Potato PCN Resistance: Cloning effective resistances against potato cyst nematodes
Lead Research Organisation:
University of East Anglia
Department Name: Sainsbury Laboratory
Abstract
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Technical Summary
Potato Cyst Nematodes (PCN) are a persistent threat to potato production and could lead to the demise of the UK's seed potato industry in the next 10 years if not controlled. Resistances against the PCN species Globodera rostochiensis and G. pallida are available in selected cultivars, but the genes, H1 (G. rostochiensis) and Gpa5 and/or Gpa4 (G. pallida), that underpin these resistances remain elusive.
Using state of the art genetics and genomics, our evidence strongly supports that H1, Gpa5 and Gpa4 are members of the NLR gene family. To specifically study NLRs, this consortium has jointly developed RenSeq-based technologies that enable the rapid identification of candidates for these resistances. Using existing RenSeq data from 380 cultivars and breeding clones alongside established computational approaches for SMRT-AgRenSeq-based analysis, we have identified five candidates for H1 and nine candidates for Gpa5. For Gpa4, we have in place populations and phenotypic information that will enable similar studies and can draw on resources from our partners Solynta and Averis.
In addition to cloning H1, Gpa5 and Gpa4, this project aims to identify the corresponding PCN Avr genes. By comparing the effector repertoires of avirulent PCN populations, populations selected for virulence on these resistances, and recently identified virulent populations from the Netherlands, we will be able to identify Avr candidate and, simultaneously, virulent variants thereof.
This knowledge will aid the mechanistic understanding of host resistances against plant-parasitic nematodes. In addition, we will reach a position through these studies where we can facilitate the stacking of complimentary resistances and predict their durability in light of Avr gene diversity in the pathogen population. With the help of our commercial partners, PepsiCo, Solynta, Averis and the 2Blades foundation, we will be able to deliver impact for the international potato market.
Using state of the art genetics and genomics, our evidence strongly supports that H1, Gpa5 and Gpa4 are members of the NLR gene family. To specifically study NLRs, this consortium has jointly developed RenSeq-based technologies that enable the rapid identification of candidates for these resistances. Using existing RenSeq data from 380 cultivars and breeding clones alongside established computational approaches for SMRT-AgRenSeq-based analysis, we have identified five candidates for H1 and nine candidates for Gpa5. For Gpa4, we have in place populations and phenotypic information that will enable similar studies and can draw on resources from our partners Solynta and Averis.
In addition to cloning H1, Gpa5 and Gpa4, this project aims to identify the corresponding PCN Avr genes. By comparing the effector repertoires of avirulent PCN populations, populations selected for virulence on these resistances, and recently identified virulent populations from the Netherlands, we will be able to identify Avr candidate and, simultaneously, virulent variants thereof.
This knowledge will aid the mechanistic understanding of host resistances against plant-parasitic nematodes. In addition, we will reach a position through these studies where we can facilitate the stacking of complimentary resistances and predict their durability in light of Avr gene diversity in the pathogen population. With the help of our commercial partners, PepsiCo, Solynta, Averis and the 2Blades foundation, we will be able to deliver impact for the international potato market.
Organisations
| Title | High-throughput screening of candidate effectors in potato protoplasts |
| Description | Identification of molecules (effectors) recognized by resistance genes (NLRs) has multiple benefits for the durable deployment of resistance in the field. Assessing the polymorphism and diversity of the effectors enables monitoring of the effectivity of the corresponding recognitions in the lab and field setting and the search for novel recognition capacities. Moreover, in case functional NLR is known, the method can be tested to identify recognised effector. Current methods for effector identification usually rely on model plants like Nicotiana benthamiana, and require laborious infiltrations and manual scoring of results several days later. The additional drawback is that this is not a native system and, if required downstream signaling components are not present, the candidate effectors will not be detected. To overcome these challenges, we have developed a high-throughput screening system directly in potato lines of interest. We optimized protocols to isolate potato protoplasts on a large scale, which are then transfected with plasmids containing candidate effectors (or effectors together with NLRs) on a large scale, in 96 or 384-well plates. The assay is based on measuring the activity of luciferase in multimodal microplate readers, allowing for quick analysis in software like R-studio. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2024 |
| Provided To Others? | No |
| Impact | The method allows high-throughput screening of candidate effectors and NLRs directly in potato lines, overcoming the need to use non-native system like N. benthamiana. It is also much faster and more sensitive than the standard co-infiltration. This method offers the potential to scale up the screening process. It can be also easily adaptable to other plant systems. |