Our studies can be helpful for soybean scientists to further learn about the molecular mechanism of resistance to soybean cyst nematode in soybean.

NemaNet: A convolutional neural network model for identification of soybean nematodes

Phytoparasitic nematodes (or phytonematodes) are causing severe damage to crops and generating large-scale economic losses worldwide. In soybean crops, annual losses are estimated at 10.6% of the world production. Besides, the identification of these species through microscopic analysis by an expert with taxonomic knowledge is often laborious, time-consuming, and susceptible to failure. From this perspective, robust and automatic approaches are necessary for identifying phytonematodes that are capable of providing correct diagnoses for the classification of species and subsidizing of all control and prevention measures. This work presents a new public data set called NemaDataset containing 3063 microscopic images from five nematode species with the most significant damage relevance for the soybean crop. Additionally, we propose a new Convolutional Neural Network (CNN) model defined as NemaNet and present a comparative assessment with thirteen popular models of CNNs, all of them representing state-of-the art classification and recognition. The general average was calculated for each model, on a from-scratch training; the NemaNet model reached 96.76% accuracy, while the best evaluation fold reached 98.04%. When training with transfer learning was performed, the average accuracy reached 98.82%. The best evaluation fold reached 99.35%, and overall accuracy improvements of over 6.83% and 4.1%, for from-scratch and transfer learning training, respectively, compared to other popular models were achieved. • Detect phytonematodes in soybean crops in Brazil using convolutional neural network. • A new dataset with five main species of phytonematodes from Brazil's soybean culture. • Evaluation of thirteen most popular CNN's architectures and new model (NemaNet). • Results describe NemaNet reaches best results in identifying nematodes overall.

Genome-wide association study for resistance to the Meloidogyne javanica causing root-knot nematode in soybean.

A locus on chromosome 13, containing multiple TIR-NB-LRR genes and SNPs associated with M. javanica resistance, was identified using a combination of GWAS, resequencing, genetic mapping and expression profiling. Meloidogyne javanica, a root-knot nematode, is an important problem in soybean-growing areas, leading to severe yield losses. Some accessions have been identified carrying resistance loci to this nematode. In this study, a set of 317 soybean accessions was characterized for resistance to M. javanica. A genome-wide association study was performed using SNPs from genotyping-by-sequencing, and a region of 29.2kb on chromosome 13 was identified. An analysis of haplotypes showed that SNPs were able to discriminate between susceptible and resistant accessions, with 25 accessions sharing the haplotype associated with resistance. Furthermore, five accessions that exhibited resistance without carrying this haplotype may carry different loci conferring resistance to M. javanica. We also conducted the screening of the SNPs in the USDA soybean germplasm, revealing that several soybean accessions previously reported as resistant to other nematodes also shared the resistance haplotype on chromosome 13. Two SNP-based TaqMan® assays were developed and validated in two panels of soybean cultivars and in biparental populations. In silico analysis of the region associated with resistance identified the occurrence of genes with structural similarity with classical major resistance genes (NBS-LRR genes). Specifically, several nonsynonymous SNPs were observed in Glyma.13g194800 and Glyma.13g194900. The expression profile of these candidate genes demonstrated that the two gene models were up-regulated in the resistance source PI 505,099 after nematode infection. Overall, the SNPs associated with resistance and the genes identified constitute an important tool for introgression of resistance to the root-knot nematode by marker-assisted selection in soybean breeding programs.

Spectral detection of nematodes in soybean at flowering growth stage using unmanned aerial vehicles

ABSTRACT: Soybean is one of the main crop species grown in the world. However, there is a decline in productivity due to the various types of stress, including the nematodes Heterodera glycines and Pratylenchus brachyurus. The objectives were to determine the best spectral band for detecting H. glycines and P. brachyurus at the beginning of flowering (R1). Soil and root sampling was conducted at nine sampling sites in each of the five nematode-infested regions, totaling 45 sampling points. Flights were made at all regions using Phantom 4 Advanced, Sequoia and 14-band customized Sentera. For H. glycines, the red spectral band best explained the variability on soil and root nematode counts as well as the second stage of juveniles in soil. For P. brachyurus, Sentera RedEdge best explained the variability in root nematode counts and Sequoia NIR best explained soil juveniles. A multiple linear regression model using spectral data for detecting P. brachyurus and H. glycines improved R² compared to simple linear regressions. At flowering growth stage (R1), soybean spectral reflectance was associated with the number of H. glycines and P. brachyurus on soil and roots using low-cost and multispectral sensors.

Effects of yeast fermentation broths on the Meloidogyne incognita population in soybean

Root-knot nematodes are pathogenic to a wide range of plants worldwide and can reduce the yield potential of important crops. The objective of this study was to investigate the potential effects of yeast fermentation broths (YFBs) on the hatching of Meloidogyne incognita second-stage juveniles (J2s) in vitro. In addition, application methods of the yeasts for the control of the nematode in soybean were evaluated. Fermentation broths (FBs) of Pichia manshurica CCMA0762, Pichia caribbica CCMA0759, Lachancea thermotolerans CCMA0763, Hanseniaspora opuntiae CCMA0760 and Kodamaea (Pichia) ohmeri CCMA0758 were evaluated in the hatching test in vitro. The same treatments were separately applied to the soil, soil+shoot and shoots of plants inoculated with M. incognita, and the results were compared with those of the control and those from a yeast-based commercial product. L. thermotolerans CCMA0763 and P. caribbica CCMA0759 FBs were selected for evaluation of nematode infection. All YFBs inhibited J2 hatching. The L. thermotolerans FB reduced the number of nematodes in one experiment when applied to soil. The most effective application mode differed by FB type. L. thermotolerans and P. caribbica FBs, when applied to shoots, decreased the number of J2s, sausage-shaped juveniles, adult females and total nematodes at different evaluation times.

Biological Control Associated With Plant Nutrition for Meloidogyne javanica and Pratylenchus brachyurus Management in Soybean

Meloidogyne javanica and Pratylenchus brachyurus stand out among the main nematodes in soybean crops. Research on integrated management are often conducted, due to the low efficiency of the main control methods when they are applied alone. Thus, the aim of the present study was to assess the potential of biological control and plant nutrition products to control these nematodes in soybean. The effect of each product alone on nematode hatching and mortality was also assessed. A greenhouse experiment was also carried out, evaluating five doses of the product for biological control based on Bacillus and Trichoderma, with and without the presence of the product for nutrition, inoculated with 2000 eggs and juveniles for the gall nematode or 1000 specimens for the nematode lesions. After 30 days of multiplication, the aerial part was removed and the soil was revolved to receive the new sowing of the soybean with the respective treatments mentioned above. After 60 days, the experiments were evaluated for nematological parameters. Both products reduced hatching and increased nematode mortality. Treatments with biological control were efficient in reducing M. javanica and P. brachyurus, mainly when applied at doses close to 5 and 8 kg ha-1, respectively. The nutrition product negatively influences the biological control.

Deep genotyping of the gene GmSNAP facilitates pyramiding resistance to cyst nematode in soybean

Soybean cyst nematode (SCN) is a highly destructive pathogen. The soybean host genome harbors at least two major genes for resistance (rhg1 and Rhg4), as well as a minor locus (SCN3-11). In the present study, a splicing site in GmSNAP11, the potential causal gene of SCN3-11, was identified by comparison of the GmSNAP11 cDNA sequences generated from resistant and susceptible soybean accessions. The sequence information was used to design a codominant CAPS marker, GmSNAP11-2565, which was used to genotype a panel of 209 soybean accessions varying with respect to SCN resistance. Analyses of the effect of the haplotypes formed by GmSNAP11-2565 and another large-effect (nonsynonymous) locus, GmSNAP11-2307, previously identified in GmSNAP11, revealed linkage disequilibrium (P < 0.0001) between the two loci, suggesting that GmSNAP11-2565 could be used as a marker for GmSNAP11. GmSNAP11-2565 was accordingly used, along with established markers for GmSNAP18 (rhg1) and GmSHMT (Rhg4), to characterize the panel accessions. The mean SCN female index of accessions carrying only the GmSNAP11 allele associated with resistance (20.3%) was higher than that associated with accessions carrying alleles for resistance at both GmSNAP11 and GmSNAP18 (12.4%), while the index for accessions carrying alleles for resistance at all of GmSNAP11, GmSNAP18, and GmSHMT was very low (1.9%). Selection on all three markers was effective for maintaining a high level of resistance to SCN race 3.

Transcriptomic and metabolomic analyses reveal that bacteria promote plant defense during infection of soybean cyst nematode in soybean

BackgroundSoybean cyst nematode (SCN) is the most devastating pathogen of soybean. Our previous study showed that the plant growth-promoting rhizobacterium Bacillus simplex strain Sneb545 promotes soybean resistance to SCN. Here, we conducted a combined metabolomic and transcriptomic analysis to gain information regarding the biological mechanism of defence enhancement against SCN in Sneb545-treated soybean. To this end, we compared the transcriptome and metabolome of Sneb545-treated and non-treated soybeans under SCN infection.ResultsTranscriptomic analysis showed that 6792 gene transcripts were common in Sneb545-treated and non-treated soybeans. However, Sneb545-treated soybeans showed a higher concentration of various nematicidal metabolites, including 4-vinylphenol, methionine, piperine, and palmitic acid, than non-treated soybeans under SCN infection.ConclusionsOverall, our results validated and expanded the existing models regarding the co-regulation of gene expression and metabolites in plants, indicating the advantage of integrated system-oriented analysis.

Suscetibilidade de cultivares de soja ao nematoide das lesões radiculares

RESUMO O nematoide das lesões radiculares, Pratylenchus brachyurus, têm causado significativas perdas na cultura da soja, sobretudo, em regiões do Centro-oeste do Brasil. Em função da atual importância deste nematoide em áreas de cultivo de soja e pela pouca disponibilidade de genótipos resistentes no mercado brasileiro, este experimento foi conduzido em casa de vegetação com o objetivo de avaliar a reação de oito cultivares de soja (‘CD 202’; ‘CD 215’; ‘CD 239’; ‘CD 226 RR’; ‘CD 231 RR’; ‘CD 235 RR’; ‘BRS 1841 e ‘BRS 283’) a P. brachyurus. O delineamento experimental foi inteiramente casualizado com oito repetições. A densidade populacional inicial (Pi) utilizada foi de 200 espécimes/planta. A população final (Pf) foi obtida por meio da extração dos nematoides do substrato e das raízes e quantificadas 90 dias após a inoculação. Todas as cultivares de soja foram suscetíveis a P. brachyurus, porém em diferentes graus, FR entre 1,24 e 2,80.

Plant elicitor peptides promote plant defences against nematodes in soybean.

Plant elicitor peptides (Peps) are widely distributed among angiosperms, and have been shown to amplify immune responses in multiple plant families. Here, we characterize three Peps from soybean (Glycine max) and describe their effects on plant defences against two damaging agricultural pests, the root-knot nematode (Meloidogyne incognita) and the soybean cyst nematode (Heterodera glycines). Seed treatments with exogenous GmPep1, GmPep2 or GmPep3 significantly reduced the reproduction of both nematodes. Pep treatment also protected plants from the inhibitory effects of root-knot nematodes on above-ground growth, and up-regulated basal expression levels of nematode-responsive defence genes. GmPep1 induced the expression of its propeptide precursor (GmPROPEP1), a nucleotide-binding site leucine-rich repeat protein (NBS-LRR), a pectin methylesterase inhibitor (PMEI), Respiratory Burst Oxidase Protein D (RBOHD) and the accumulation of reactive oxygen species (ROS) in leaves. In addition, GmPep2 and GmPep3 seed treatments up-regulated RBOHD expression and ROS accumulation in roots and leaves. These results suggest that GmPeps activate plant defences through systemic transcriptional reprogramming and ROS signalling, and that Pep seed treatments represent a potential strategy for nematode management.

ダイズの病害虫抵抗性検定法および選抜手法に関する研究(北陸作物学会賞(奨励賞))

ダイズの病害虫抵抗性検定法および選抜手法に関する研究(北陸作物学会賞(奨励賞))

English

The soybean cyst nematode (SCN), Heterodera glycines, is present in more than 150 municipalities in Brazil, and the long persistence of the cysts in the soil combined with the severe degree of parasitism induces high soybean production losses. The objective of this study was to evaluate the biofumigant effect of Crambe abyssinica on the SCN population in the second soybean crop season. The experiment was conducted on a rural property whose soil was naturally infested with SCN. Crambe abyssinica was planted in the second crop season following harvest, and in the subsequent crop season, 4 soybean varieties, 2 resistant and 2 susceptible to SCN, were planted. The nematode population was evaluated every month for 90 days after planting. In the second crop season, when C. abyssinica was in the field, there was a significant decrease in the number of adult SCN females and cysts. During the 90-day period after C. abyssinica cultivation, when plant residues were incorporated into the soil and the area was planted with soybeans, both the number of adult SCN females / 10 g roots and the number of cysts decreased. This result indicates that C. abyssinica reduced the nematode population during its time in the field. Key words: Crambe, Glycine max, soybean nematode cyst, culture control.