Hypersensitive response to Potato virus Y in potato cultivar Sárpo Mira is conferred by the Ny-Smira gene located on the long arm of chromosome IX

Rychc Confers Extreme Resistance to Potato virus Y in Potato

The Potato virus Y (PVY) is responsible for huge economic losses for the potato industry worldwide and is the fifth most consequential plant virus globally. The main strategies for virus control are to limit aphid vectors, produce virus-free seed potatoes, and breed virus-resistant varieties. The breeding of PVY-resistant varieties is the safest and most effective method in terms of cost and environmental protection. Rychc, a gene that confers extreme resistance to PVY, is from S. chacoense, which is a wild diploid potato species that is widely used in many PVY-resistant breeding projects. In this study, Rychc was fine mapped and successfully cloned from S. chacoense accession 40-3. We demonstrated that Rychc encodes a TIR-NLR protein by stably transforming a diploid susceptible cultivar named AC142 and a tetraploid potato variety named E3. The Rychc conferred extreme resistance to PVYO, PVYN:O and PVYNTN in both of the genotypes. To investigate the genetic events occurring during the evolution of the Rychc locus, we sequenced 160 Rychc homologs from 13 S. chacoense genotypes. Based on the pattern of sequence identities, 160 Rychc homologs were divided into 11 families. In Family 11 including Rychc, we found evidence for Type I evolutionary patterns with frequent sequence exchanges, obscured orthologous relationships and high non-synonymous to synonymous substitutions (Ka/Ks), which is consistent with rapid diversification and positive selection in response to rapid changes in the PVY genomes. Furthermore, a functional marker named MG64-17 was developed in this study that indicates the phenotype with 100% accuracy and, therefore, can be used for marker-assisted selection in breeding programs that use S. chacoense as a breeding resource.

Natural resistance to Potato virus Y in Solanum tuberosum Group Phureja

Novel major gene resistance against Potato virus Y in diploid populations of Solanum tuberosum Groups Phureja and Tuberosum was biologically and genetically characterised. Named Ry(o)_phu, it mapped to chromosome 9. A new source of genetic resistance derived from Solanum tuberosum Group Phureja against Potato virus Y (PVY) was identified and genetically characterised in three diploid biparental potato populations. Segregation data for two populations (05H1 and 08H1) suggested the presence of a single dominant gene for resistance to PVY which, following DaRT analysis of the 08H1 cross, was mapped to chromosome 9. More detailed genetic analysis of resistance utilised a well-characterised SNP-linkage map for the 06H1 population, together with newly generated marker data. In these plants, which have both S. tuberosum Group Phureja and S. tuberosum Group Tuberosum in their pedigree, the resistance was shown to map to chromosome 9 at a locus not previously associated with PVY resistance, although there is evidence for at least one other genetic factor controlling PVY infection. The resistance factor location on chromosome 9 (named as Ry(o)phu) suggests a potential role of NB-LRR genes in this resistance. Phenotypic analysis using a GUS-tagged virus revealed that a small amount of PVY replication occurred in occasional groups of epidermal cells in inoculated leaves of resistant plants, without inducing any visible hypersensitive response. However, the virus did not enter the vascular system and systemic spread was completely prevented.

Plant Molecular Responses to Potato Virus Y: A Continuum of Outcomes from Sensitivity and Tolerance to Resistance

Potato virus Y (PVY) is the most economically important virus affecting potato production. PVY manipulates the plant cell machinery in order to successfully complete the infecting cycle. On the other side, the plant activates a sophisticated multilayer immune defense response to combat viral infection. The balance between these mechanisms, depending on the plant genotype and environment, results in a specific outcome that can be resistance, sensitivity, or tolerance. In this review, we summarize and compare the current knowledge on molecular events, leading to different phenotypic outcomes in response to PVY and try to link them with the known molecular mechanisms.

The Expression of Potato Expansin A3 (StEXPA3) and Extensin4 (StEXT4) Genes with Distribution of StEXPAs and HRGPs-Extensin Changes as an Effect of Cell Wall Rebuilding in Two Types of PVYNTN-Solanum tuberosum Interactions

The plant cell wall acts not only as a physical barrier, but also as a complex and dynamic structure that actively changes under different biotic and abiotic stress conditions. The question is, how are the different cell wall compounds modified during different interactions with exogenous stimuli such as pathogens? Plants exposed to viral pathogens respond to unfavorable conditions on multiple levels. One challenge that plants face under viral stress is the number of processes required for differential cell wall remodeling. The key players in these conditions are the cell wall genes and proteins, which can be regulated in specific ways during the interactions and have direct influences on the rebuilding of the cell wall structure. The cell wall modifications occurring in plants during viral infection remain poorly described. Therefore, this study focuses on cell wall dynamics as an effect of incompatible interactions between the potato virus Y (PVY^NTN) and resistant potatoes (hypersensitive plant), as well as compatible (susceptible plant) interactions. Our analysis describes, for the first time, the expression of the potato expansin A3 (StEXPA3) and potato extensin 4 (StEXT4) genes in PVY^NTN-susceptible and -resistant potato plant interactions. The results indicated a statistically significant induction of the StEXPA3 gene during a susceptible response. By contrast, we demonstrated the predominantly gradual activation of the StEXT4 gene during the hypersensitive response to PVY^NTN inoculation. Moreover, the in situ distributions of expansins (StEXPAs), which are essential cell wall-associated proteins, and the hydroxyproline-rich glycoprotein (HRGP) extensin were investigated in two types of interactions. Furthermore, cell wall loosening was accompanied by an increase in StEXPA deposition in a PVY^NTN-susceptible potato, whereas the HRGP content dynamically increased during the hypersensitive response, when the cell wall was reinforced. Ultrastructural localization and quantification revealed that the HRGP extensin was preferably located in the apoplast, but deposition in the symplast was also observed in resistant plants. Interestingly, during the hypersensitive response, StEXPA proteins were mainly located in the symplast area, in contrast to the susceptible potato where StEXPA proteins were mainly observed in the cell wall. These findings revealed that changes in the intracellular distribution and abundance of StEXPAs and HRGPs can be differentially regulated, depending on different types of PVY^NTN–potato plant interactions, and confirmed the involvement of apoplast and symplast activation as a defense response mechanism.

HCPro Suppression of Callose Deposition Contributes to Strain-Specific Resistance Against Potato Virus Y

Potato virus Y (PVY; Potyviridae) is a continuing challenge for potato production owing to the increasing popularity of strain-specific resistant cultivars. Hypersensitive resistance (HR) is one type of plant defense responses to restrict virus spread. In many potato cultivars, such as cultivar Premier Russet (PR), local necrosis at the site of infection protects against the most common PVY^O strain, but the HR often fails to restrain necrotic strains, which spread systemically. Here, we established the role of callose accumulation in the strain-specific resistance responses to PVY infection. We first uncovered that PVY, independent of the strain, is naturally capable of suppressing pathogenesis-related callose formation in a susceptible host. Such activity can be dissociated from viral replication by the transient expression of the viral-encoded helper component proteinase (HCPro) protein, identifying it as the pathogen elicitor. However, unlike the necrotic strain, PVY^O and its corresponding HCPro are unable to block callose accumulation in resistant PR potatoes, in which we observed an abundance of callose deposition and the inability of the virus to spread. The substitution of eight amino acid residues within the HCPro C-terminal region that differ between PVY^O and PVY^N strains and were previously shown to be responsible for eliciting the HR response, are sufficient to restore the ability of HCPro^O to suppress callose accumulation, despite the resistant host background, in line with a new viral function in pathogenicity.

The Respiratory Burst Oxidase Homolog D (RbohD) Cell and Tissue Distribution in Potato-Potato Virus Y (PVYNTN) Hypersensitive and Susceptible Reactions

The respiratory burst oxidase homolog D (RbohD) acts as a central driving force of reactive oxygen species signaling in plant cells by integrating many different signal transduction pathways in plants, including incompatible interactions with pathogens. This study demonstrated the localization and distribution of RbohD in two types of potato–potato virus Y (PVY) interactions: Compatible and incompatible (resistant). The results indicated a statistically significant induction of the RbohD antigen signal in both interaction types. In the hypersensitive response (resistant reaction) of potato with a high level of resistance to the potato tuber necrotic strain of PVY (PVY^NTN), RbohD localization followed by hydrogen peroxide (H₂O₂) detection was concentrated in the apoplast. In contrast, in the hypersensitive response of potato with a low resistance level to PVY^NTN, the distribution of RbohD was concentrated more in the plant cell organelles than in the apoplast, resulting in the virus particles being present outside the inoculation area. Moreover, when compared to mock-inoculated plants and to the hypersensitive response, the PVY^NTN-compatible potato interaction triggered high induction in the RbohD distribution, which was associated with necrotization. Our findings indicated that RbohD and hydrogen peroxide deposition was associated with the hypersensitive response, and both were detected in the vascular tissues and chloroplasts. These results suggest that the RbohD distribution is actively dependent on different types of PVY ^NTN-potato plant interactions. Additionally, the RbohD may be involved in the PVY^NTN tissue limitation during the hypersensitive response, and it could be an active component of the systemic signal transduction in the susceptible host reaction.

Molecular and genetic characterization of the Ryadg locus on chromosome XI from Andigena potatoes conferring extreme resistance to potato virus Y

KEY MESSAGE

We have elucidated the Andigena origin of the potato Ryadg gene on chromosome XI of CIP breeding lines and developed two marker assays to facilitate its introgression in potato by marker-assisted selection. Potato virus Y (PVY) is causing yield and quality losses forcing farmers to renew periodically their seeds from clean stocks. Two loci for extreme resistance to PVY, one on chromosome XI and the other on XII, have been identified and used in breeding. The latter corresponds to a well-known source of resistance (Solanum stoloniferum), whereas the one on chromosome XI was reported from S. stoloniferum and S. tuberosum group Andigena as well. To elucidate its taxonomic origin in our breeding lines, we analyzed the nucleotide sequences of tightly linked markers (M45, M6) and screened 251 landraces of S. tuberosum group Andigena for the presence of this gene. Our results indicate that the PVY resistance allele on chromosome XI in our breeding lines originated from S. tuberosum group Andigena. We have developed two marker assays to accelerate the introgression of Ryadg gene into breeding lines by marker-assisted selection (MAS). First, we have multiplexed RYSC3, M6 and M45 DNA markers flanking the Ryadg gene and validated it on potato varieties with known presence/absence of the Ryadg gene and a progeny of 6,521 individuals. Secondly, we developed an allele-dosage assay particularly useful to identify multiplex Ryadg progenitors. The assay based on high-resolution melting analysis at the M6 marker confirmed Ryadg plex level as nulliplex, simplex and duplex progenitors and few triplex progenies. These marker assays have been validated and can be used to facilitate MAS in potato breeding.

Spatiotemporal Changes in Xylan-1/Xyloglucan and Xyloglucan Xyloglucosyl Transferase (XTH-Xet5) as a Step-In of Ultrastructural Cell Wall Remodelling in Potato⁻Potato Virus Y (PVYNTN) Hypersensitive and Susceptible Reaction

One type of monitoring system in a plant cell is the cell wall, which intensively changes its structure during interaction with pathogen-stress factors. The wall plays a role as a dynamic and controlled structure, although it is not fully understood how relevant these modifications are to the molecular mechanisms during plant–virus interactions. In this work we localise the non-cellulosic polysaccharides such as xyloglucan, xylan (xylan-1) and xyloglucosyl transferase (XTH-Xet5), the enzyme that participates in the metabolism of xyloglucan. This provided us with information about the in situ distribution of the components of the hemicellulotic cell wall matrix in hypersensitive and susceptible potato–PVY^NTN interactions. The loosening of the cell wall was accompanied by an increase in xylan depositions during susceptible interactions, whereas, during the hypersensitive response, when the cell wall was reinforced, the xylan content decreased. Moreover, the PVY inoculation significantly redirected XTH-Xet5 depositions, regardless of types of interactions, compared to mock-inoculated tissues. Furthermore, the immunogold localisation clearly revealed the domination of Xet5 in the cell wall and in vesicles in the susceptible host. In contrast, in the resistant host increased levels of Xet5 were observed in cytoplasm, in the cell wall and in the trans-Golgi network. These findings show that the hypersensitive reaction activated XTH-Xet5 in the areas of xyloglucan endo-transglycosylase (XET) synthesis, which was then actively transported to cytoplasm, cell wall and to vacuoles. Our results provide novel insight into cell wall reorganisation during PVY^NTN infection as a response to biotic stress factors. These novel findings help us to understand the mechanisms of defence responses that are incorporated into the cell wall signalling network.

Plant Cell Wall Dynamics in Compatible and Incompatible Potato Response to Infection Caused by Potato Virus Y (PVYNTN)

The cell wall provides the structure of the plant, and also acts as a barier against biotic stress. The vein necrosis strain of Potato virus Y (PVY^NTN) induces necrotic disease symptoms that affect both plant growth and yield. Virus infection triggers a number of inducible basal defense responses, including defense proteins, especially those involved in cell wall metabolism. This study investigates the comparison of cell wall host dynamics induced in a compatible (potato cv. Irys) and incompatible (potato cv. Sárpo Mira with hypersensitive reaction gene Ny-Smira) PVY^NTN–host–plant interaction. Ultrastructural analyses revealed numerous cell wall changes induced by virus infection. Furthermore, the localization of essential defensive wall-associated proteins in susceptible and resistant potato host to PVY^NTN infection were investigated. The data revealed a higher level of detection of pathogenesis-related protein 2 (PR-2) in a compatible compared to an incompatible (HR) interaction. Immunofluorescence analyses indicated that hydroxyproline-rich glycoproteins (HRGP) (extensin) synthesis was induced, whereas that of cellulose synthase catalytic subunits (CesA4) decreased as a result of PVY^NTN infection. The highest level of extensin localization was found in HR potato plants. Proteins involved in cell wall metabolism play a crucial role in the interaction because they affect the spread of the virus. Analysis of CesA4, PR-2 and HRGP deposition within the apoplast and symplast confirmed the active trafficking of these proteins as a step-in potato cell wall remodeling in response to PVY^NTN infection. Therefore, cell wall reorganization may be regarded as an element of “signWALLing”—involving apoplast and symplast activation as a specific response to viruses.

Graphical genotyping as a method to map Ny (o,n)sto and Gpa5 using a reference panel of tetraploid potato cultivars

The method of graphical genotyping is applied to a panel of tetraploid potato cultivars to visualize haplotype sharing. The method allowed to map genes involved in virus and nematode resistance. The physical coordinates of the amount of linkage drag surrounding these genes are easily interpretable. Graphical genotyping is a visually attractive and easily interpretable method to represent genetic marker data. In this paper, the method is extended from diploids to a panel of tetraploid potato cultivars. Application of filters to select a subset of SNPs allows one to visualize haplotype sharing between individuals that also share a specific locus. The method is illustrated with cultivars resistant to Potato virus Y (PVY), while simultaneously selecting for the absence of the SNPs in susceptible clones. SNP data will then merge into an image which displays the coordinates of a distal genomic region on the northern arm of chromosome 11 where a specific haplotype is introgressed from the wild potato species S. stoloniferum (CPC 2093) carrying a gene (Ny _(o,n)sto ) conferring resistance to two PVY strains, PVY^O and PVY^NTN. Graphical genotyping was also successful in showing the haplotypes on chromosome 12 carrying Ry-f _sto , another resistance gene derived from S. stoloniferum conferring broad-spectrum resistance to PVY, as well as chromosome 5 haplotypes from S. vernei, with the Gpa5 locus involved in resistance against Globodera pallida cyst nematodes. The image also shows shortening of linkage drag by meiotic recombination of the introgression segment in more recent breeding material. Identity-by-descent was found to be a requirement for using graphical genotyping, which is proposed as a non-statistical alternative method for gene discovery, as compared with genome-wide association studies. The potential and limitations of the method are discussed.

The Solanum demissum R8 late blight resistance gene is an Sw-5 homologue that has been deployed worldwide in late blight resistant varieties

The potato late blight resistance gene R8 has been cloned. R8 is found in five late blight resistant varieties deployed in three different continents. R8 recognises Avr8 and is homologous to the NB-LRR protein Sw-5 from tomato. The broad spectrum late blight resistance gene R8 from Solanum demissum was cloned based on a previously published coarse map position on the lower arm of chromosome IX. Fine mapping in a recombinant population and bacterial artificial chromosome (BAC) library screening resulted in a BAC contig spanning 170 kb of the R8 haplotype. Sequencing revealed a cluster of at least ten R gene analogues (RGAs). The seven RGAs in the genetic window were subcloned for complementation analysis. Only one RGA provided late blight resistance and caused recognition of Avr8. From these results, it was concluded that the newly cloned resistance gene was indeed R8. R8 encodes a typical intracellular immune receptor with an N-terminal coiled coil, a central nucleotide binding site and 13 C-terminal leucine rich repeats. Phylogenetic analysis of a set of representative Solanaceae R proteins shows that R8 resides in a clearly distinct clade together with the Sw-5 tospovirus R protein from tomato. It was found that the R8 gene is present in late blight resistant potato varieties from Europe (Sarpo Mira), USA (Jacqueline Lee, Missaukee) and China (PB-06, S-60). Indeed, when tested under field conditions, R8 transgenic potato plants showed broad spectrum resistance to the current late blight population in the Netherlands, similar to Sarpo Mira.