Expression of the Potato Late Blight Resistance Gene Rpi-phu1 and Phytophthora infestans Effectors in the Compatible and Incompatible Interactions in Potato

Recent advances of NLR receptors in vegetable disease resistance

Plants mainly depend on both cell-surface and intracellular receptors to defend against various pathogens. The nucleotide-binding leucine-rich repeat (NLR) proteins are intracellular receptors that recognize pathogen effectors. The first NLR was cloned thirty years ago. Genomic sequencing and biotechnologies accelerated NLR gene isolation. NLR genes have been proven useful in breeding disease resistant crops. Here, we summarized the current knowledge of strategies for NLR gene isolation and provided a list of NLRs cloned in vegetables. We also discussed the mechanisms underlying NLR gene function, the challenges of NLRs in vegetable breeding and directions for future studies.

Evolution of Phytophthora infestans on its potato host since the Irish potato famine

Phytophthora infestans is a major oomycete plant pathogen, responsible for potato late blight, which led to the Irish Potato Famine from 1845-1852. Since then, potatoes resistant to this disease have been bred and deployed worldwide. Their resistance (R) genes recognize pathogen effectors responsible for virulence and then induce a plant response stopping disease progression. However, most deployed R genes are quickly overcome by the pathogen. We use targeted sequencing of effector and R genes on herbarium specimens to examine the joint evolution in both P. infestans and potato from 1845-1954. Currently relevant effectors are historically present in P. infestans, but with alternative alleles compared to modern reference genomes. The historic FAM-1 lineage has the virulent Avr1 allele and the ability to break the R1 resistance gene before breeders deployed it in potato. The FAM-1 lineage is diploid, but later, triploid US-1 lineages appear. We show that pathogen virulence genes and host resistance genes have undergone significant changes since the Famine, from both natural and artificial selection.

Foliar transcriptomes reveal candidate genes for late blight resistance in cultivars of diploid potato Solanum tuberosum L. Andigenum Group

Characterization of major resistance (R) genes to late blight (LB) -caused by the oomycete Phytophthora infestans- is very important for potato breeding. The objective of this study was to identify novel genes for resistance to LB from diploid Solanum tuberosum L. Andigenum Group (StAG) cultivar accessions. Using comparative analysis with a edgeR bioconductor package for differential expression analysis of transcriptomes, two of these accessions with contrasting levels of resistance to LB were analyzed using digital gene expression data. As a result, various differentially expressed genes (P ≤ 0.0001, Log2FC ≥ 2, FDR < 0.001) were noted. The combination of transcriptomic analysis provided 303 candidate genes that are overexpressed and underexpressed, thereby giving high resistance to LB. The functional analysis showed differential expression of R genes and their corresponding proteins related to disease resistance, NBS-LRR domain proteins, and specific disease resistance proteins. Comparative analysis of specific tissue transcriptomes in resistant and susceptible genotypes can be used for rapidly identifying candidate R genes, thus adding novel genes from diploid StAG cultivar accessions for host plant resistance to P. infestans in potato.

Characterization of host-effector transcription dynamics during pathogen infection in engineered late blight resistant potato

Phytophthora infestans, the etiologic agent of late blight, is a threat to potato production in areas with high humidity during the growing season. The oomycete pathogen is hemi-biotrophic, it establishes infection on living plant cells and then spreads, kills, and feeds off the necrotized plant tissue material. The interaction between host and pathogen is complex with dynamic pathogen RXLR effectors and potato NB-LRR resistance proteins actively competing for dominance and survival. Late blight protection was brought to several cultivars of potato through insertion of the wild potato (Solanum venturii) NB-LRR resistance gene Rpi-vnt1.1. We have established that the late blight protection trait, mediated by Rpi-vnt1.1, is effective despite low expression of RNA. The RNA expression dynamics of Rpi-vnt1.1 and the cognate pathogen RXLR effector, Avr-vnt1, were evaluated following spray inoculation with up to five different contemporary late blight isolates from North America and South America. Following inoculations, RXLR effector transcript profiles provided insight into interaction compatibility in relation to markers of the late blight hemi-biotrophic lifecycle.

Strive or thrive: Trends in Phytophthora capsici gene expression in partially resistant pepper

Partial resistance in plants generally exerts a low selective pressure on pathogens, and thus ensuring their durability in agrosystems. However, little is known about the effect of partial resistance on the molecular mechanisms of pathogenicity, a knowledge that could advance plant breeding for sustainable plant health. Here we investigate the gene expression of Phytophthora capsici during infection of pepper (Capsicum annuum L.), where only partial genetic resistance is reported, using Illumina RNA-seq. Comparison of transcriptomes of P. capsici infecting susceptible and partially resistant peppers identified a small number of genes that redirected its own resources into lipid biosynthesis to subsist on partially resistant plants. The adapted and non-adapted isolates of P. capsici differed in expression of genes involved in nucleic acid synthesis and transporters. Transient ectopic expression of the RxLR effector genes CUST_2407 and CUST_16519 in pepper lines differing in resistance levels revealed specific host-isolate interactions that either triggered local necrotic lesions (hypersensitive response or HR) or elicited leave abscission (extreme resistance or ER), preventing the spread of the pathogen to healthy tissue. Although these effectors did not unequivocally explain the quantitative host resistance, our findings highlight the importance of plant genes limiting nutrient resources to select pepper cultivars with sustainable resistance to P. capsici.

Late Blight Resistance Conferred by Rpi-Smira2/R8 in Potato Genotypes In Vitro Depends on the Genetic Background

Potato production worldwide is threatened by late blight, caused by the oomycete Phytophthora infestans (Mont.) de Bary. Highly resistant potato cultivars were developed in breeding programs, using resistance gene pyramiding methods. In Sárpo Mira potatoes, five resistance genes (R3a, R3b, R4, Rpi-Smira1, and Rpi-Smira2/R8) are reported, with the latter gene assumed to be the major contributor. To study the level of late blight resistance conferred by the Rpi-Smira2/R8 gene, potato genotypes with only the Rpi-Smira2/R8 gene were selected from progeny population in which susceptible cultivars were crossed with Sárpo Mira. Ten R8 potato genotypes were obtained using stepwise marker-assisted selection, and agroinfiltration of the avirulence effector gene Avr4. Nine of these R8 genotypes were infected with both Slovenian P. infestans isolates and aggressive foreign isolates. All the progeny R8 genotypes are resistant to the Slovenian P. infestans isolate 02_07, and several show milder late blight symptoms than the corresponding susceptible parent after inoculation with other isolates. When inoculated with foreign P. infestans isolates, the genotype C571 shows intermediate resistance, similar to that of Sárpo Mira. These results suggest that Rpi-Smira2/R8 contributes to late blight resistance, although this resistance is not guaranteed solely by the presence of the R8 in the genome.

Late blight resistance genes in potato breeding

Using late blight resistance genes targeting conservative effectors of Phytophthora infestans and the constructing gene pyramids may lead to durable, broad-spectrum resistance, which could be accelerated through genetic engineering. Potato (Solanum tuberosum L.) is one of the most important food crops worldwide. In 2020, potato production was estimated to be more than 359 million tons according to the Food and Agriculture Organization (FAO). Potato is affected by many pathogens, among which Phytophthora infestans, causing late blight, is of the most economic importance. Crop protection against late blight requires intensive use of fungicides, which has an impact on the environment and humans. Therefore, new potato cultivars have been bred using resistance genes against P. infestans (Rpi genes) that originate from wild relatives of potato. Such programmes were initiated 100 years ago, but the process is complex and long. The development of genetic engineering techniques has enabled the direct transfer of resistance genes from potato wild species to cultivars and easier pyramiding of multiple Rpi genes, which potentially increases the durability and spectrum of potato resistance to rapidly evolving P. infestans strains. In this review, we summarize the current knowledge concerning Rpi genes. We also discuss the use of Rpi genes in breeding as well as their detection in existing potato cultivars. Last, we review new sources of Rpi genes and new methods used to identify them and discuss interactions between P. infestans and host.

Dual RNA Sequencing Reveals the Genome-Wide Expression Profiles During the Compatible and Incompatible Interactions Between Solanum tuberosum and Phytophthora infestans

Late blight, caused by Phytophthora infestans (P. infestans), is a devastating plant disease. P. infestans genome encodes hundreds of effectors, complicating the interaction between the pathogen and its host and making it difficult to understand the interaction mechanisms. In this study, the late blight-resistant potato cultivar Ziyun No.1 and the susceptible potato cultivar Favorita were infected with P. infestans isolate SCPZ16-3-1 to investigate the global expression profiles during the compatible and incompatible interactions using dual RNA sequencing (RNA-seq). Most of the expressed Arg-X-Leu-Arg (RXLR) effector genes were suppressed during the first 24 h of infection, but upregulated after 24 h. Moreover, P. infestans induced more specifically expressed genes (SEGs), including RXLR effectors and cell wall-degrading enzymes (CWDEs)-encoding genes, in the compatible interaction. The resistant potato activated a set of biotic stimulus responses and phenylpropanoid biosynthesis SEGs, including kirola-like protein, nucleotide-binding site-leucine-rich repeat (NBS-LRR), disease resistance, and kinase genes. Conversely, the susceptible potato cultivar upregulated more kinase, pathogenesis-related genes than the resistant cultivar. This study is the first study to characterize the compatible and incompatible interactions between P. infestans and different potato cultivars and provides the genome-wide expression profiles for RXLR effector, CWDEs, NBS-LRR protein, and kinase-encoding genes.

Genomic Approaches to Identify Molecular Bases of Crop Resistance to Diseases and to Develop Future Breeding Strategies

Plant diseases are responsible for substantial crop losses each year and affect food security and agricultural sustainability. The improvement of crop resistance to pathogens through breeding represents an environmentally sound method for managing disease and minimizing these losses. The challenge is to breed varieties with a stable and broad-spectrum resistance. Different approaches, from markers to recent genomic and 'post-genomic era' technologies, will be reviewed in order to contribute to a better understanding of the complexity of host-pathogen interactions and genes, including those with small phenotypic effects and mechanisms that underlie resistance. An efficient combination of these approaches is herein proposed as the basis to develop a successful breeding strategy to obtain resistant crop varieties that yield higher in increasing disease scenarios.

Identification of Natural Resistance Mediated by Recognition of Phytophthora infestans Effector Gene Avr3aEM in Potato

Late blight is considered the most renowned devastating potato disease worldwide. Resistance gene (R)-based resistance to late blight is the most effective method to inhibit infection by the causal agent Phytophthora infestans. However, the limited availability of resistant potato varieties and the rapid loss of R resistance, caused by P. infestans virulence variability, make disease control rely on fungicide application. We employed an Agrobacterium tumefaciens-mediated transient gene expression assay and effector biology approach to understand late blight resistance of Chinese varieties that showed years of promising field performance. We are particularly interested in PiAvr3a^EM , the most common virulent allele of PiAvr3a^KI that triggers a R3a-mediated hypersensitive response (HR) and late blight resistance. Through our significantly improved A. tumefaciens-mediated transient gene expression assay in potato using cultured seedlings, we characterized two dominant potato varieties, Qingshu9 and Longshu7, in China by transient expression of P. infestans effector genes. Transient expression of 10 known avirulence genes showed that PiAvr4 and PiAvr8 (PiAvrsmira2) could induce HR in Qingshu9, and PiAvrvnt1.1 in Longshu7, respectively. Our study also indicated that PiAvr3a^EM is recognized by these two potato varieties, and is likely involved in their significant field performance of late blight resistance. The identification of natural resistance mediated by PiAvr3a^EM recognition in Qingshu9 and Longshu7 will facilitate breeding for improved potato resistance against P. infestans.

Stacking three late blight resistance genes from wild species directly into African highland potato varieties confers complete field resistance to local blight races

Considered responsible for one million deaths in Ireland and widespread famine in the European continent during the 1840s, late blight, caused by Phytophthora infestans, remains the most devastating disease of potato (Solanum tuberosum L.) with about 15%-30% annual yield loss in sub-Saharan Africa, affecting mainly smallholder farmers. We show here that the transfer of three resistance (R) genes from wild relatives [RB, Rpi-blb2 from Solanum bulbocastanum and Rpi-vnt1.1 from S. venturii] into potato provided complete resistance in the field over several seasons. We observed that the stacking of the three R genes produced a high frequency of transgenic events with resistance to late blight. In the field, 13 resistant transgenic events with the 3R-gene stack from the potato varieties 'Desiree' and 'Victoria' grew normally without showing pathogen damage and without any fungicide spray, whereas their non-transgenic equivalent varieties were rapidly killed. Characteristics of the local pathogen population suggest that the resistance to late blight may be long-lasting because it has low diversity, and essentially consists of the single lineage, 2_A1, which expresses the cognate avirulence effector genes. Yields of two transgenic events from 'Desiree' and 'Victoria' grown without fungicide to reflect small-scale farm holders were estimated to be 29 and 45 t/ha respectively. This represents a three to four-fold increase over the national average. Thus, these late blight resistant potato varieties, which are the farmers' preferred varieties, could be rapidly adopted and bring significant income to smallholder farmers in sub-Saharan Africa.

A comprehensive analysis of the Lactuca sativa, L. transcriptome during different stages of the compatible interaction with Rhizoctonia solani

The leafy green vegetable Lactuca sativa, L. is susceptible to the soil-born fungus Rhizoctonia solani AG1-IB. In a previous study, we reported on the transcriptional response of R. solani AG1-IB (isolate 7/3/14) during the interspecies interaction with L. sativa cv. Tizian by means of RNA sequencing. Here we present the L. sativa transcriptome and metabolome from the same experimental approach. Three distinct interaction zones were sampled and compared to a blank (non-inoculated) sample: symptomless zone 1, zone 2 showing light brown discoloration, and a dark brown zone 3 characterized by necrotic lesions. Throughout the interaction, we observed a massive reprogramming of the L. sativa transcriptome, with 9231 unique genes matching the threshold criteria for differential expression. The lettuce transcriptome of the light brown zone 2 presents the most dissimilar profile compared to the uninoculated zone 4, marking the main stage of interaction. Transcripts putatively encoding several essential proteins that are involved in maintaining jasmonic acid and auxin homeostasis were found to be negatively regulated. These and other indicator transcripts mark a potentially inadequate defence response, leading to a compatible interaction. KEGG pathway mapping and GC-MS metabolome data revealed large changes in amino acid, lignin and hemicellulose related pathways and related metabolites.

Plant NLRs: From discovery to application

Plants require a complex immune system to defend themselves against a wide range of pathogens which threaten their growth and development. The nucleotide-binding leucine-rich repeat proteins (NLRs) are immune sensors that recognize effectors delivered by pathogens. The first NLR was cloned more than twenty years ago. Since this initial discovery, NLRs have been described as key components of plant immunity responsible for pathogen recognition and triggering defense responses. They have now been described in most of the well-studied mulitcellular plant species, with most having large NLR repertoires. As research has progressed so has the understanding of how NLRs interact with their recognition substrates and how they in turn activate downstream signalling. It has also become apparent that NLR regulation occurs at the transcriptional, post-transcriptional, translational, and post-translational levels. Even before the first NLR was cloned, breeders were utilising such genes to increase crop performance. Increased understanding of the mechanistic details of the plant immune system enable the generation of plants resistant against devastating pathogens. This review aims to give an updated summary of the NLR field.