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

2020 ◽  
pp. PHYTO-08-20-034 ◽  
Author(s):  
Dave T. Ste-Croix ◽  
Anne-Frédérique Gendron St-Marseille ◽  
Etienne Lord ◽  
Richard R. Bélanger ◽  
Jacques Brodeur ◽  
...  
Keyword(s):  
Soybean Cyst Nematode ◽  
Differential Expression Analysis ◽  
Cyst Nematode ◽  
Interesting Phenomenon ◽  
Specific Sequence ◽  
Sequence Polymorphisms ◽  
Resistance Breakdown ◽  
Pi 88788 ◽  
Nematode Virulence ◽  
Selection Of

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.

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

Plant Disease ◽  
2021 ◽  
Author(s):  
Clinton Meinhardt ◽  
Amanda Howland ◽  
Mark Ellersieck ◽  
Andrew Scaboo ◽  
Brian Diers ◽  
...  
Keyword(s):  
Population Density ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Soybean Cyst Nematode ◽  
Cyst Nematode ◽  
Single Type ◽  
Resistant Cultivars ◽  
Scn Resistance ◽  
Pi 88788 ◽  
Selection Of

Soybean cyst nematode (SCN) is an important pathogen of soybean causing more than $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 introductions (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 US. The widespread use of PI 88788 rhg1-b has led to limited options for farmers to rotate resistance sources to manage SCN. Consequently, an over reliance 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 either continuous selection of a virulent SCN field population (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.

scholarly journals A SNARE-Like Protein and Biotin Are Implicated in Soybean Cyst Nematode Virulence

PLoS ONE ◽  
2015 ◽  
Vol 10 (12) ◽  
pp. e0145601 ◽  
Author(s):  
Sadia Bekal ◽  
Leslie L. Domier ◽  
Biruk Gonfa ◽  
Naoufal Lakhssassi ◽  
Khalid Meksem ◽  
...  
Keyword(s):  
Soybean Cyst Nematode ◽  
Cyst Nematode ◽  
Nematode Virulence

scholarly journals Marker-assisted selection strategies for developing resistant soybean plants to cyst nematode

2014 ◽  
Vol 14 (3) ◽  
pp. 180-186 ◽  
Author(s):  
Fernanda Abreu Santana ◽  
Martha Freire da Silva ◽  
Julierme Kellen Freitas Guimarães ◽  
Marcia Flores da Silva Ferreira ◽  
Waldir Dias Pereira ◽  
...  
Keyword(s):  
Marker Assisted Selection ◽  
Soybean Cyst Nematode ◽  
Cyst Nematode ◽  
Selection Strategies ◽  
Resistant Lines ◽  
Resistance Trait ◽  
Scn Resistance ◽  
Soybean Plants ◽  
Moderate Resistance ◽  
Selection Of

Resistant lines can be identified by marker-assisted selection(MAS), based on alleles of genetic markers linked to the resistance trait. This reduces the number of phenotypically evaluated lines, one of the limitations in the development of cultivars with resistance to soybean cyst nematode (SCN).This study evaluated the efficiency of microsatellites near quantitative traitloci (QTL) for SCN resistance, in the linkage groups (LG) G and A2 of soybean, for the selection of resistant genotypes in populations originated from crosses between the cultivars Vmax and CD201. The QTL of LG A2 was not detected in 'Vmax' (derived from PI 88788). In MAS, the microsatellites of LG G were efficient in selecting F6:7 families with resistance and moderate resistance to SCN race 3. The selection efficiency of the microsatellites Sat_168, Satt309 and Sat_141 was greater than 93%.

scholarly journals Increase in Soybean Cyst Nematode Virulence and Reproduction on Resistant Soybean Varieties in Iowa From 2001 to 2015 and the Effects on Soybean Yields

2017 ◽  
Vol 18 (3) ◽  
pp. 146-155 ◽  
Author(s):  
Michael T. McCarville ◽  
Christopher C. Marett ◽  
Mark P. Mullaney ◽  
Gregory D. Gebhart ◽  
Gregory L. Tylka
Keyword(s):  
Soybean Cyst Nematode ◽  
Field Experiments ◽  
Yield Loss ◽  
Plant Introduction ◽  
Cyst Nematode ◽  
Population Densities ◽  
Sources Of Resistance ◽  
Nematode Reproduction ◽  
Soybean Yield ◽  
Pi 88788

Management of the soybean cyst nematode (SCN) relies heavily on use of SCN-resistant soybean varieties to limit nematode reproduction and minimize yield loss. For Iowa, almost all SCN-resistant soybean varieties contain SCN resistance genes from a breeding line named Plant Introduction (PI) 88788. Iowa State University conducts experiments to evaluate numerous SCN-resistant and three to four SCN-susceptible soybean varieties in up to nine field experiments across Iowa each year. Data on SCN population density, virulence (SCN race and HG type), soybean yield, precipitation, and growing degree days from more than 25,000 four-row plots in field experiments conducted from 2001 to 2015 were analyzed to determine how these factors affected SCN reproduction and yield. SCN population densities were positively correlated with temperatures and negatively associated with precipitation during the growing seasons, indicating that SCN reproduction was greatest in hot, dry years. Over the years, virulence of SCN populations on PI 88788 increased in the fields in which the experiments were conducted, resulting in increased end-of-season SCN population densities and reduced yields of SCN-resistant soybean varieties with the PI 88788 source of resistance. These results indicate that soybean yield loss caused by SCN on resistant varieties with the common PI 88788 source of resistance likely will increase as virulence of SCN populations increases unless new sources of resistance become widely available and used in the future.

scholarly journals Resistance to Brown Stem Rot in Soybean Germ Plasm with Resistance to the Soybean Cyst Nematode

Plant Disease ◽  
2004 ◽  
Vol 88 (7) ◽  
pp. 761-768 ◽  
Author(s):  
T. J. Hughes ◽  
N. C. Kurtzweil ◽  
B. W. Diers ◽  
C. R. Grau
Keyword(s):  
Soybean Cyst Nematode ◽  
Field Experiments ◽  
Germ Plasm ◽  
Cyst Nematode ◽  
Stem Rot ◽  
Brown Stem Rot ◽  
Resistant Cultivars ◽  
Greenhouse Experiments ◽  
Scn Resistance ◽  
Pi 88788

The soybean cyst nematode (SCN) and Phialophora gregata f. sp. sojae, the causal agent of brown stem rot (BSR), are two pathogens of soybean commonly found in the same field throughout the north-central United States. Field experiments designed to study the role of SCN-resistant germ plasm in soybean production have led to data suggesting that some sources of SCN resistance also may provide resistance to BSR. Soybean germ plasm with resistance to SCN was evaluated in greenhouse and field environments for resistance to BSR development based on the percentage of host tissue symptomatic of BSR. Comparison of SCN-resistant cultivars and plant introductions (PI) to standard BSR-resistant and -susceptible checks were conducted in two greenhouse experiments using a root-dip inoculation with a single isolate of P. gregata. For both greenhouse experiments, PI 209332 was the only source of SCN resistance with resistance to BSR similar to standard BSR-resistant checks. Nine other sources of SCN resistance, including PI 88788 and Peking, expressed BSR symptom severity similar to BSR-susceptible checks. Cultivars derived from most SCN-resistant sources, including PI 209332, also were susceptible to BSR development, while four of the five cultivars derived from PI 88788 were highly resistant to BSR development. SCN-resistant cultivars derived from PI 88788, Peking, and PI 209332 were planted along with standard BSR-resistant and -susceptible checks at two field locations naturally infested with P. gregata and SCN or P. gregata alone. As in greenhouse experiments, four of the five cultivars derived from PI 88788 expressed resistance to BSR development equal to or better than standard BSR-resistant checks at both locations. In contrast, cultivars derived from PI 209332 and Peking expressed varying levels of disease development depending on field environment. Yields observed for PI 88788-derived cultivars were higher than BSR-resistant checks regardless of the presence of SCN. Data from both greenhouse and field experiments suggest that cvs. Williams and Williams 82 may contain a gene or genes for BSR resistance that require one or more modifier genes, possibly located in the genome of PI 88788, for complete expression.

scholarly journals Genetic Analysis of Parasitism in the Soybean Cyst Nematode Heterodera glycines

Genetics ◽  
1997 ◽  
Vol 146 (4) ◽  
pp. 1311-1318 ◽  
Author(s):  
Ke Dong ◽  
Charles H Opperman
Keyword(s):  
Genetic Analysis ◽  
Host Range ◽  
Soybean Cyst Nematode ◽  
Heterodera Glycines ◽  
Cyst Nematode ◽  
Generation Progeny ◽  
Pi 88788 ◽  
Parasitism Genes ◽  
Parasitism Gene ◽  
F1 Generation

A genetic analysis of parasitic ability in the soybean cyst nematode Heterodera glycines was performed. To identify and characterize genes involved in parasitism, we developed three highly inbred H. glycines lines, OP20, OP25 and OP50, for use as parents for controlled crosses. Through these crosses, we have identified genes in the inbred parents that control reproduction of the nematode on hosts that carry resistance genes. These genes, designated as ror-* for reproduction on a resistant host, segregate in a normal Mendelian fashion as independent loci. Host range tests of F1 generation progeny indicated that at least one parasitism gene in both the OP20 and OP50 lines for host PI 88788 was dominant. Parasitism genes in OP50 for hosts “Peking” and PI 90763 are recessive. Two types of single female descent populations, a single backcrossed BC1F2-derived and a double backcrossed BC2F1-derived, were established on the susceptible soybean cultivar “Lee 68.” Host range tests for parasitism in these lines demonstrated the presence of two independent genes in OP50, one for host PI 88788 designated ror-1 and one for host PI 90763 designated ror-2. OP20 carries two independent genes for parasitism on PI 88788, designated as alleles kr3 and kr4.

scholarly journals Variability in Distribution and Virulence Phenotypes of Heterodera glycines in Missouri During 2005

Plant Disease ◽  
2007 ◽  
Vol 91 (11) ◽  
pp. 1473-1476 ◽  
Author(s):  
Melissa G. Mitchum ◽  
J. Allen Wrather ◽  
Robert D. Heinz ◽  
J. Grover Shannon ◽  
Gene Danekas
Keyword(s):  
Soybean Cyst Nematode ◽  
Heterodera Glycines ◽  
Cyst Nematode ◽  
Common Source ◽  
Sources Of Resistance ◽  
Resistant Cultivars ◽  
Soybean Cultivars ◽  
Geographical Regions ◽  
Two Samples ◽  
Pi 88788

The soybean cyst nematode, Heterodera glycines, is a serious economic threat to soybean producers in Missouri. Periodic monitoring for the presence, population densities, and virulence phenotypes of H. glycines is essential for determining crop losses and devising management strategies implementing the use of resistant cultivars. A survey using area-frame sampling was conducted to determine the distribution and virulence phenotypes of H. glycines in Missouri during 2005. Two samples from each of 125 fields representing eight geographical regions of Missouri were collected; 243 samples were processed for extraction of cysts and eggs. In all, 49% of samples had detectable cyst nematode populations, which ranged from 138 to 85,250 eggs per 250 cm3 of soil. Race and H. glycines type tests were conducted on populations from 45 samples. Nearly 80% of the populations that were tested, irrespective of the region, were virulent on the indicator line plant introduction (PI) 88788, which is the source of resistance for most H. glycines-resistant cultivars. More than 70% of populations could reproduce on the indicator lines PI 88788, PI 209332, and PI 548316 (Cloud), indicating that soybean cultivars with resistance derived from these sources need to be carefully monitored and used only in rotation with nonhost crops and soybean cultivars with resistance from other sources. Approximately one-third of the populations, primarily in the southern regions of Missouri, could reproduce on PI 548402 (Peking), another common source of resistance. Fewer than 10% of the populations could reproduce on PI 90763, PI 437654, PI 89772, or PI 438489B, suggesting that these sources of resistance should be used in soybean breeding programs to develop H. glycines-resistant soybean cultivars.

scholarly journals First Report of Soybean Cyst Nematode (Heterodera glycines) on Soybean in North Dakota

Plant Disease ◽  
2004 ◽  
Vol 88 (11) ◽  
pp. 1287-1287 ◽  
Author(s):  
C. A. Bradley ◽  
C. R. Biller ◽  
B. D. Nelson
Keyword(s):  
North Dakota ◽  
Soybean Cyst Nematode ◽  
Heterodera Glycines ◽  
Plant Introduction ◽  
Cyst Nematode ◽  
Diagnostic Laboratory ◽  
First Report ◽  
Second Stage ◽  
The North ◽  
Pi 88788

During August 2003, soybean (Glycine max) plants from Richland County, North Dakota with white-to-yellow, lemon-shaped structures on the roots were brought to the North Dakota State University Plant Diagnostic Laboratory. To confirm that the structures were females of a cyst nematode, they were crushed and observed microscopically to determine if nematode eggs and second-stage juveniles were present. Morphology of the second-stage juveniles was consistent with Heterodera glycines, the soybean cyst nematode (SCN). A survey was conducted in soybean fields in 34 km2 around the field in which the samples originated. Ten of twenty fields surveyed had visible females on the roots of plants. Symptoms observed in those fields included patches of stunted, chlorotic, and dead plants. Soil samples were collected from selected areas within eight fields, eggs were extracted using standard soil sieving techniques, and egg numbers were determined. Egg numbers ranged from 550 to 20,000 eggs per 100 cm3 of soil. SCN collected from two different fields, designated as Dwight and LaMars, were used to determine their HG Type. Standardized procedures (1) were used in a growth chamber set at 27°C with 16-h days. Pots in the test were organized in a completely randomized design with three replicates; the test was repeated over time. After 30 days, females were extracted from roots and counted, and a female index (FI) was calculated for each indicator line (1). The mean number of females on susceptible standard cv. Lee 74, was 110. The Dwight SCN population had an FI of 5.3 on plant introduction (PI) 88788, 1.5 on PI 209332, 5.8 on PI 548316 (Cloud), and 0 on all other indicator lines. The LaMars population had an FI of 1.0 on PI 88788, 3.1 on PI 548316 (Cloud), and 0 on all other indicator lines. These results indicate that both SCN populations tested are HG Type 0. To our knowledge, this is the first report of SCN on soybean in North Dakota. Because other hosts of SCN, as well as soybean, are economically important in North Dakota, such as dry edible bean (Phaseolus vulgaris) and dry pea (Pisum sativum), this disease could adversely impact several commodities throughout the state. Reference: (1) T. L. Niblack et al. J. Nematol. 34:279, 2002.

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