Soybean Cyst Nematode Population Research Articles

Registration of ‘TN14‐5021’, a conventional soybean cultivar with elevated seed protein and resistance to soybean cyst nematode races 2, 3, and 5

Abstract‘TN14‐5021’ (Reg. no. CV‐543, PI 699124) is a late maturity group IV (relative maturity 4.9) determinate conventional soybean [Glycine max (L.) Merr.] cultivar developed and released by the University of Tennessee soybean breeding program. Soybean cultivars with resistance to soybean cyst nematode (SCN) race 2 are rare, but race 2 is becoming a predominant SCN population infecting farmers’ fields in regions of the U.S. Southeast and Mid‐South. TN14‐5021 also conveys resistance to stem canker [caused by Diaporthe phaseolorum (Cooke & Ellis) Sacc. var. caulivora K.L. Athow & R.M. Caldwell] and strong resistance to SCN races 3 and 5. In replicated trials across 70 environments from the Mid‐South to the Southeast, TN‐5021 showed high yield potential and adaptation to a broad range of growing conditions. TN14‐5021 has white flowers and gray pubescence. The pods have a tan pod coat, and the seeds are yellow with smooth seed coats. Across 48 environments over a 4‐yr period, with testing locations from Kansas to Alabama, TN14‐5021 averaged 406 and 226 g kg–1 protein and oil content, respectively. In comparison, the average protein and oil content of commercial cultivars grown in the same tests averaged 397 and 224 g kg–1, respectively. Its high yield coupled with elevated seed protein concentration and nematode resistance package make TN14‐5021 a valuable cultivar for Tennessee and the Mid‐South region.

Soybean cyst nematode (Heterodera glycines) resistant cultivar rotation system impacts nematode population density, virulence, and yield

Soybean cyst nematode (SCN) is the most economically important pathogen of soybeans in the United States. The most effective SCN management practice is the use of resistant cultivars; however, continuous use of cultivars derived from a single line of resistance results in selection for SCN virulent populations. A four-year field study (2017–2020) was conducted in Michigan to evaluate the impact of six soybean rotation systems with cultivars derived from PI548402 (5DV) and PI88788 (8DV) on SCN population development, virulence, and soybean yield. The rotation systems were: 1) 8DV/5DV/8DV/5DV, 2) 5DV/5DV/5DV/5DV, 3) 8DV/Susceptible (SDV)/5DV/8DV, 4) 5DV/SDV/8DV/5DV, 5) 8DV/8DV/8DV/8DV, and 6) 5DV/SDV/SDV/SDV. SCN population levels were significantly lower in the 5DV/8DV rotation in 2018 compared to the 5DV/SDV rotation. In 2020, SCN population levels were the lowest in the rotation system 8DV/5DV/8DV/5DV and the highest in the continuous 5DV soybeans. In 2017, there were no substantial soybean yield differences among the differing systems, but for the remainder of the trial, the 5DV/8DV rotations had the highest yields. HG type tests showed that rotation of resistance sources can alter the virulence of the SCN population. The initial 2017 SCN population was HG type 1.2. The final populations in 2020 for the rotation systems 8DV/5DV/8DV/5DV, 5DV/5DV/5DV/5DV, and 8DV/SDV/5DV/8DV was HG type 1.2.5.7, and HG type 1.2.3.5.6.7 for the other rotation systems 5DV/SDV/8DV/5DV, 8DV/8DV/8DV/8DV, and 5DV/SDV/SDV/SDV. Based on the results of the field trial, a greenhouse trial was conducted where we found that a Michigan SCN population from continuous PI88788 sources of resistance can also reproduce on Peking. These findings indicate rotating PI548402- and PI88788-derived cultivars can reduce SCN density and maintain high soybean yields; thus rotating these two sources of resistance with non-host rotations might delay the aggressiveness of SCN populations further, reducing soybean yield loss.

Evaluation of Scopoletin from Penicillium janthinellum Snef1650 for the Control of Heterodera glycines in Soybean.

Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is responsible for causing a major soybean disease globally. The fungal strain Penicillium janthinellum Snef1650 was evaluated against H. glycines. However, the effective determinants of the P. janthinellum strain are unknown. By performing pot experiments, a functioning compound was isolated from P. janthinellum Snef1650 through organic solvent extraction, semi-preparative HPLC, Sephadex LH-20 column chromatography, and silica gel column chromatography, and the isolated compound was identified to be scopoletin through 1H NMR, 13C NMR, and HPLC–MS. The pot experiments indicated that the treatment of soybean seeds with scopoletin drastically reduced the SCN population. The field experiments performed in 2017 and 2018 revealed that scopoletin decreased over 43.7% juveniles in the roots and over 61.55% cysts in the soil. Scopoletin treatment also promoted soybean growth and improved its yield, with an increase in plot yield by >5.33%. Scopoletin obtained from P. janthinellum Snef1650 could be used as an anti-H. glycines biocontrol agent.

Resistance Gene Pyramiding and Rotation to Combat Widespread Soybean Cyst Nematode Virulence

Soybean cyst nematode (SCN) is an important pathogen of soybean causing >$1 billion in yield losses annually in the United States. Planting SCN-resistant soybean cultivars is the primary management strategy. Resistance genes derived from the plant introduction (PI) 88788 (rhg1-b) and PI 548402 (Peking; rhg1-a and Rhg4) are the main types of resistance available in commercial cultivars. The PI 88788 rhg1-b resistance allele is found in the majority of SCN-resistant cultivars in the north central United States. The widespread use of PI 88788 rhg1-b has led to limited options for farmers to rotate resistance sources to manage SCN. Consequently, overreliance on a single type of resistance has resulted in the selection of SCN populations that have adapted to reproduce on these resistant cultivars. Here we evaluated the effectiveness of rotating soybean lines with different combinations of resistance genes to determine the best strategy for combating the widespread increase in virulent SCN and limit future nematode adaptation to resistant cultivars. Eight SCN populations were developed by continuous selection of a virulent SCN field population (Heterodera glycines [HG] type 1.2.5.7) on a single resistance source or in rotation with soybean pyramiding different resistance gene alleles derived from PI 88788 (rhg1-b), PI 437654 (rhg1-a and Rhg4), PI 468916 (cqSCN-006 and cqSCN-007), and PI 567516C (Chr10). SCN population densities were determined for eight generations. HG type tests were conducted after the eighth generation to evaluate population shifts. The continued use of rhg1-b or 006/007 had limited effectiveness for reducing SCN type 1.2.5.7 population density, whereas rotation to the use of rhg1-a/Rhg4 resistance significantly reduced SCN population density but selected for broader SCN virulence (HG type 1.2.3.5.6.7). A rotation of rhg1-a/Rhg4 with a pyramid of rhg1-b/006/007/Chr10 was the most effective combination at both reducing population density and minimizing selection pressure. Our results provide guidance for implementation of a strategic SCN resistance rotation plan to manage the widespread virulence on PI 88788 and sustain the future durability of SCN resistance genes.

Impact of Wheat on Soybean Cyst Nematode Population Density in Double-Cropping Soybean Production.

Double-cropping is defined as producing more than one crop on the same parcel of land in a single growing season. It is reported to have many benefits when incorporated in cropping systems, including improving soil health. In some double-cropping systems, soybean is planted following winter wheat. The soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is a major soybean pathogen, and several reports suggest suppressive effects of wheat on SCN populations. Field trials were conducted from 2017 to 2018 to investigate the effect of wheat on SCN populations in double-cropping soybean. Nine fields with three levels of initial SCN populations (low, moderate, and high) were selected in Illinois. Wheat was planted in strips alternating with strips-maintained weed-free and under fallow over winter and early spring. Soybean was planted in all strips after wheat harvest. SCN egg densities were acquired at four time points: wheat establishment, post-wheat/pre-soybean, mid-soybean (R1 growth stage or beginning of flowering), and post-soybean harvest. Wheat strips reduced SCN egg densities compared with fallow strips at the R1 stage (−31.8%) and after soybean harvest (−32.7%). Double-cropping soybean with wheat has the potential to suppress SCN field populations and is a system with the potential to provide additional farm income. This study is meant to be a first step toward a better understanding of the mechanisms that govern the suppression of SCN by wheat.

Robotic agricultural instrument for automated extraction of nematode cysts and eggs from soil to improve integrated pest management

Soybeans are an important crop for global food security. Every year, soybean yields are reduced by numerous soybean diseases, particularly the soybean cyst nematode (SCN). It is difficult to visually identify the presence of SCN in the field, let alone its population densities or numbers, as there are no obvious aboveground disease symptoms. The only definitive way to assess SCN population densities is to directly extract the SCN cysts from soil and then extract the eggs from cysts and count them. Extraction is typically conducted in commercial soil analysis laboratories and university plant diagnostic clinics and involves repeated steps of sieving, washing, collecting, grinding, and cleaning. Here we present a robotic instrument to reproduce and automate the functions of the conventional methods to extract nematode cysts from soil and subsequently extract eggs from the recovered nematode cysts. We incorporated mechanisms to actuate the stage system, manipulate positions of individual sieves using the gripper, recover cysts and cyst-sized objects from soil suspended in water, and grind the cysts to release their eggs. All system functions are controlled and operated by a touchscreen interface software. The performance of the robotic instrument is evaluated using soil samples infested with SCN from two farms at different locations and results were comparable to the conventional technique. Our new technology brings the benefits of automation to SCN soil diagnostics, a step towards long-term integrated pest management of this serious soybean pest.

Genomic Profiling of Virulence in the Soybean Cyst Nematode Using Single-Nematode Sequencing.

Soybean cyst nematode (SCN) is one of the most important diseases in soybean. Currently, the main management strategy relies on planting resistant cultivars. However, the overuse of a single resistance source has led to the selection of virulent SCN populations, although the mechanisms by which the nematode overcomes the resistance genes remain unknown. In this study, we used a nematode-adapted single-cell RNA-seq approach to identify SCN genes potentially involved in resistance breakdown in Peking and PI 88788 parental soybean lines. We established for the first time the full transcriptome of single SCN individuals allowing us to identify a list of putative virulence genes against both major SCN resistance sources. Our analysis identified 48 differentially expressed putative effectors (secreted proteins required for infection) alongside 40 effectors showing evidence of novel structural variants, and 11 effector genes containing phenotype-specific sequence polymorphisms. Additionally, a differential expression analysis revealed an interesting phenomenon of coexpressed gene regions with some containing putative effectors. The selection of virulent SCN individuals on Peking resulted in a profoundly altered transcriptome, especially for genes known to be involved in parasitism. Several sequence polymorphisms were also specific to these virulent nematodes and could potentially play a role in the acquisition of nematode virulence. On the other hand, the transcriptome of virulent individuals on PI 88788 was very similar to avirulent ones with the exception of a few genes, which suggest a distinct virulence strategy to Peking.

Genetic diversity of Soybean Cyst Nematode (Heterodera glycines) populations in Southeastern Goiás state, Brasil

Heterodera glycines, also known as Soybean Cyst Nematode (SCN), is one of the phytosanitary issues that prevents high soybean yields (Glycine max) due to its dissemination capacity and high physiological race variability. The first step towards the proper and safe use of resistant cultivars lies on correctly identifying the physiological race of this nematode in the crop in order to avoid new breed-selection pressure. Thus, the aim of the present study was to genetically characterize the races of Heterodera glycines populations from soybean-producer counties belonging to the Railroad (Estrada de Ferro) Region (Goiás State, Brazil), as well as to investigate their molecular characterization based on RAPD markers. RAPD data were evaluated in a binary way, in which values (1) and (0) were attributed to the presence and absence of amplified bands for each primer, respectively. The binary matrix was used to estimate the genetic distance between populations, based on the Jaccard dissimilarity index. The clustering analysis was carried out based on the calculated genetic dissimilarity matrix, according to Ward’s method. Eight (8) different physiological Heterodera glycines races were found in the investigated counties. Only 10 out of 28 RAPD primers were polymorphic among SCN populations, whereas the remaining primers either did not amplify, or presented low amplification of the DNA fragment. Five genetically-different groups were recorded among H. glycines population accessions, which presented high genetic variability rate.

Targeted suppression of soybean BAG6-induced cell death in yeast by soybean cyst nematode effectors.

While numerous effectors that suppress plant immunity have been identified from bacteria, fungi, and oomycete pathogens, relatively little is known for nematode effectors. Several dozen effectors have been reported from the soybean cyst nematode (SCN). Previous studies suggest that a hypersensitive response‐like programmed cell death is triggered at nematode feeding sites in soybean during an incompatible interaction. However, virulent SCN populations overcome this incompatibility using unknown mechanisms. A soybean BAG6 (Bcl‐2 associated anthanogene 6) gene previously reported by us to be highly up‐regulated in degenerating feeding sites induced by SCN in a resistant soybean line was attenuated in response to a virulent SCN population. We show that GmBAG6‐1 induces cell death in yeast like its Arabidopsis homolog AtBAG6 and also in soybean. This led us to hypothesize that virulent SCN may target GmBAG6‐1 as part of their strategy to overcome soybean defence responses during infection. Thus, we used a yeast viability assay to screen SCN effector candidates for their ability to specifically suppress GmBAG6‐1‐induced cell death. We identified several effectors that strongly suppressed cell death mediated by GmBAG6‐1. Two effectors identified as suppressors showed direct interaction with GmBAG6‐1 in yeast, suggesting that one mechanism of cell death suppression may occur through an interaction with this host protein.

Dynamics of Population Density and Virulence Phenotype of the Soybean Cyst Nematode as Influenced by Resistance Source Sequence and Tillage.

The soybean cyst nematode (SCN), Heterodera glycines, is the most damaging pathogen of soybean. Use of resistant cultivars is an effective strategy to manage SCN, but it also selects for virulent populations over time. A 12-year field experiment was initiated in 2003 to study how tillage and 11 different sequences of four cultivars impact SCN population dynamics and virulence. An SCN-susceptible cultivar and three resistant cultivars (R1, R2, and R3 derived from cultivars PI 88788, Peking, and PI 437654, respectively) were used. Tillage had minimal effect on SCN population density. Compared with no till, conventional tillage resulted in a faster increase of SCN virulence to Peking when the SCN was selected by R2 and virulence to PI 88788 by R3. Among the three SCN-resistant cultivars, R1 supported the greatest population density, R2 supported intermediate population density, and R3 supported the least SCN population density. The SCN populations selected by R1 overcame the resistance in PI 88788 but not in Peking and PI 437654. R2 selected SCN populations that overcame the resistance in Peking but not in PI 88788 and PI 437654. In contrast, R3 selected SCN populations that overcame both PI 88788 and Peking sources of resistance. There was no increase of virulence to PI 437654 in any cultivar sequence. R1 in rotation with R2 or R3 had a negative effect on female index on Peking. Susceptible soybean reduced SCN virulence to Peking, indicating that there was fitness cost of the Peking virulent SCN type. These results suggest that rotation of Peking with PI 88788 is a good strategy for managing the SCN, and susceptible cultivar and no till may reduce SCN virulence selection pressure in some rotations.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Characterizing resistance to soybean cyst nematode in PI 494182, an early maturing soybean accession

AbstractThe soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) generates more damage to soybean [Glycine max (L.) Merr.] than any other parasite in most soybean‐producing countries. The use of SCN‐resistant cultivars remains the most effective method to limit losses caused by SCN. The SCN‐resistant accession PI 88788 has been used almost exclusively to control SCN over the past decades, inducing a shift in nematode virulence to overcome the resistance. Furthermore, PI 88788 and other sources of resistance characterized to date belong to maturity groups (MGs) III and higher, making them less attractive to develop early maturing soybean varieties (MGs 0‐000). In this work, we performed a quantitative trait loci (QTL) analysis of the SCN‐resistant soybean accession PI 494182 (MG 0). A recombinant inbred lines (RILs) population (‘Costaud’ × PI 494182) segregating for SCN resistance was challenged with SCN (H. glycines [HG] type 0) and genotyped via genotyping‐by‐sequencing (GBS) to produce a genetic map. Six resistance QTL were identified, including a potentially new resistance locus on chromosome 07. A subset of the RIL population was confronted to a HG type 2.5.7 SCN population and some of these exhibited resistance toward this type. Whole‐genome sequencing of PI 494182 and Costaud allowed us to determine the alleles and their copy number for three candidate genes: GmSNAP11, GmSNAP18 (Rhg1), and GmSHMT08 (Rhg4). Finally, we determined that selecting for PI 494182 alleles at some SCN‐resistance QTL could entail linkage drag (decrease in protein concentration and 100‐seed weight, increase in oil concentration). This work provides useful markers for introgressing SCN resistance in early maturing soybean varieties.

Effects of ILeVO Seed Treatment on Heterodera glycines Reproduction and Soybean Yield in Small-Plot and Strip-Trial Experiments in Iowa.

ILeVO (fluopyram) is a fungicide seed treatment for soybean sudden death syndrome (SDS) that also has nematicidal activity. ILeVO is sold with a base of insecticide Poncho (clothianidin), nematode-protectant VOTiVO (Bacillus firmus), and Acceleron fungicides (metalaxyl, fluxapyroxad, and pyraclostrobin). Yield and reproduction of the soybean cyst nematode (SCN) (Heterodera glycines) on soybean plants grown from seed treated with ILeVO plus the base were compared with those treated with only the base in 27 small-plot experiments and 12 strip-trial experiments across Iowa from 2015 to 2017. To increase the likelihood that yield results were related to effects on SCN, data were used only from 26 small-plot experiments and 12 strip trials in which symptoms of SDS were low or nonexistent. An SCN reproductive factor (RF) was calculated for each experimental unit by dividing the SCN population density at harvest by the population density at planting. ILeVO significantly reduced SCN RF by 50% in one strip-trial experiment and by 36 to 60% in four small-plot experiments but yields were not increased by ILeVO in any of those five experiments. Soybean yields were 2.8 to 3.7 bushels/acre (bu/ac) (188.3 to 248.8 kg/ha) greater with ILeVO in three small-plot experiments but SCN RF was not reduced in those experiments. Also, yield was 1.9 bu/ac (127.8 kg/ha) greater with ILeVO in one strip-trial experiment in 2016 but SCN samples were not collected at harvest from the study to assess the possible effects of ILeVO on SCN reproduction. When strip-trial data from 2015 and 2016 were combined, there was a small but significant 0.8 bu/ac (52.2 kg/ha) yield increase with ILeVO. Overall, the effects of ILeVO on SCN reproduction and soybean yield were variable in these field studies.

Evaluation of diverse cover crops as hosts of two populations of soybean cyst nematode, Heterodera glycines

Soybean cyst nematode (SCN; Heterodera glycines) reproduces on a wide range of plants, including some cover crops. However, reproduction of SCN populations on a number of cover crops has not been investigated in the northern Great Plains. Thirty-five cover crop species/cultivars from four plant families were evaluated as hosts for SCN. Greenhouse evaluations were done with two common SCN populations, SCN103 (HG type 0) and SCN2W (HG type 7) under controlled conditions. The sources of two SCN populations were two soybean fields of North Dakota. After 35 days of growth, white SCN females were extracted from individual plants and counted to determine a female index (FI = average number of females on a tested crop/average number of females in a susceptible check x 100) for each crop. Out of the 35 cover crop species/cultivars tested, at least one of the SCN populations reproduced on seven crops/cultivars but did not reproduce on the other 28 crops/cultivars. Out of these seven crops, only white lupine (Lupinus albus L.) was a suitable host (FI ≥ 10) for both SCN populations in all the experiments, while others showed varied responses from poor host to suitable host for the SCN populations. The host crops were from the family Brassicaceae or Fabaceae, while all the crops in the Linaceae or Poaceae family tested were non-hosts. The non-host crops can be planted in SCN-infested fields without the concern of increasing SCN populations, while poor hosts with low female index should be evaluated for effects on reduction of SCN numbers in the fields before they are used as cover crops in a soybean cropping system.

Fluopyram Suppresses Population Densities of Heterodera glycines in Field and Greenhouse Studies in Michigan.

The soybean cyst nematode (SCN), Heterodera glycines Ichinohe, causes significant damage to soybean production annually. Fluopyram is a fungicide commonly used in soybean seed treatments intended to control soilborne fungal pathogens; however, recent studies have also suggested inhibitory effects on SCN. We examined the effects of a fluopyram seed treatment, ILeVO, on SCN reproduction, sudden death syndrome (SDS) development, and yield in a 3-year field study. Overall, fluopyram had a significant effect on yield (P = 0.046) and end-of-season SCN eggs and second-stage juveniles (Pf, P = 0.033) but no significant effect on SCN reproduction (Rf) or SDS disease index (P > 0.05). Post hoc tests indicated that fluopyram increased yield and suppressed SCN quantities. However, Rf was consistently greater than 1 whether or not the seed was treated with fluopyram, indicating that SCN populations were still increasing in the presence of fluopyram. A follow-up greenhouse study indicated that fluopyram reduced SCN relative to nontreated controls, as observed in the field, but only reduced SCN DNA within roots of a susceptible cultivar. These results indicate that fluopyram can suppress SCN quantities relative to nontreated seed but may not successfully reduce nematode populations without the use of additional management strategies.

Can winter camelina, crambe, and brown mustard reduce soybean cyst nematode populations?

Industrial oilseeds have a great potential in the northern Great Plains both as oilseeds and as cover crops sown following wheat (Triticum aestivum L.) harvest and before soybean [Glycine max (L.) Merr.] sowing in the following spring. One of the most important biotic stresses in soybean production is soybean cyst nematode (Heterodera glycines Ichinohe, SCN), a serious pest that affects 90% of the soybean producing areas in the U.S. The objective of this study was to evaluate the host status of and the SCN population reduction by, winter camelina [Camelina sativa (L.) Crantz, cv. Joelle], crambe (Crambe abyssinica Hochst. Ex R.E.Fr., cv. BelAnn), and brown mustard (Brassica juncea L. cv. Kodiak). The experiments were performed in a growth chamber at 27°C for 35 days by planting the crops in soil naturally infested with SCN and autoclaved sandy soil artificially inoculated with two SCN populations from two fields in North Dakota. Soybean cyst nematode did not reproduce on brown mustard or camelina with a female index (FI) of 0, suggesting these are non-hosts, while it reproduced on crambe. The numbers of white females on crambe ranged from 1 to 13 per plant with FI of 0.2 to 1.1 in naturally infested soils, and 1 to 4 per plant with FI of 1.2 to 2.5 in artificially infested soils, thus crambe would be classified as a poor-host (FI < 10). Brown mustard and winter camelina reduced the SCN populations by an average of 51% and 48%, respectively, while crambe only reduced the populations by an average of 24%, across all the experiments with naturally infested soils when compared with the initial population levels. Both brown mustard and camelina consistently reduced the SCN populations but crambe did not steadily reduce the SCN populations when compared with the non-planted control (fallow). Further understanding the effects of these crops on SCN populations under natural field conditions is needed to determine if cover crops can be used for sustainable SCN management in SCN-infested soybean fields.

The rhg1-a (Rhg1 low-copy) nematode resistance source harbors a copia-family retrotransposon within the Rhg1-encoded α-SNAP gene.

Soybean growers widely use the Resistance to Heterodera glycines 1 (Rhg1) locus to reduce yield losses caused by soybean cyst nematode (SCN). Rhg1 is a tandemly repeated four gene block. Two classes of SCN resistance‐conferring Rhg1 haplotypes are recognized: rhg1‐a (“Peking‐type,” low‐copy number, three or fewer Rhg1 repeats) and rhg1‐b (“PI 88788‐type,” high‐copy number, four or more Rhg1 repeats). The rhg1‐a and rhg1‐b haplotypes encode α‐SNAP (alpha‐Soluble NSF Attachment Protein) variants α‐SNAPRhg1LC and α‐SNAPRhg1HC, respectively, with differing atypical C‐terminal domains, that contribute to SCN resistance. Here we report that rhg1‐a soybean accessions harbor a copia retrotransposon within their Rhg1 Glyma.18G022500 (α‐SNAP‐encoding) gene. We termed this retrotransposon “RAC,” for Rhg1 alpha‐SNAP copia. Soybean carries multiple RAC‐like retrotransposon sequences. The Rhg1 RAC insertion is in the Glyma.18G022500 genes of all true rhg1‐a haplotypes we tested and was not detected in any examined rhg1‐b or Rhg1WT (single‐copy) soybeans. RAC is an intact element residing within intron 1, anti‐sense to the rhg1‐a α‐SNAP open reading frame. RAC has intrinsic promoter activities, but overt impacts of RAC on transgenic α‐SNAPRhg1LC mRNA and protein abundance were not detected. From the native rhg1‐a RAC+ genomic context, elevated α‐SNAPRhg1LC protein abundance was observed in syncytium cells, as was previously observed for α‐SNAPRhg1HC (whose rhg1‐b does not carry RAC). Using a SoySNP50K SNP corresponding with RAC presence, just ~42% of USDA accessions bearing previously identified rhg1‐a SoySNP50K SNP signatures harbor the RAC insertion. Subsequent analysis of several of these putative rhg1‐a accessions lacking RAC revealed that none encoded α‐SNAPRhg1LC, and thus, they are not rhg1‐a. rhg1‐a haplotypes are of rising interest, with Rhg4, for combating SCN populations that exhibit increased virulence against the widely used rhg1‐b resistance. The present study reveals another unexpected structural feature of many Rhg1 loci, and a selectable feature that is predictive of rhg1‐a haplotypes.

Field and greenhouse evaluations of soil suppressiveness to Heterodera glycines in the Midwest corn-soybean production systems.

Soil suppressive to the soybean cyst nematode (SCN), a major yield-limiting pathogen of soybean, plays an important role in biological control. Field and greenhouse experiments were conducted to evaluate the effects of tillage, crop sequence, and biocide application on SCN suppression in corn-soybean cropping systems in Minnesota. The experiment was a split-plot design with no-tillage and conventional tillage as main plots, and six crop-biocide treatments (CRCS, CSCS, SSSS, SSSS + streptomycin, SSSS + captan, and SSSS + formaldehyde – the four letters represent crops in 2009 to 2012, respectively; C is corn, R is SCN-resistant soybean, and S is SCN-susceptible soybean) as subplots with four replicates. Soil samples were taken from each plot at planting, midseason, and harvest each year for SCN egg counts, and soybean yield was determined. In addition, soil samples collected from each plot at midseason were assayed for suppressiveness to SCN. Tillage had minimal effect on SCN population density and soybean yield. Annual rotation with corn reduced SCN population density, but also reduced soil suppressiveness as SCN egg population density increased in the following SCN-susceptible soybean compared with soybean monoculture. Rotation with SCN-resistant soybean and corn was the most effective in reducing SCN population density. The bactericide streptomycin did not affect SCN populations but the fungicide captan increased SCN population density. The biocide formaldehyde was the most effective in reducing the level of suppressiveness to SCN. The greenhouse study confirmed that the soil was suppressive to SCN, but failed to detect effects of tillage, crop sequence, and biocide field treatments. This study demonstrated that the soil in the fields was suppressive to the SCN, and biological agents, especially fungal antagonists, were involved in nematode suppression.

SCNBase: a genomics portal for the soybean cyst nematode (Heterodera glycines).

Soybean is an important worldwide crop, and farmers continue to experience significant yield loss due to the soybean cyst nematode (SCN), Heterodera glycines. This soil-borne roundworm parasite is rated the most important pathogen problem in soybean production. The infective nematodes enter into complex interactions with their host plant by inducing the development of specialized plant feeding cells that provide the parasites with nourishment. Addressing the SCN problem will require the development of genomic resources and a global collaboration of scientists to analyze and use these resources. SCNBase.org was designed as a collaborative hub for the SCN genome. All data and analyses are downloadable and can be analyzed with three integrated genomic tools: JBrowse, Feature Search and BLAST. At the time of this writing, a number of genomic and transcriptomic data sets are already available, with 43 JBrowse tracks and 21 category pages describing SCN genomic analyses on gene predictions, transcriptome and read alignments, effector-like genes, expansion and contraction of genomic repeats, orthology and synteny with related nematode species, Single Nucleotide Polymorphism (SNPs) from 15 SCN populations and novel splice sites. Standard functional gene annotations were supplemented with orthologous gene annotations using a comparison to nine related plant-parasitic nematodes, thereby enabling functional annotations for 85% of genes. These annotations led to a greater grasp on the SCN effectorome, which include over 3324 putative effector genes. By designing SCNBase as a hub, future research findings and genomic resources can easily be uploaded and made available for use by others with minimal needs for further curation. By providing these resources to nematode research community, scientists will be empowered to develop novel, more effective SCN management tools.

Genome Scans Reveal Homogenization and Local Adaptations in Populations of the Soybean Cyst Nematode.

Determining the adaptive potential of alien invasive species in a new environment is a key concern for risk assessment. As climate change is affecting local climatic conditions, widespread modifications in species distribution are expected. Therefore, the genetic mechanisms underlying local adaptations must be understood in order to predict future species distribution. The soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is a major pathogen of soybean that was accidentally introduced in most soybean-producing countries. In this study, we explored patterns of genetic exchange between North American populations of SCN and the effect of isolation by geographical distance. Genotyping-by-sequencing was used to sequence and compare 64 SCN populations from the United States and Canada. At large scale, only a weak correlation was found between genetic distance (Wright's fixation index, FST) and geographic distance, but local effects were strong in recently infested states. Our results also showed a high level of genetic differentiation within some populations, allowing them to adapt to new environments and become established in new soybean-producing areas. Bayesian genome scan methods identified 15 loci under selection for climatic or geographic co-variables. Among these loci, two non-synonymous mutations were detected in SMAD-4 (mothers against decapentaplegic homolog 4) and DOP-3 (dopamine receptor 3). High-impact variants linked to these loci by genetic hitchhiking were also highlighted as putatively involved in local adaptation of SCN populations to new environments. Overall, it appears that strong selective pressure by resistant cultivars is causing a large scale homogenization with virulent populations.

Microbial communities in soils with different population densities of soybean cyst nematode

The relationship of abiotic factors with soybean cyst nematode (SCN), the most damaging pathogen of soybean, has been studied extensively, but characterization of microbial communities in infested soils and on soybean roots under field conditions remains unknown. This study investigated the relationship of different SCN population density levels with soil physical, chemical and microbial properties in soils and on soybean roots. A commercial soybean field with different levels of SCN densities (low, medium, high) was sampled, and microbial communities were characterized using both dilution plating assays and molecular approaches. Population densities of species of Trichoderma, actinomycetes, Pseudomonas and other bacteria were significantly higher (P ≤ 0.05) in soils with low SCN (SCN-C) compared with high (SCN-A) and medium levels (SCN-B). Diversity indices of Trichoderma communities on roots based on denaturing gradient gel electrophoresis (DGGE) were significantly higher in soils with SCN-C compared with SCN-A and SCN-B. Cluster analyses and canonical correspondence analysis (CCA) generally separated microbial communities into three groups based on different SCN levels, and CCA showed that low SCN population levels were positively correlated with high levels of nitrogen (N), potassium (K), calcium (Ca), magnesium (Mg), sodium (Na), cation exchange capacity (CEC), base saturation (BS), the populations of Trichoderma and bacteria. Moreover, diverse Trichoderma, Pseudomonas, Bacillus and actinomycetes were found on roots in SCN-C soils based on dilution plating and DGGE, suggesting that the presence of these microbes on soybean roots might be associated with improved plant health and reduction of SCN.