Warts wars : The resistant potatoes strike back

Abstract

Potato wart disease, caused by the obligate biotrophic Chytrid fungus Synchytrium endobioticum, is one of the most important quarantine diseases of potato. This disease was named after the symptoms caused by the pathogen, which are the proliferation of meristematic tissues leading to the formation of warts, mainly on the below-ground sprouts of potato plants. The quarantine status of S. endobioticum is due to the production of spores that can remain viable in the soil for more than 40 years, the lack of chemical control and the severe yield losses. In Europe, more than 40 different pathotypes of S. endobioticum have been recorded and only resistance to pathotype 1 is commonly deployed in the breeding germplasm. The breeding and cultivation of potato varieties resistant to a wider spectrum of pathotypes is crucial for quarantine practice to reduce the propagation of the pathogen. Therefore, the identification of genes bringing resistance to the most frequent pathotypes of the pathogen and the development of diagnostic markers for marker assisted selection (MAS) is urgently needed. In this thesis, genes involved in resistance to pathotypes 1, 2, 6 and 18 of S. endobioticum were identified to make an inventory of the different resistance sources at hand for potato breeders. In Chapter 2, we investigated the distribution of the pathotype 1 resistance in a variety panel representative of the potato breeding material. Breeding programs of the 20th century were very successful in producing varieties resistant to pathotype 1 as 77% of the panel varieties were found to be resistant. To identify markers linked with pathotype 1 resistance, we used previously produced genotypic and phenotypic data to perform a Genome-Wide Association Study (GWAS). The GWAS resulted in the identification of markers associated with pathotype 1 resistance on the north arm of chromosome 11. In this region, the major effect gene Sen1 was previously identified. Sen1 is the main source of pathotype 1 resistance in the variety panel and no common ancestral donor could be identified due to the inability to define identity-by-descent (IBD). As we faced limitations to design markers fully diagnostic for pathotype 1 resistance using the GWAS approach, we aimed to develop new tools to identify haplotype specific SNPs. In Chapter 3, we developed a new set of workflows, called Comparative Subsequence Sets Analysis (CoSSA), for the genetic analysis of traits of interest and the identification of haplotype specific SNPs. CoSSA can be used for any crop as it is suitable for polyploids and can be used with or without a reference genome. We applied CoSSA to identify Sen3, a dominant gene conferring resistance to all tested pathotypes. Sen3 was fine-mapped to the resistance gene cluster C76 on the north arm of chromosome 11. Furthermore, we used CoSSA for the fine-mapping of Sen1 in Chapter 4. Sen1 was mapped to the same R gene cluster as Sen3. We performed a candidate gene analysis and showed that Sen1 encodes a nucleotide-binding domain, leucine rich containing (NLR) protein from the TNL group. The two identified candidate genes were cloned and tested in complementation assays with AvrSen1, the S. endobioticum effector protein which triggers Hypersensitive Responses (HR) in Sen1 plants. These findings will serve as novel tools to study the interactions between potato and S. endobioticum. In Chapter 5, we made an, as complete as possible at this moment, inventory of the dominant potato wart disease resistance (Sen) genes and QTLs present in the potato breeding germplasm. We combined the GWAS and CoSSA strategies to identify two new major genes, Sen4 and Sen5, which are involved in resistance to pathotypes 2, 6 and 18. We also identified several wart disease resistance QTLs which, in combination with the dominant genes, can contribute to improve resistance to the higher pathotypes. To avoid any confusion between the previously and newly identified QTLs, we introduced a new naming system which allows to differentiate each resistant haplotype identified. Finally, we screened a broad panel of potato varieties and wild Solanum species for the genes Sen1, Sen2, Sen3, Sen4 and Sen5. To put it in a nutshell, a complete picture of the major potato wart disease resistance sources present in the breeding germplasm is given in this thesis. Haplotype specific markers have been designed for all the major genes and QTLs mapped, which will facilitate the breeding of resistant varieties. Finally, the development of CoSSA will facilitate the mapping of traits of interest and the design of haplotype specific markers for any crop.