A Predictive Risk Model Analysis of the Potato Cyst Nematode Globodera pallida in Idaho
J. Bertrand Contina (University of Idaho); Louise-Marie Dandurand (University of Idaho); Guy R. Knudsen (University of Idaho)
Globodera pallida is a major nematode pest of potato (Solanum tuberosum) and is of great economic importance for the potato industry. Assessing potato yield loss caused by the Idaho G. pallida population under field conditions was not performed due to its quarantine status in Idaho, where it is prohibited by regulatory statutes to grow potato in any infested fields. The experimental data came from three trials that were conducted under greenhouse conditions. A predictive risk model analysis was performed to: (i) determine the effect of the Idaho population of G. pallida on potato yield; (ii) estimate reproduction rate from different initial nematode densities; and (iii) simulate potato yield losses in Idaho field conditions by integrating the coefficients of potato yield into the SUBSTOR-DSSAT crop simulation model. Experiments were conducted under greenhouse conditions using five initial G. pallida soil infestation levels (0, 10, 20, 40, and 80 eggs/g soil). The coefficients of potato yield achieved under each initial nematode density were integrated into the SUBSTOR-DSSAT potato growth simulation model. The model showed that tuber weight reached a maximum yield of 96 ton/ha in noninfested soil. Based on the greenhouse trials, the model predicted a minimum yield of 12 and 58 ton/ha in trial 1 and trial 2/3 respectively, when initial nematode density was 80 eggs/g soil. In trial 1, tuber weight was significantly reduced by 44% at 40 eggs/g soil and by 87% at 80 eggs/g soil, and 20% at 40 eggs/g soil and by 39% at 80 eggs/g soil in trial 2/3. The outputs of this study should facilitate common understanding between regulators, policymakers, and potato growers on the challenges and opportunities for controlling this economically important pest in Idaho.
Contina, J. B., L. M. Dandurand, and G. R. Knudsen. 2019. A predictive Risk Model Analysis of the Potato Cyst Nematode Globodera pallida in Idaho. Plant Disease 103:3117-3128. https://doi.org/10.1094/PDIS-04-19-0717-RE
A Spatiotemporal Analysis and Dispersal Patterns of the Potato Cyst Nematode, Globodera pallida, in Idaho.
Jean Bertrand Contina (University of Idaho); Louise-Marie Dandurand (University of Idaho); Guy R. Knudsen (University of Idaho)
The potato cyst nematode, Globodera pallida, is a globally regulated potato pest. Detected in the U.S. in the state of Idaho in 2006, the infestation, as of February 2019, is limited to 1,326 hectares. Globodera pallida is an obligate sedentary endoparasite that reduces yields up to 80% and is spread through movement of soil, tubers or equipment. The objectives of this study were to describe the spatiotemporal pattern of G. pallida in infested fields and to model its dispersal patterns in Idaho. We used geostatistical tools and simulation models for mapping and description of the relationships between G. pallida incidence and spatial configurations. We found that the nematode is spatially clustered, prevalent around field edges, and its dispersal pattern followed the direction of cultivation. The absence of potato in an infested field significantly reduced the number of cysts sampled each year subsequent to the initial delimitation sampling in 2007. Phytosanitary measures prohibiting potato contributed in stopping nematode reproduction, and the use of chemical fumigants and biofumigant cover crops contributed to a significant reduction in egg viability. We observed a process of a non-linear decline in the prevalence of cysts as the distance separation from the primary infestation focus increased. A power-law model was used to fit G. pallida dispersal capabilities. This study contributed in describing G. pallida infestation for Idaho and provided information on the spatial pattern and landscape ecology of G. pallida in Idaho to facilitate common understandings on the challenges and opportunities for controlling this pest in Idaho.
Contina, J. B., L. M. Dandurand, and G. R. Knudsen. 2019. A Spatiotemporal Analysis and Dispersal Patterns of the Potato Cyst Nematode, Globodera pallida, in Idaho. Phytopathology. https://doi.org/10.1094/PHYTO-04-19-0113-R
Evaluation of Fluorescent Stains for Viability Assessment of the Potato Cyst Nematodes Globodera pallida and G. ellingtonae
Syamkumar Sivasankara Pillai (University of Idaho); Louise-Marie Dandurand (University of Idaho)
Potato cyst nematodes (PCNs), Globodera pallida and Globodera rostochiensis, are quarantine pests of potato which cause significant damage to production and farm gate revenue worldwide. Accurately assessing viability of PCN eggs is important for eradication and management programs. The goal of this study was to develop a quick and reliable fluorescent staining method to evaluate viability of G. pallida and Globodera ellingtonae eggs. The staining efficiency of eight fluorescent stains was evaluated using G. pallida eggs compared with the conventional Meldola’s Blue (MB) staining method. The staining efficiency of the fluorescent stains ranged from 80.33 ± 2.99 (Sytox Green) to 100% (Acridine Orange) for non-viable eggs. Two stains were further evaluated for their efficiency in assessing viability of encysted eggs from five different greenhouse-reared G. pallida cyst sources which contained both viable and non-viable eggs. For the G. pallida cyst sources, viability ofencysted eggs were estimated to be 41.02 ± 3.81 to 62.66% ± 3.12% when stained with Acridine Orange (AO) and 79.52% ± 1.54% viability for G. ellingtonae. Both staining time and stain concentration were significant for staining efficiency of released and encysted eggs. Staining time and concentration were optimized for released eggs at 4 h at 10 μg/ml and for encysted eggs at 16 h at 25 μg/ml respectively for AO. Fluorescent stains accurately and rapidly assessed percent egg viability and were determined to be as sensitive as a seven-day incubation with the Meldola’s Blue staining method.
Pillai, S. S., and L. M. Dandurand. 2019. Evaluation of Fluorescent Stains for Viability Assessment of the Potato Cyst Nematodes Globodera pallida and G. ellingtonae. Advances in Bioscience and Biotechnology, 10:244-258. DOI: 10.4236/abb.2019.108019
"Piler Dirt" Survey for the Sampling and Detection of Potato Cyst Nematodes
Benjamin Mimee (Agriculture and Agri-Food Canada); Nathalie Dauphinais (Agriculture and Agri-Food Canada); Guy Bélair (Agriculture and Agri-Food Canada)
Potato cyst nematodes are a significant threat to potato production worldwide and have important economic impacts due to yield losses but also because of the expenses associated with regulation procedures. In order to reduce the sampling labor, an alternative strategy named the “Piler Dirt” that collects the soil carried with potato tubers during their transfer to storage was proposed. The method showed a better sensitivity than the reference method to detect fields infested with G. rostochiensis. The quantification of the number of cysts per kilogram of soil was proportional between the two methods at low and moderate population densities (R2 = 0.885) but no correlations were found at high density. However, the quantity of soil generated by the method was exceedingly large to be treated by diagnostic labs. It was shown that subsampling six aliquots, each equivalent to 5,000 cm3/ha, from the total quantity of soil generated by the Piler Dirt method, resulted in a probability of 97% to detect infested fields, 95% of the time in our dataset. Overall, Piler Dirt appears as a good compromise to reduce labor time and cost without significantly affecting sensitivity. However, it will be challenging to implement because it needs to be done simultaneously with harvest and will require the participation of farmers during a busy period.
Mimee, B., N. Dauphinais, and G.Bélair. 2019. "Piler Dirt" Survey for the Sampling and Detection of Potato Cyst Nematodes. Plant Dis 2019 https://doi.org/10.1094/PDIS-12-18-2188-RE
What determines host specificity in hyperspecialized plant parasitic nematodes?
Michael Sabeh (Agriculture and Agri-Food Canada); Etienne Lord (Agriculture and Agri-Food Canada); Marc St-Arnaud (University of Montreal); Benjamin Mimee (Agriculture and Agri-Food Canada)
In hyperspecialized parasites, the ability to grow on a particular host relies on specific virulence factors called effectors. These excreted proteins are involved in the molecular mechanisms of parasitism and distinguish virulent pathogens from non-virulent related species. The potato cyst nematodes (PCN) Globodera rostochiensis and G. pallida are major plant-parasitic nematodes developing on numerous solanaceous species including potato. Their close relatives, G. tabacum and G. mexicana are stimulated by potato root diffusate but unable to establish a feeding site on this plant host.
RNA sequencing was used to characterize transcriptomic differences among these four Globodera species and to identify genes associated with host specificity. We identified seven transcripts that were unique to PCN species, including a protein involved in ubiquitination. We also found 545 genes that were differentially expressed between PCN and non-PCN species, including 78 genes coding for effector proteins, which represent more than a 6-fold enrichment compared to the whole transcriptome. Gene polymorphism analysis identified 359 homozygous non-synonymous variants showing a strong evidence for selection in PCN species.
Overall, we demonstrated that the determinant of host specificity resides in the regulation of essential effector gene expression that could be under the control of a single or of very few regulatory genes. Such genes are therefore promising targets for the development of novel and more sustainable resistances against potato cyst nematodes.
Sabeh, M., E. Lord, É. Grenier, M, St-Arnaud, and B. Mimee. 2019. What determines host specificity in hyperspecialized plant parasitic nematodes? BMC Genomics 20:457 https://doi.org/10.1186/s12864-019-5853-4
Transcriptome-wide selection of a reliable set of reference genes for gene expression studies in potato cyst nematodes (Globodera spp.).
Relative gene expression analyses by qRT-PCR (quantitative reverse transcription PCR) require an internal control to normalize the expression data of genes of interest and eliminate the unwanted variation introduced by sample preparation. A perfect reference gene should have a constant expression level under all the experimental conditions. However, the same few housekeeping genes selected from the literature or successfully used in previous unrelated experiments are often routinely used in new conditions without proper validation of their stability across treatments. The advent of RNA-Seq and the availability of public datasets for numerous organisms are opening the way to finding better reference genes for expression studies. Globodera rostochiensis is a plant-parasitic nematode that is particularly yield-limiting for potato. The aim of our study was to identify a reliable set of reference genes to study G. rostochiensis gene expression. Gene expression levels from an RNA-Seq database were used to identify putative reference genes and were validated with qRT-PCR analysis. Three genes, GR, PMP-3, and aaRS, were found to be very stable within the experimental conditions of this study and are proposed as reference genes for future work.
Sabeh, M., Duceppe, M. O., St-Arnaud, M., & Mimee, B. (2018). Transcriptome-wide selection of a reliable set of reference genes for gene expression studies in potato cyst nematodes (Globodera spp.). PloS one, 13(3), e0193840. DOI:10.137/journal.pone.0193840.
An Evaluation of two H1-Linked Markers and their Suitability for Selecting Globodera rostochiensis Resistant Potatoes in the New York Breeding Program
Jaebum Park; Huijun Yang; Walter S. De Jong; Xiaohong Wang
The golden cyst nematode (Globodera rostochiensis) is a serious pest that can dramatically reduce potato crop yield. Pathotype Ro1 of G. rostochiensis was first detected in the United States in 1941 and is still present on several farms in New York State. The H1 gene confers high levels of resistance to pathotype Ro1 but screening for it with a bioassay is time consuming and expensive. In this study two known molecular markers, 57R and TG689, were evaluated for their ability to identify resistant clones among 38 global cultivars and 350 New York breeding clones. The ability of either marker to predict resistance was high – 99.7% and 98.3% for 57R and TG689, respectively – but the ability to predict susceptibility was much lower, 47% and 41%, respectively. As resistance is the trait of interest, either of these markers is sufficient to make selection decisions in a practical breeding program. Cases exhibiting discordance between presence/absence of diagnostic markers and bioassay results were investigated further. Recombination, inflow of other resistance genes, and occasional failure of marker- and/or bio-assays are discussed as potential causes.
Park, J., H. Yang, W. S. De Jong, X. Wang. 2018. An Evaluation of two H1-Linked Markers and their Suitability for Selecting Globodera rostochiensis Resistant Potatoes in the New York Breeding Program. American Journal of Potato Research. https://link.springer.com/article/10.1007/s12230-017-9623-z
A qRT-PCR method to evaluate viability of potato cyst nematode (Globodera spp.)
Benjamin Mimee; Brahim Soufiane; Nathalie Dauphinais; Guy Bélair
One of the main challenges to PCN management is the ability of PCN to remain dormant in the soil for several decades. For that reason, many countries have strict quarantine regulations for PCN. These regulations, although expensive and restrictive for growers, are necessary to prevent further spread of PCN but should be lifted when no more viable cysts are found. Here, we report a promising qRT-PCR method for the quantification of viable eggs and propose that this method be included in routine testing. The method was successful for quantifying G. ellingtonae, G. rostochiensis and G. pallida and was found to be very sensitive with the systematic detection of a single larva.
Citation: Mimee, B., B. Soufiane, N. Dauphinais, and G. Bélair. 2017. A qRT-PCR method to evaluate viability of potato cyst nematode (Globodera spp.). Canadian Journal of Plant Pathology. http://dx.doi.org/10.1080/07060661.2017.1382574
Analysis of survival and hatching transcriptomes from potato cyst nematodes, Globodera rostochiensis and G. pallida
Marc-Olivier Duceppe ; Joël Lafond-Lapalme; Juan Emilio Palomares-Rius; Michaël Sabeh; Vivian Blok; Peter Moffet; Benjamin Mimee
Citation: Duceppe, M.-O., J. Lafond-Lapalme, J. E. Palomares-Rius, M. Sabeh, V. Blok, P. Moffett, and B. Mimee. 2017. Analysis of survival and hatching transcriptomes from potato cyst nematodes, Globodera rostochiensis and G. pallida. Scientific Reports 7, Article number: 3882. doi:10.1038/s41598-017-03871-x
The Draft Genome of Globodera ellingtonae
Wendy S. Phillips; Danna K. Howe; Amanda M.V. Brown; Sebastian Eves-Van Den Akker; Levi Dettwyler; Amy B. Peetz; Dee R. Denver; and Inga A. Zasada
Globodera ellingtonae is a newly described potato cyst nematode (PCN) found in Idaho, Oregon, and Argentina. Here, we present a genome assembly for G. ellingtonae, a relative of the quarantine nematodes G. pallida and G. rostochiensis, produced using data from Illumina and Pacific Biosciences DNA sequencing technologies.
Phillips, W. S., Howe, D. K., Brown, A. M. V., Eves-van den Akker, S., Dettwyler, L., Peetz, A. B., Denver, R.E., Zasada, I. A. (2017). The Draft Genome of Globodera ellingtonae. Journal of Nematology, 49(2), 127–128. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5507130/