Location: Emerging Pests and Pathogens Research
2024 Annual Report
Objectives
Objective 1: Identify and characterize soybean cyst nematode (SCN) populations in newly detected regions in New York. (NP303, C1, PS1B)
Objective 2: Discover and characterize genes and proteins regulating the interactions between potato and its associated pathogens. (NP303, C2, PS2A)
Sub-Objective 2.A: Characterize AIM-containing effector protein-encoding genes from PCN and their associated host proteins contributing to nematode parasitism or virulence.
Sub-Objective 2.B: Investigate a role of autophagy in potato diseases caused by other invasive potato pathogens.
Objective 3: Investigate novel or improved strategies to manage potato cyst nematodes and/or other invasive potato pathogens. (NP303, C3, PS3A)
Sub-Objective 3.A: Determine the resistance of breeding potato clones as well as wild potato clones to G. rostochiensis pathotypes.
Sub-Objective 3.B: Clone the novel R gene present in the broad-spectrum resistant clone Y1-5.
Sub-Objective 3.C: Determine the resistance of wild potato clones to G. pallida.
Approach
In general, nematodes and other invasive pathogens of potato and soybean crops cause severe yield loss, and effective control measures are often lacking. In addition, most nematicides are no longer available; thus alternative control strategies for emerging nematode species and pathotypes are critically needed. New plant biotechnologies will likely provide the basis for the development of novel methods of controlling nematode and other invasive pathogens, but the success of these methods will be dependent upon a complete understanding of the fundamental mechanisms of host-pathogen interactions. One approach is to identify and characterize soybean cyst nematode (SCN) populations in newly detected regions in New York. An extensive statewide SCN survey in NY will be condicted and soli samples will be analyzed to determine SCN population densities. A modified HG type test will be used to determine the virulence phenotypes of selected SCN pouplations. The data on SCN population density and virulence diversity will be used to develop recommendations on SCN management in New York. A second approach is to discover and characterize genes and proteins regulating the interactions between potato and its associated pathogens. AIM-containing effector protein-encoding genes from potato cyst nematodes (PCN) that potentially target the host autophagy machinery will be cloned and characterized by multiple technologies to better understand the function of these effectors in nematode parasitism and virulence. The third approach is to investigate novel or improved strategies to manage potato cyst nematodes and/or other invasive potato pathogens. Working with potato breeders we will continue to use bioassays to evaluate breeding clones and wild potato germplasm for nematode resistance. We will conduct nematode phenotyping of the Y1-5 F1 population and use a RenSeq approach coupled with long-read PacBio SMRT sequencing to identify the novel resistance gene(s) present in the wild potato clone Y1-5. Conceptually novel information on the population dynamics of nematode and other invasive pests of potato and soybean crops, and on host–pathogen interactions will aid in the development of new effective biologically-based disease control strategies. Novel genes and germplasm for disease resistance that are identified will accelerate resistance breeding in potatoes and disease resistant cultivars developed through conventional breeding and genetic engineering can be transferred readily to customers.
Progress Report
Objective 1: Identify and characterize soybean cyst nematode (SCN) populations in newly detected regions in New York.
The soybean cyst nematode (SCN) is consistently the most economically damaging pathogen of soybean, causing tremendous yield loss in the U.S. First detected in New York in 2016, SCN has since spread to at least 36 counties. If left unmanaged, SCN population densities and the potential for yield reduction will keep increasing. Unfortunately, there are often no obvious aboveground symptoms of plant damage caused by SCN, and yield loss may not be readily visible. Thus, regular monitoring of SCN population densities and virulence phenotypes is necessary for developing management strategies based on the use of resistant cultivars. In collaboration with Cornell Cooperation Extension educators, we collected and analyzed fifty-five soil samples from soybean fields in New York. The soil analysis showed that ten field samples contained suspicious nematode cysts. We further conducted bioassay tests to verify the nematode species. The results showed that six of the ten cyst samples could reproduce on susceptible soybean plants, indicating that six fields are infested with SCN. Bioassays will be further conducted to determine the ability of these field populations to reproduce on commonly used resistant soybean cultivars. The knowledge obtained on SCN virulence phenotypes in soybean fields will be used to develop recommendations for SCN management in New York.
Objective 2: Discover and characterize genes and proteins regulating the interactions between potato and its associated pathogens.
The potato cyst nematodes (PCN), Globodera rostochiensis and G. pallida, are pests of regulatory concern worldwide and pose a continued threat to the U.S. potato industry. During infection, PCN secretes an arsenal of proteins known as effectors into host root cells to induce disease. Understanding how nematode effectors function in host root cells is necessary for developing effective and sustainable means for combating nematode diseases. Our studies this year focused on a better understanding of the function of a conserved effector, NMAS1 (Nematode Manipulator of Autophagy System 1), from PCN. We previously showed that the NMAS1 effector targets the plant host autophagy machinery to promote disease. We identified two additional host proteins, SNX1 (sorting nexin 1) and CHMP1 (CHARGED MULTIVESICULAR BODY PROTEIN 1), that interact with the NMAS1 effector. By using transgenic lines to reveal gene expression, we showed that both SNX1 and CHMP1 genes are regulated in nematode feeding structures (NFS), indicating a role of SNX1 and CHMP1 in nematode parasitism. We also utilized the Arabidopsis-beet cyst nematode pathosystem to better understand the function of SNX1 and CHMP1 in nematode parasitism. Interestingly, we found that the size of NFS formed on snx1 or chmp1 mutants is altered compared to those formed on wild-type Arabidopsis plants. The phytohormone auxin is known to be pivotal for the formation of NFS in roots. Since both SNX1 and CHMP1 proteins have been implicated in the cellular trafficking of auxin carriers, we hypothesize that targeting SNX1 and CHMP1 by the NMAS1 effector might result in the autophagic turnover of auxin carriers, leading to increased auxin levels in cells that favor the formation of NFS. We are currently testing this hypothesis. A better understanding of the mechanistic details of the interaction between NMAS1 and its host targets may help develop innovative tools for generating novel resistance in potatoes against PCN. Moreover, we continued to make progress on the functional characterization of several candidate effectors that contain motifs potentially responsible for interacting with the host autophagy machinery. Some of these PCN effectors were shown to function in suppressing host defenses. Interestingly, mutations in their interacting motifs abolished the ability of these effectors to suppress defense. These results corroborate our previous finding that PCNs have evolved effectors capable of manipulating the host autophagy system to promote parasitism.
Phytophthora infestans, the cause of potato and tomato late blight, remains one of the most devastating diseases of these crops. The pathogen persists in the U.S. as clonal strains, which have predictable characteristics such as host preference, fungicide sensitivity, and reaction to host-resistance genes. Late blight outbreaks must be continuously monitored for emergence of new strains, resulting from sexual recombination, importation through trade, or both. New strains must be identified and characterized as they emerge to determine the most effective management strategies. We collected six isolates of P. infestans originated from potato or tomato. Five out of six isolates originated in New York State, and one isolate was from Washington State. These isolates were further characterized and genotyped, and subsequently determined to be US-11, US-23, and US-25.
Populations of fungal and oomycete pathogens are under constant selection pressure imposed by agricultural management practices. One of the most common examples of this is the use of fungicides and the subsequent development of fungicide resistance. It is important to monitor these pathogen populations for fungicide resistance to ensure the most efficient, sustainable, and environmentally conscious approach to disease management is employed. We collected 11 isolates of Colletotrichum coccodes, one isolate of Verticullium dahliae, and six isolates of Phytophthora infestans. Two of the P. infestans clonal lineages were evaluated for sensitivity to mefenoxam, one of the most important late blight fungicides. One lineage, US-23, was sensitive to mefenoxam and the other lineage, US-25, was found to be highly resistant. This information is crucial for growers to make informed disease management decisions that promote effective and efficient fungicide use, environmental stewardship, and economical farming practices.
Objective 3: Investigate novel or improved strategies to manage potato cyst nematodes and/or other invasive potato pathogens.
Our research program plays an essential role in the control and eradication of potato cyst nematodes (PCN; golden nematode and pale cyst nematode) in the U.S. One of the key factors that has contributed to the success of golden nematode (GN) containment in New York is the availability of potato cultivars with resistance to GN. Two pathotypes of GN, Ro1 and Ro2, have been detected in NY. Many potato cultivars with Ro1 resistance have been developed and are available to growers. Ro2 is a new virulent pathotype that can reproduce well on Ro1-resistant potato cultivars. Tools for controlling Ro2 are very limited, as there are currently only two potato cultivars that offer Ro2 resistance. We continued our collaboration with potato breeders in at Cornell University and other major U.S. potato breeding programs to evaluate potato breeding clones for resistance against GN. A total of 110 breeding clones were screened using marker tests and pot bioassays; 56 of them showed resistance to Ro1, and six of them showed resistance to Ro2. These clones will be retested for GN resistance multiple times and further evaluated in fields until they may be released as GN-resistant cultivars. We also evaluated ten existing European potato cultivars and identified two cultivars that showed strong resistance to Ro2. These two commercially available cultivars may serve as an alternative tool for Ro2 control in NY. In addition, we have re-evaluated twenty-four wild potato clones and identified fourteen clones that showed robust resistance to Ro2. These newly identified resistant clones can be introduced to potato breeding programs to accelerate breeding for durable GN resistance in U.S. potato cultivars.
We previously identified Y1-5, a Solanum brevicaule clone that showed robust and broad-spectrum resistance to both PCN species. We further generated a mapping population derived from Y1-5 and conducted bioassays to determine resistance or susceptibility of the Y1-5-derived offspring to nematode infection. Our bioassay results indicated that the genes playing a large effect on nematode resistance are not segregating in this Y1-5-derived population. To address this issue, we are in the process of generating a new mapping population from a genetic cross between Y1-5 and Yoshi-6, a fully susceptible and self-compatible parent. The collection of the phenotypic data of this new mapping population is needed to guide downstream discovery of candidate resistance genes that are expressed in Y1-5.
We previously identified a group of wild potato clones that showed resistance to the Ro2 pathotype of GN. We have re-evaluated these clones for their responses to infection by the pale cyst nematode, a pest detected only in Idaho. Our results confirmed that five of these clones offer extreme resistance to the pale cyst nematode. These newly identified resistant clones have been shared with potato breeding programs in Idaho and New York to help accelerate breeding for durable PCN resistance in U.S. potato cultivars.
Natural genetic sources of disease resistance are vital to supporting efforts to breed potato varieties with resistance to existing and emerging Phytophthora infestans strains. Sixty wild potato clones were evaluated in growth chamber experiments using previously established methods. Clones were inoculated with P. infestans lineage US-23, which has been the predominant lineage in the U.S. for over a decade. One clone showed a high level of resistance to late blight. Several more clones showed moderate levels of resistance. Results from this work will aid efforts to breed robust late blight resistance into commercial potato cultivars.
Accomplishments
1. Collection of genetic and genomic resources for novel resistance against quarantine nematodes. Potato cyst nematodes (PCN; golden nematode and pale cyst nematode) are among the most devastating potato diseases threatening the U.S. potato production. Deploying naturally occurring resistance genes is the most effective and environmentally friendly means for combating crop diseases. Wild potato species offer desirable agricultural traits, such as disease resistance, making them an invaluable genetic resource for potato improvement. Through screening of a large collection of wild potato clones at the U.S. Potato Genebank collection, ARS researchers in Ithaca, New York, identified several wild potato clones that exhibit extreme and broad-spectrum resistance to PCN. Additionally, in collaboration with university scientists, a high-quality genome sequence of a wild potato clone that offers robust resistance to PCN was obtained. The availability of these new resistant germplasm and genomic resources will help expedite the breeding of U.S. potato cultivars with durable PCN resistance.