Functional stacking of three resistance genes against Phytophthora infestans in potato

Identification of New Isolates of Phytophthora sojae and Selection of Resistant Soybean Genotypes

Phytophthora root and stem rot (PRR), caused by Phytophthora sojae, can occur at any growth stage under poorly drained and humid conditions. The expansion of soybean cultivation in South Korean paddy fields has increased the frequency of PRR outbreaks. This study aimed to identify four P. sojae isolates newly collected from domestic fields and evaluate race-specific resistance using the hypocotyl inoculation technique. The four isolates exhibited various pathotypes, with GJ3053 exhibiting the highest virulence complexity. Two isolates, GJ3053 and AD3617, were screened from 205 soybeans, and 182 and 190 genotypes (88.8 and 92.7%, respectively) were susceptible to each isolate. Among these accessions, five genotypes resistant to both isolates were selected. These promising genotypes are candidates for the development of resistant soybean cultivars that can effectively control PRR through gene stacking.

T-DNA characterization of genetically modified 3-R-gene late blight-resistant potato events with a novel procedure utilizing the Samplix Xdrop® enrichment technology

Before the commercialization of genetically modified crops, the events carrying the novel DNA must be thoroughly evaluated for agronomic, nutritional, and molecular characteristics. Over the years, polymerase chain reaction-based methods, Southern blot, and short-read sequencing techniques have been utilized for collecting molecular characterization data. Multiple genomic applications are necessary to determine the insert location, flanking sequence analysis, characterization of the inserted DNA, and determination of any interruption of native genes. These techniques are time-consuming and labor-intensive, making it difficult to characterize multiple events. Current advances in sequencing technologies are enabling whole-genomic sequencing of modified crops to obtain full molecular characterization. However, in polyploids, such as the tetraploid potato, it is a challenge to obtain whole-genomic sequencing coverage that meets the regulatory approval of the genetic modification. Here we describe an alternative to labor-intensive applications with a novel procedure using Samplix Xdrop® enrichment technology and next-generation Nanopore sequencing technology to more efficiently characterize the T-DNA insertions of four genetically modified potato events developed by the Feed the Future Global Biotech Potato Partnership: DIA_MSU_UB015, DIA_MSU_UB255, GRA_MSU_UG234, and GRA_MSU_UG265 (derived from regionally important varieties Diamant and Granola). Using the Xdrop® /Nanopore technique, we obtained a very high sequence read coverage within the T-DNA and junction regions. In three of the four events, we were able to use the data to confirm single T-DNA insertions, identify insert locations, identify flanking sequences, and characterize the inserted T-DNA. We further used the characterization data to identify native gene interruption and confirm the stability of the T-DNA across clonal cycles. These results demonstrate the functionality of using the Xdrop® /Nanopore technique for T-DNA characterization. This research will contribute to meeting regulatory safety and regulatory approval requirements for commercialization with small shareholder farmers in target countries within our partnership.

CRISPR/Cas StNRL1 gene knockout increases resistance to late blight and susceptibility to early blight in potato

With the development of genome editing technologies, editing susceptible genes is a promising method to modify plants for resistance to stress. NPH3/RPT2-LIKE1 protein (NRL1) interacts with effector Pi02860 of Phytophthora infestans and creates a protein complex, promoting the proteasome-mediated degradation of the guanine nucleotide exchange factor SWAP70. SWAP70, as a positive regulator, enhances cell death triggered by the perception of the P. infestans pathogen-associated molecular pattern (PAMP) INF1. Using a clustered regularly interspaced short palindrome repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, a construct was made to introduce four guide RNAs into the potato cultivar Agria. A total of 60 putative transgenic lines were regenerated, in which 10 transgenic lines with deletions were selected and analyzed. A mutant line with a four-allelic knockdown of StNRL1 gene was obtained, showing an ~90% reduction in StNRL1 expression level, resulting in enhanced resistance to P. infestans. Surprisingly, mutant lines were susceptible to Alternaria alternata, suggesting that StNRL1 may play a role as a resistance gene; hence, silencing StNRL1 enhances resistance to P. infestans.

Tetraose steroidal glycoalkaloids from potato provide resistance against Alternaria solani and Colorado potato beetle

Plants with innate disease and pest resistance can contribute to more sustainable agriculture. Natural defence compounds produced by plants have the potential to provide a general protective effect against pathogens and pests, but they are not a primary target in resistance breeding. Here, we identified a wild relative of potato, Solanum commersonii, that provides us with unique insight in the role of glycoalkaloids in plant immunity. We cloned two atypical resistance genes that provide resistance to Alternaria solani and Colorado potato beetle through the production of tetraose steroidal glycoalkaloids (SGA). Moreover, we provide in vitro evidence to show that these compounds have potential against a range of different (potato pathogenic) fungi. This research links structural variation in SGAs to resistance against potato diseases and pests. Further research on the biosynthesis of plant defence compounds in different tissues, their toxicity, and the mechanisms for detoxification, can aid the effective use of such compounds to improve sustainability of our food production.

Plant and pathogen genomics: essential approaches for stem rust resistance gene stacks in wheat

The deployment of disease resistance genes is currently the most economical and environmentally sustainable method of crop protection. However, disease resistance genes can rapidly break down because of constant pathogen evolution, particularly when they are deployed singularly. Polygenic resistance is, therefore, considered the most durable, but combining and maintaining these genes by breeding is a laborious process as effective genes are usually unlinked. The deployment of polygenic resistance with single-locus inheritance is a promising innovation that overcomes these difficulties while enhancing resistance durability. Because of major advances in genomic technologies, increasing numbers of plant resistance genes have been cloned, enabling the development of resistance transgene stacks (RTGSs) that encode multiple genes all located at a single genetic locus. Gene stacks encoding five stem rust resistance genes have now been developed in transgenic wheat and offer both breeding simplicity and potential resistance durability. The development of similar genomic resources in phytopathogens has advanced effector gene isolation and, in some instances, enabled functional validation of individual resistance genes in RTGS. Here, the wheat stem rust pathosystem is used as an illustrative example of how host and pathogen genomic advances have been instrumental in the development of RTGS, which is a strategy applicable to many other agricultural crop species.

Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors

Potato (Solanum tuberosum) and tomato (Solanum lycopersicon) crops suffer severe losses to late blight caused by the oomycete pathogen Phytophthora infestans. Solanum americanum, a relative of potato and tomato, is globally distributed and most accessions are highly blight resistant. We generated high-quality reference genomes of four S. americanum accessions, resequenced 52 accessions, and defined a pan-NLRome of S. americanum immune receptor genes. We further screened for variation in recognition of 315P. infestans RXLR effectors in 52 S. americanum accessions. Using these genomic and phenotypic data, we cloned three NLR-encoding genes, Rpi-amr4, R02860 and R04373, that recognize cognate P. infestans RXLR effectors PITG_22825 (AVRamr4), PITG_02860 and PITG_04373. These genomic resources and methodologies will support efforts to engineer potatoes with durable late blight resistance and can be applied to diseases of other crops.

Breeding strategies for late blight resistance in potato crop: recent developments

Late blight (LB) is a serious disease that affects potato crop and is caused by Phytophthora infestans. Fungicides are commonly used to manage this disease, but this practice has led to the development of resistant strains and it also poses serious environmental and health risks. Therefore, breeding for resistance development can be the most effective strategies to control late blight. Various Solanum species have been utilized as a source of resistance genes to combat late blight disease. Several potential resistance genes and quantitative resistance loci (QRLs) have been identified and mapped through the application of molecular techniques. Furthermore, molecular markers closely linked to resistance genes or QRLs have been utilized to hasten the breeding process. However, the use of single-gene resistance can lead to the breakdown of resistance within a short period. To address this, breeding programs are now being focused on development of durable and broad-spectrum resistant cultivars by combining multiple resistant genes and QRLs using advanced molecular breeding tools such as marker-assisted selection (MAS) and cis-genic approaches. In addition to the strategies mentioned earlier, somatic hybridization has been utilized for the development and characterization of interspecific somatic hybrids. To further broaden the scope of late blight resistance breeding, approaches such as genomic selection, RNAi silencing, and various genome editing techniques can be employed. This study provides an overview of recent advances in various breeding strategies and their applications in improving the late blight resistance breeding program.

Pathways to engineering plant intracellular NLR immune receptors

Factors including climate change and increased global exchange are set to escalate the prevalence of plant diseases, posing an unprecedented threat to global food security and making it more challenging to meet the demands of an ever-growing population. As such, new methods of pathogen control are essential to help with the growing danger of crop losses to plant diseases. The intracellular immune system of plants utilizes nucleotide-binding leucine-rich repeat (NLR) receptors to recognize and activate defense responses to pathogen virulence proteins (effectors) delivered to the host. Engineering the recognition properties of plant NLRs toward pathogen effectors is a genetic solution to plant diseases with high specificity, and it is more sustainable than several current methods for pathogen control that frequently rely on agrochemicals. Here, we highlight the pioneering approaches toward enhancing effector recognition in plant NLRs and discuss the barriers and solutions in engineering the plant intracellular immune system.

Insights on cisgenic plants with durable disease resistance under the European Green Deal

Significant shares of harvests are lost to pests and diseases, therefore, minimizing these losses could solve part of the supply constraints to feed the world. Cisgenesis is defined as the insertion of genetic material into a recipient organism from a donor that is sexually compatible. Here, we review (i) conventional plant breeding, (ii) cisgenesis, (iii) current pesticide-based disease management, (iv) potential economic implications of cultivating cisgenic crops with durable disease resistances, and (v) potential environmental implications of cultivating such crops; focusing mostly on potatoes, but also apples, with resistances to Phytophthora infestans and Venturia inaequalis, respectively. Adopting cisgenic varieties could provide benefits to farmers and to the environment through lower pesticide use, thus contributing to the European Green Deal target.

The northern corn leaf blight resistance gene Ht1 encodes an nucleotide-binding, leucine-rich repeat immune receptor

Northern corn leaf blight, caused by the fungal pathogen Exserohilum turcicum, is a major disease of maize. The first major locus conferring resistance to E. turcicum race 0, Ht1, was identified over 50 years ago, but the underlying gene has remained unknown. We employed a map-based cloning strategy to identify the Ht1 causal gene, which was found to be a coiled-coil nucleotide-binding, leucine-rich repeat (NLR) gene, which we named PH4GP-Ht1. Transgenic testing confirmed that introducing the native PH4GP-Ht1 sequence to a susceptible maize variety resulted in resistance to E. turcicum race 0. A survey of the maize nested association mapping genomes revealed that susceptible Ht1 alleles had very low to no expression of the gene. Overexpression of the susceptible B73 allele, however, did not result in resistant plants, indicating that sequence variations may underlie the difference between resistant and susceptible phenotypes. Modelling of the PH4GP-Ht1 protein indicated that it has structural homology to the Arabidopsis NLR resistance gene ZAR1, and probably forms a similar homopentamer structure following activation. RNA sequencing data from an infection time course revealed that 1 week after inoculation there was a threefold reduction in fungal biomass in the PH4GP-Ht1 transgenic plants compared to wild-type plants. Furthermore, PH4GP-Ht1 transgenics had significantly more inoculation-responsive differentially expressed genes than wild-type plants, with enrichment seen in genes associated with both defence and photosynthesis. These results demonstrate that the NLR PH4GP-Ht1 is the causal gene underlying Ht1, which represents a different mode of action compared to the previously reported wall-associated kinase northern corn leaf blight resistance gene Htn1/Ht2/Ht3.

Stacking Multiple Genes Improves Resistance to Chilo suppressalis, Magnaporthe oryzae, and Nilaparvata lugens in Transgenic Rice

The ability of various pests and diseases to adapt to a single plant resistance gene over time leads to loss of resistance in transgenic rice. Therefore, introduction of different pest and disease resistance genes is critical for successful cultivation of transgenic rice strains with broad-spectrum resistance to multiple pathogens. Here, we produced resistance rice lines with multiple, stacked resistance genes by stacking breeding and comprehensively evaluated their resistance to Chilo suppressalis (striped rice stemborer), Magnaporthe oryzae (rice blast), and Nilaparvata lugens (brown planthopper) in a pesticide-free environment. CRY1C and CRY2A are exogenous genes from Bacillus thuringiensis. Pib, Pikm, and Bph29 are natural genes in rice. CH121TJH was introduced into CRY 1C, Pib, Pikm, and Bph29. CH891TJH and R205XTJH were introduced into CRY 2A, Pib, Pikm, and Bph29. Compared with those observed in their recurrent parents, CH121TJH significantly increased the mortality of borers. The other two lines CH891TJH and R205XTJH are the same result. Three lines introduction of Pib and Pikm significantly reduced the area of rice blast lesions, and introduction of Bph29 significantly reduced seedling mortality from N. lugens. Introduction of the exogenous genes had relatively few effects on agronomic and yield traits of the original parents. These findings suggest that stacking of rice resistance genes through molecular marker-assisted backcross breeding can confer broad spectrum and multiple resistance in differently genetic backgrounds.

NLR immune receptor-nanobody fusions confer plant disease resistance

Plant pathogens cause recurrent epidemics, threatening crop yield and global food security. Efforts to retool the plant immune system have been limited to modifying natural components and can be nullified by the emergence of new pathogen strains. Made-to-order synthetic plant immune receptors provide an opportunity to tailor resistance to pathogen genotypes present in the field. In this work, we show that plant nucleotide-binding, leucine-rich repeat immune receptors (NLRs) can be used as scaffolds for nanobody (single-domain antibody fragment) fusions that bind fluorescent proteins (FPs). These fusions trigger immune responses in the presence of the corresponding FP and confer resistance against plant viruses expressing FPs. Because nanobodies can be raised against most molecules, immune receptor-nanobody fusions have the potential to generate resistance against plant pathogens and pests delivering effectors inside host cells.

Will genetically modified late blight resistant potatoes be the first GM crops to be approved for commercial growing in Norway?

Last decade's advances in biotechnology, with the introduction of CRISPR, have challenged the regulatory framework for competent authorities all over the world. Hence, regulatory issues related to gene editing are currently high on the agenda both in the EU and in the European Economic Area (EEA) Agreement country of Norway, particularly with regards to sustainable agriculture. During the negotiations on the EEA Agreement, Norway was allowed to retain three extra aims in the Gene Technology Act: "That the production and use of GMO happens in an ethical way, is beneficial to society and is in accordance with the principle of sustainable development". We argue the case that taking sustainability into the decisions on regulating gene edited products could be easier in Norway than in the EU because of these extra aims. Late blight is our chosen example, as a devastating disease in potato that is controlled in Norway primarily by high levels of fungicide use. Also, many of these fungicides are being banned due to negative environmental and health effects. The costs of controlling late blight in Norway were calculated in 2006, and since then there have been new cultivars developed, inflation and an outbreak of war in Europe increasing farm input costs. A genetically modified (GM) cisgenic late blight resistant (LBR) potato presents a possible solution that could reduce fungicide use, but this could still be controversial. This paper aims to discuss the advantages and disadvantages of approving the commercial use of a GM LBR potato cultivar in Norway and compare these against currently used late blight management methods and conventional potato resistance breeding. We argue that a possible route for future regulatory framework could build upon the proposal by the Norwegian Biotechnology Advisory Board from 2019, also taking sustainability goals into account. This could favour a positive response from the Competent Authorities without breeching the European Economic Area (EEA) Agreement. Perhaps the EU could adopt a similar approach to fulfil their obligations towards a more sustainable agriculture?

Canola with Stacked Genes Shows Moderate Resistance and Resilience against a Field Population of Plasmodiophora brassicae (Clubroot) Pathotype X

Genetic resistance is a cornerstone for managing clubroot (Plasmodiophora brassicae). However, when used repeatedly, a clubroot resistance (CR) gene can be broken rapidly. In this study, canola inbred/hybrid lines carrying one or two CR genes (Rcr1/CRa^M and Crr1^rutb) were assessed against P. brassicae pathotype X by repeated exposure to the same inoculum source under a controlled environment. Lines carrying two CR genes, either Rcr1 + Crr1^rutb or CRa^M + Crr1^rutb, showed partial resistance. Selected lines were inoculated with a field pathotype X population (L-G3) at 5 × 10⁶ resting spores/g soil, and all clubs were returned to the soil they came from six weeks after inoculation. The planting was repeated for five cycles, with diseased roots being returned to the soil after each cycle. The soil inoculum was quantified using qPCR before each planting cycle. All lines with a single CR gene were consistently susceptible, maintaining high soil inoculum levels over time. The lines carrying two CR genes showed much lower clubroot severity, resulting in a 10-fold decline in soil inoculum. These results showed that the CR-gene stacking provided moderate resistance against P. brassicae pathotype X, which may also help reduce the pathogen inoculum buildup in soil.

Engineering Resistance against Sclerotinia sclerotiorum Using a Truncated NLR (TNx) and a Defense-Priming Gene

The association of both cell-surface PRRs (Pattern Recognition Receptors) and intracellular receptor NLRs (Nucleotide-Binding Leucine-Rich Repeat) in engineered plants have the potential to activate strong defenses against a broad range of pathogens. Here, we describe the identification, characterization, and in planta functional analysis of a novel truncated NLR (TNx) gene from the wild species Arachis stenosperma (AsTIR19), with a protein structure lacking the C-terminal LRR (Leucine Rich Repeat) domain involved in pathogen perception. Overexpression of AsTIR19 in tobacco plants led to a significant reduction in infection caused by Sclerotinia sclerotiorum, with a further reduction in pyramid lines containing an expansin-like B gene (AdEXLB8) potentially involved in defense priming. Transcription analysis of tobacco transgenic lines revealed induction of hormone defense pathways (SA; JA-ET) and PRs (Pathogenesis-Related proteins) production. The strong upregulation of the respiratory burst oxidase homolog D (RbohD) gene in the pyramid lines suggests its central role in mediating immune responses in plants co-expressing the two transgenes, with reactive oxygen species (ROS) production enhanced by AdEXLB8 cues leading to stronger defense response. Here, we demonstrate that the association of potential priming elicitors and truncated NLRs can produce a synergistic effect on fungal resistance, constituting a promising strategy for improved, non-specific resistance to plant pathogens.

Emerging principles in the design of bioengineered made-to-order plant immune receptors

Crop yield and global food security are under constant threat from plant pathogens with the potential to cause epidemics. Traditional breeding for disease resistance can be too slow to counteract these emerging threats, resulting in the need to retool the plant immune system using bioengineered made-to-order immune receptors. Efforts to engineer immune receptors have focused primarily on nucleotide-binding domain and leucine-rich repeat (NLR) immune receptors and proof-of-principles studies. Based upon a near-exhaustive literature search of previously engineered plant immune systems we distil five emerging principles in the design of bioengineered made-to-order plant NLRs and describe approaches based on other components. These emerging principles are anticipated to assist the functional understanding of plant immune receptors, as well as bioengineering novel disease resistance specificities.

CRISPR/Cas mediated genome editing in potato: Past achievements and future directions

Genome engineering has been re-shaping plant biotechnology and agriculture. Crop improvement using the recently developed gene editing techniques is now easier, faster, and more precise than ever. Although considered to be a global food security crop, potato has not benefitted enough from diverse collection of these techniques. Unique genetic features of cultivated potatoes such as tetrasomic inheritance, high genomic heterozygosity, and inbreeding depression hamper conventional breeding of this important crop. Therefore, genome editing provides an excellent arsenal of tools for trait improvement in potato. Moreover, using specific transformation protocols, it is possible to engineer transgene free commercial varieties. In this review we first describe the past achievements in potato genome editing and highlight some of the missing aspects of these efforts. Then, we discuss about technical challenges of genome editing in potato and present approaches to overcome these difficulties. Finally, we talk about genome editing applications that have not been explored in potato and point out some of the missing venues in literature.

From plant immunity to crop disease resistance

Plant diseases caused by diverse pathogens lead to serious reduction in crop yield and threaten food security worldwide. Genetic improvement of plant immunity is considered as the most effective and sustainable approach to control crop diseases. In the last decade, our understanding of plant immunity at both molecular and genomic levels has improved greatly. Combined with advances in biotechnologies, particularly CRISPR/Cas9-based genome editing, we can now rapidly identify new resistance genes and engineer disease resistance crop plants like never before. In this review, we summarize the current knowledge of plant immunity and outline existing and new strategies for disease resistance improvement in crop plants. We also discuss existing challenges in this field and suggest directions for future studies.

Genome Engineering Technology for Durable Disease Resistance: Recent Progress and Future Outlooks for Sustainable Agriculture

Crop production worldwide is under pressure from multiple factors, including reductions in available arable land and sources of water, along with the emergence of new pathogens and development of resistance in pre-existing pathogens. In addition, the ever-growing world population has increased the demand for food, which is predicted to increase by more than 100% by 2050. To meet these needs, different techniques have been deployed to produce new cultivars with novel heritable mutations. Although traditional breeding continues to play a vital role in crop improvement, it typically involves long and laborious artificial planting over multiple generations. Recently, the application of innovative genome engineering techniques, particularly CRISPR-Cas9-based systems, has opened up new avenues that offer the prospects of sustainable farming in the modern agricultural industry. In addition, the emergence of novel editing systems has enabled the development of transgene-free non-genetically modified plants, which represent a suitable option for improving desired traits in a range of crop plants. To date, a number of disease-resistant crops have been produced using gene-editing tools, which can make a significant contribution to overcoming disease-related problems. Not only does this directly minimize yield losses but also reduces the reliance on pesticide application, thereby enhancing crop productivity that can meet the globally increasing demand for food. In this review, we describe recent progress in genome engineering techniques, particularly CRISPR-Cas9 systems, in development of disease-resistant crop plants. In addition, we describe the role of CRISPR-Cas9-mediated genome editing in sustainable agriculture.

Silencing susceptibility genes in potato hinders primary infection of Phytophthora infestans at different stages

Most potato cultivars are susceptible to late blight disease caused by the oomycete pathogen Phytophthora infestans. A new source of resistance to prevent or diminish pathogen infection is found in the genetic loss of host susceptibility. Previously, we showed that RNAi-mediated silencing of the potato susceptibility (S) genes StDND1, StDMR1 and StDMR6 leads to increased late blight resistance. The mechanisms underlying this S-gene mediated resistance have thus far not been identified. In this study, we examined the infection process of P. infestans on StDND1-, StDMR1- and StDMR6-silenced potato lines. Microscopic analysis showed that penetration of P. infestans spores was hampered on StDND1-silenced plants. On StDMR1- and StDMR6-silenced plants, P. infestans infection was arrested at a primary infection stage by enhanced cell death responses. Histochemical staining revealed that StDMR1- and StDMR6-silenced plants display elevated ROS levels in cells at the infection sites. Resistance in StDND1-silenced plants, however, seems not to rely on a cell death response as ROS accumulation was found to be absent at most inoculated sites. Quantitative analysis of marker gene expression suggests that the increased resistance observed in StDND1- and StDMR6-silenced plants relies on an early onset of SA- and ET-mediated signalling pathways. Resistance mediated by silencing StDMR1 was found to be correlated with the early induction of SA-mediated signalling. These data provide evidence that different defense mechanisms are involved in late blight resistance mediated by functional impairment of different potato S-genes.

"Core" RxLR effectors in phytopathogenic oomycetes: A promising way to breeding for durable resistance in plants?

Phytopathogenic oomycetes are known to successfully infect their hosts due to their ability to secrete effector proteins. Of interest to many researchers are effectors with the N-terminal RxLR motif (Arginine-any amino acid-Leucine-Arginine). Owing to advances in genome sequencing, we can now comprehend the high level of diversity among oomycete effectors, and similarly, their conservation within and among species referred to here as "core" RxLR effectors (CREs). Currently, there is a considerable number of CREs that have been identified in oomycetes. Functional characterization of these CREs propose their virulence role with the potential of targeting central cellular processes that are conserved across diverse plant species. We reason that effectors that are highly conserved and recognized by the host, could be harnessed in engineering plants for durable as well as broad-spectrum resistance.

Visualising the ionome in resistant and susceptible plant-pathogen interactions

At the morphological and anatomical levels, the ionome, or the elemental composition of an organism, is an understudied area of plant biology. In particular, the ionomic responses of plant-pathogen interactions are scarcely described, and there are no studies on immune reactions. In this study we explored two X-ray fluorescence (XRF)-based ionome visualisation methods (benchtop- and synchrotron-based micro-XRF [µXRF]), as well as the quantitative inductively coupled plasma optical emission spectroscopy (ICP-OES) method, to investigate the changes that occur in the ionome of compatible and incompatible plant-pathogen interactions. We utilised the agronomically important and comprehensively studied interaction between potato (Solanum tuberosum) and the late blight oomycete pathogen Phytophthora infestans as an example. We used one late blight-susceptible potato cultivar and two resistant transgenic plant lines (only differing from the susceptible cultivar in one or three resistance genes) both in control and P. infestans-inoculated conditions. In the lesions from the compatible interaction, we observed rearrangements of several elements, including a decrease of the mobile macronutrient potassium (K) and an increase in iron (Fe) and manganese (Mn), compared with the tissue outside the lesion. Interestingly, we observed distinctly different distribution patterns of accumulation at the site of inoculation in the resistant lines for calcium (Ca), magnesium (Mg), Mn and silicon (Si) compared to the susceptible cultivar. The results reveal different ionomes in diseased plants compared to resistant plants. Our results demonstrate a technical advance and pave the way for deeper studies of the plant-pathogen ionome in the future.

Breeding for Resistance to Fusarium Wilt of Tomato: A Review

For over a century, breeders have worked to develop tomato (Solanum lycopersicum) cultivars with resistance to Fusarium wilt (Fol) caused by the soilborne fungus Fusarium oxysporum f. sp. lycopersici. Host resistance is the most effective strategy for the management of this disease. For each of the three Fol races, resistance has been introgressed from wild tomato species, predominately in the form of R genes. The I, I-2, I-3, and I-7 R genes have each been identified, as well as the corresponding Avr effectors in the fungus with the exception of Avr7. The mechanisms by which the R gene protein products recognize these effectors, however, has not been elucidated. Extensive genetic mapping, gene cloning, and genome sequencing efforts support the development of tightly-linked molecular markers, which greatly expedite tomato breeding and the development of elite, Fol resistant cultivars. These resources also provide important tools for pyramiding resistance genes and should support the durability of host resistance.

Comparative Phenotypic and Agronomic Assessment of Transgenic Potato with 3R-Gene Stack with Complete Resistance to Late Blight Disease

Transgenic potato event Vic.172, expressing three naturally occurring resistance genes (R genes) conferring complete protection against late blight disease, was evaluated for resistance to late blight, phenotypic characterization, and agronomic performance in field conditions at three locations during three seasons in Uganda. These trials were conducted by comparison to the variety Victoria from which Vic.172 derives, using identical fungicide treatment, except when evaluating disease resistance. During all seasons, the transgenic event Vic.172 was confirmed to have complete resistance to late blight disease, whereas Victoria plants were completely dead by 60-80 days after planting. Tubers from Vic.172 were completely resistant to LB after artificial inoculation. The phenotypic characterization included observations of the characteristics and development of the stems, leaves, flowers, and tubers. Differences in phenotypic parameters between Vic.172 and Victoria were not statistically significant across locations and seasons. The agronomic performance observations covered sprouting, emergence, vigor, foliage growth, and yield. Differences in agronomic performance were not statistically significant except for marketable yield in one location under high productivity conditions. However, yield variation across locations and seasons was not statistically significant, but was influenced by the environment. Hence, the results of the comparative assessment of the phenotype and agronomic performance revealed that transgenic event Vic.172 did not present biologically significant differences in comparison to the variety Victoria it derives from.

Targeting of anti-microbial proteins to the hyphal surface amplifies protection of crop plants against Phytophthora pathogens

Phytophthora pathogens are a persistent threat to the world's commercially important agricultural crops, including potato and soybean. Current strategies aim at reducing crop losses rely mostly on disease-resistance breeding and chemical pesticides, which can be frequently overcome by the rapid adaptive evolution of pathogens. Transgenic crops with intrinsic disease resistance offer a promising alternative and continue to be developed. Here, we explored Phytophthora-derived PI3P (phosphatidylinositol 3-phosphate) as a novel control target, using proteins that bind this lipid to direct secreted anti-microbial peptides and proteins (AMPs) to the surface of Phytophthora pathogens. In transgenic Nicotiana benthamiana, soybean, and potato plants, significantly enhanced resistance to different pathogen isolates was achieved by expression of two AMPs (GAFP1 or GAFP3 from the Chinese medicinal herb Gastrodia elata) fused with a PI3P-specific binding domain (FYVE). Using the soybean pathogen P. sojae as an example, we demonstrated that the FYVE domain could boost the activities of GAFPs in multiple independent assays, including those performed in vitro, in vivo, and in planta. Mutational analysis of P. sojae PI3K1 and PI3K2 genes of this pathogen confirmed that the enhanced activities of the targeted GAFPs were correlated with PI3P levels in the pathogen. Collectively, our study provides a new strategy that could be used to confer resistance not only to Phytophthora pathogens in many plants but also potentially to many other kinds of plant pathogens with unique targets.

A playbook for developing disease-resistant crops through immune receptor identification and transfer

Plants are resistant to most pathogens because of an immune system that perceives invading microbes and activates defense. A large repertoire of innate immune receptors mediates specific direct or indirect recognition of pathogen-derived molecules. Disease is often a consequence of insufficient immune surveillance, and the transfer of immune receptor genes from resistant plants to susceptible crop varieties is an effective strategy for combating disease outbreaks. We discuss approaches for identifying intracellular and cell surface immune receptors, with particular focus on recently developed and emerging methodologies. We also review considerations for the transfer of immune receptor genes into crop species, including additional host factors that may be required for immune receptor function. Together, these concepts lay out a broadly applicable playbook for developing crop varieties with durable disease resistance.

Characterization and elimination of linkage-drag associated with Fusarium wilt race 3 resistance genes

Reducing the size of the I-3 introgression resulted in eliminating linkage-drag contributing to increased sensitivity to bacterial spot and reduced fruit size. The I-7 gene was determined to have no effect on bacterial spot or fruit size, and germplasm is now available with both the reduced I-3 introgression and I-7. Tomato (Solanum lycopersicum) production is increasingly threatened by Fusarium wilt race 3 (Fol3) caused by the soilborne fungus, Fusarium oxysporum f. sp. lycopersici. Although host resistance based on the I-3 gene is the most effective management strategy, I-3 is associated with detrimental traits including reduced fruit size and increased bacterial spot sensitivity. Previous research demonstrated the association with bacterial spot is not due to the I-3 gene, itself, and we hypothesize that reducing the size of the I-3 introgression will remedy this association. Cultivars with I-7, an additional Fol3 resistance gene, are available but are not widely used commercially, and it is unclear whether I-7 also has negative horticultural associations. To characterize the effect of I-3 on fruit size, segregating populations were developed and evaluated, revealing that the large I-3 introgression decreased fruit size by approximately 21%. We reduced the I-3 introgression from 5 to 140 kb through successive recombinant screening and crossing efforts. The reduced I-3 introgression and I-7 were then separately backcrossed into elite Florida breeding lines and evaluated for effects on bacterial spot sensitivity and fruit size across multiple seasons. The reduced I-3 introgression resulted in significantly less bacterial spot and larger fruit size than the large introgression, and it had no effect on these horticultural characteristics compared with Fol3 susceptibility. I-7 was also found to have no effect on these traits compared to Fol3 susceptibility. Together, these efforts support the development of superior Fol3-resistant cultivars and more durable resistance against this pathogen.

New Sources of Eastern Filbert Blight Resistance and Simple Sequence Repeat Markers on Linkage Group 6 in Hazelnut (Corylus avellana L.)

Commercial production of hazelnut (Corylus avellana) in Oregon's Willamette Valley is threatened by eastern filbert blight (EFB), a serious canker disease caused by the pyrenomycete Anisogramma anomala (Peck) E. Müller. The fungus also prevents the establishment of hazelnut orchards in eastern North America. Genetic resistance is considered the most effective way to control the disease. A high level of EFB resistance was first discovered in 'Gasaway'. This resistance is conferred by a dominant allele at a single locus on linkage group 6 (LG6). Resistance from several additional sources has been assigned to the same chromosomal region. In this study, new simple sequence repeat (SSR) markers were developed for the resistance region on LG6 and new sources of resistance were investigated. Forty-two new SSR markers were developed from four contigs in the genome sequence of 'Jefferson' hazelnut, characterized, and nine of them were placed on LG6 of the genetic map. Accessions representing 12 new sources of EFB resistance were crossed with susceptible selections resulting in 18 seedling populations. Segregation ratios in the seedling populations fit the expected 1:1 ratio for 10 sources, while one source showed an excess of resistant seedlings and another showed an excess of susceptible seedlings. Based on correlation of disease response and scores of SSR markers in the 'Gasaway' resistance region in the seedlings, eight resistance sources were assigned to LG6. Linkage maps were constructed for each progeny using SSR markers. The LG6 resistance sources include two selections (#23 and #26) from the Russian Research Institute of Forestry and Mechanization near Moscow, four selections from southern Russia, one selection (OSU 1185.126) from Crimea, one selection (OSU 533.129) from Michigan, Corylus heterophylla 'Ogyoo' from the South Korea, and the interspecific hybrid 'Estrella #1'. These new LG6 resistance sources and SSR markers should be useful in breeding new cultivars, including the pyramiding of resistance genes. For the other four resistance sources (Moscow #37, hybrid selection OSU 401.014, C. americana 'Winkler' and C. americana OSU 366.060), SSR marker scores on linkage groups 6, 7 and 2 were not correlated with disease response and merit further investigation.

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.

Extreme Resistance to Viruses in Potato and Soybean

Plant pathogens, including viruses, negatively impact global crop production. Plants have evolved complex immune responses to pathogens. These responses are often controlled by nucleotide-binding leucine-rich repeat proteins (NLRs), which recognize intracellular, pathogen-derived proteins. Genetic resistance to plant viruses is often phenotypically characterized by programmed cell death at or near the infection site; a reaction termed the hypersensitive response. Although visualization of the hypersensitive response is often used as a hallmark of resistance, the molecular mechanisms leading to the hypersensitive response and associated cell death vary. Plants with extreme resistance to viruses rarely exhibit symptoms and have little to no detectable virus replication or spread beyond the infection site. Both extreme resistance and the hypersensitive response can be activated by the same NLR genes. In many cases, genes that normally provide an extreme resistance phenotype can be stimulated to cause a hypersensitive response by experimentally increasing cellular levels of pathogen-derived elicitor protein(s). The molecular mechanisms of extreme resistance and its relationship to the hypersensitive response are largely uncharacterized. Studies on potato and soybean cultivars that are resistant to strains of Potato virus Y (PVY), Potato virus X (PVX), and Soybean mosaic virus (SMV) indicate that abscisic acid (ABA)-mediated signaling and NLR nuclear translocation are important for the extreme resistance response. Recent research also indicates that some of the same proteins are involved in both extreme resistance and the hypersensitive response. Herein, we review and synthesize published studies on extreme resistance in potato and soybean, and describe studies in additional species, including model plant species, to highlight future research avenues that may bridge the gaps in our knowledge of plant antiviral defense mechanisms.

Engineering plant disease resistance against biotrophic pathogens

Breeding for disease resistance against microbial pathogens is essential for food security in modern agriculture. Conventional breeding, although widely accepted, is time consuming. An alternative approach is generating crop plants with desirable traits through genetic engineering. The collective efforts of many labs in the past 30 years have led to a comprehensive understanding of how plant immunity is achieved, enabling the application of genetic engineering to enhance disease resistance in crop plants. Here, we briefly review the engineering of disease resistance against biotrophic pathogens using various components of the plant immune system. Recent breakthroughs in immune receptors signaling and systemic acquired resistance (SAR), along with innovations in precise gene editing methods, provide exciting new opportunities for the development of improved environmentally friendly crop varieties that are disease resistant and high-yield.

Mutations introduced in susceptibility genes through CRISPR/Cas9 genome editing confer increased late blight resistance in potatoes

The use of pathogen-resistant cultivars is expected to increase yield and decrease fungicide use in agriculture. However, in potato breeding, increased resistance obtained via resistance genes (R-genes) is hampered because R-gene(s) are often specific for a pathogen race and can be quickly overcome by the evolution of the pathogen. In parallel, susceptibility genes (S-genes) are important for pathogenesis, and loss of S-gene function confers increased resistance in several plants, such as rice, wheat, citrus and tomatoes. In this article, we present the mutation and screening of seven putative S-genes in potatoes, including two DMR6 potato homologues. Using a CRISPR/Cas9 system, which conferred co-expression of two guide RNAs, tetra-allelic deletion mutants were generated and resistance against late blight was assayed in the plants. Functional knockouts of StDND1, StCHL1, and DMG400000582 (StDMR6-1) generated potatoes with increased resistance against late blight. Plants mutated in StDND1 showed pleiotropic effects, whereas StDMR6-1 and StCHL1 mutated plants did not exhibit any growth phenotype, making them good candidates for further agricultural studies. Additionally, we showed that DMG401026923 (here denoted StDMR6-2) knockout mutants did not demonstrate any increased late blight resistance, but exhibited a growth phenotype, indicating that StDMR6-1 and StDMR6-2 have different functions. To the best of our knowledge, this is the first report on the mutation and screening of putative S-genes in potatoes, including two DMR6 potato homologues.

Pathogen-informed breeding for crop disease resistance

The development of durable and broad-spectrum resistance is an economical and eco-friendly approach to control crop diseases for sustainable agricultural production. Emerging knowledge of the molecular basis of pathogenesis and plant-pathogen interactions has contributed to the development of novel pathogen-informed breeding strategies beyond the limits imposed by conventional breeding. Here, we review the current status of pathogen-assisted resistance-related gene cloning. We also describe how pathogen effector proteins can be used to identify resistance resources and to inform cultivar deployment. Finally, we summarize the main approaches for pathogen-directed plant improvement, including transgenesis and genome editing. Thus, we describe the emerging role of pathogen-related studies in the breeding of disease-resistant varieties, and propose innovative pathogen-informed strategies for future applications.

Screening of Wild Potatoes Identifies New Sources of Late Blight Resistance

Late blight (LB) of potato is considered one of the most devastating plant diseases in the world. Most cultivated potatoes are susceptible to this disease. However, wild relatives of potatoes are an excellent source of LB resistance. We screened 384 accessions of 72 different wild potato species available from the U.S. Potato GeneBank against the LB pathogen Phytophthora infestans in a detached leaf assay (DLA). P. infestans isolates US-23 and NL13316 were used in the DLA to screen the accessions. Although all plants in 273 accessions were susceptible, all screened plants in 39 accessions were resistant. Resistant and susceptible plants were found in 33 accessions. All tested plants showed a partial resistance phenotype in two accessions, segregation of resistant and partial resistant plants in nine accessions, segregation of partially resistant and susceptible plants in four accessions, and segregation of resistant, partially resistant, and susceptible individuals in 24 accessions. We found several species that were never before reported to be resistant to LB: Solanum albornozii, S. agrimoniifolium, S. chomatophilum, S. ehrenbergii, S. hypacrarthrum, S. iopetalum, S. palustre, S. piurae, S. morelliforme, S. neocardenasii, S. trifidum, and S. stipuloideum. These new species could provide novel sources of LB resistance. P. infestans clonal lineage-specific screening of selected species was conducted to identify the presence of RB resistance. We found LB resistant accessions in Solanum verrucosum, Solanum stoloniferum, and S. morelliforme that were susceptible to the RB overcoming isolate NL13316, indicating the presence of RB-like resistance in these species.

A five-transgene cassette confers broad-spectrum resistance to a fungal rust pathogen in wheat

Breeding wheat with durable resistance to the fungal pathogen Puccinia graminis f. sp. tritici (Pgt), a major threat to cereal production, is challenging due to the rapid evolution of pathogen virulence. Increased durability and broad-spectrum resistance can be achieved by introducing more than one resistance gene, but combining numerous unlinked genes by breeding is laborious. Here we generate polygenic Pgt resistance by introducing a transgene cassette of five resistance genes into bread wheat as a single locus and show that at least four of the five genes are functional. These wheat lines are resistant to aggressive and highly virulent Pgt isolates from around the world and show very high levels of resistance in the field. The simple monogenic inheritance of this multigene locus greatly simplifies its use in breeding. However, a new Pgt isolate with virulence to several genes at this locus suggests gene stacks will need strategic deployment to maintain their effectiveness.

Identification of Solanum Immune Receptors by Bulked Segregant RNA-Seq and High-Throughput Recombinant Screening

The identification, understanding, and deployment of immune receptors are crucial to achieve high-level and durable resistance for crops against pathogens. In potato, many R genes have been identified using map-based cloning strategies. However, this is a challenging and laborious task that involves the development of a high number of molecular markers for the initial mapping, and the screening of thousands of plants for fine mapping. Bulked segregant RNA-Seq (BSR-Seq) has proven to be an efficient technique for the mapping of resistance genes. The RNA from two bulks of plants with contrasting phenotypes is sequenced and analyzed to identify single-nucleotide polymorphism (SNPs) markers linked to the target gene. Subsequently, the SNP markers that are identified can be used to delimit the mapping interval. Additionally, we designed an in vitro recombinant screening strategy that is advantageous for analyzing a large number of plants, in terms of time, space, and cost. Tips and detailed protocols, including BSR-Seq, bioinformatic analysis, and recombinant screening, are provided in this chapter.

Opportunities and Challenges in Studies of Host-Pathogen Interactions and Management of Verticillium dahliae in Tomatoes

Tomatoes (Solanum lycopersicum L.) are a valuable horticultural crop that are grown and consumed worldwide. Optimal production is hindered by several factors, among which Verticillium dahliae, the cause of Verticillium wilt, is considered a major biological constraint in temperate production regions. V. dahliae is difficult to mitigate because it is a vascular pathogen, has a broad host range and worldwide distribution, and can persist in soil for years. Understanding pathogen virulence and genetic diversity, host resistance, and plant-pathogen interactions could ultimately inform the development of integrated strategies to manage the disease. In recent years, considerable research has focused on providing new insights into these processes, as well as the development and integration of environment-friendly management approaches. Here, we discuss the current knowledge on the race and population structure of V. dahliae, including pathogenicity factors, host genes, proteins, enzymes involved in defense, and the emergent management strategies and future research directions for managing Verticillium wilt in tomatoes.

Molecular Characterization of a Pathogen-Inducible Bidirectional Promoter from Hot Pepper (Capsicum annuum)

In hot pepper, the sesquiterpene phytoalexin capsidiol is catalyzed by the two final-step enzymes, a sesquiterpene cyclase (EAS) and a hydroxylase (EAH), which are genetically linked and present as head-to-head orientation in the genome. Transcriptomic analysis revealed that a subset of EAS and EAH is highly induced following pathogen infection, suggesting the coregulation of EAS and EAH by a potential bidirectional activity of the promoter (pCaD). A series of the nested deletions of pCaD in both directions verified the bidirectional promoter activity of the pCaD. Promoter deletion analysis revealed that the 226 bp of the adjacent promoter region of EAS and GCC-box in EAH orientation were determined as critical regulatory elements for the induction of each gene. Based on promoter analyses, we generated a set of synthetic promoters to maximize reporter gene expression within the minimal length of the promoter in both directions. We found that the reporter gene expression was remarkably induced upon infection with Phytophthora capsici, Phytophthora infestans, and bacterial pathogen Pseudomonas syringae pv. tomato DC3000 but not with necrotrophic fungi Botrytis cinerea. Our results confirmed the bidirectional activity of the pCaD located between the head-to-head oriented phytoalexin biosynthetic genes in hot pepper. Furthermore, the synthetic promoter modified in pCaD could be a potential tool for pathogen-inducible expression of target genes for developing disease-resistant crops.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Genome Wide Association Studies in Multiple Spinach Breeding Populations Refine Downy Mildew Race 13 Resistance Genes

Downy mildew, caused by the oomycete Peronospora effusa, is the most economically important disease on spinach. Fourteen new races of P. effusa have been identified in the last three decades. The frequent emergence of new races of P. effusa continually overcome the genetic resistance to the pathogen. The objectives of this research were to more clearly map the downy mildew resistance locus RPF1 in spinach, to identify single nucleotide polymorphism (SNP) markers associated with the resistance, and to refine the candidate genes responsible for the resistance. Progeny from populations generated from crosses of cultivars resistant (due to RPF1) to race 13 of P. effusa (Swan, T-Bird, Squirrel, and Tonga) with race 13 susceptible cultivars (Whale and Polka) were inoculated and the downy mildew disease response determined. Association analysis was performed in TASSEL, GAPIT, PLINK, and GENESIS programs using SNP markers identified from genotyping by sequencing (GBS). Association analysis mapped the race 13 resistance loci (RPF1) to positions 0.39, 0.69, 0.94-0.98, and 1.2 Mb of chromosome 3. The associated SNPs were within 1-7 kb of the disease resistance genes Spo12784, Spo12719, Spo12905, and Spo12821, and 11-18 Kb from Spo12903. This study extended our understanding of the genetic basis of downy mildew resistance in spinach and provided the most promising candidate genes Spo12784 and Spo12903 near the RPF1 locus, to pursue functional validation. The SNP markers may be used to select for the resistant lines to improve genetic resistance against the downy mildew pathogen and in developing durably resistant cultivars.

Global transcriptome analyses reveal the molecular signatures in the early response of potato (Solanum tuberosum L.) to Phytophthora infestans, Ralstonia solanacearum, and Potato virus Y infection

Specific and common genes including transcription factors, resistance genes and pathways were significantly induced in potato by Phytophthora infestans, Ralstonia solanacearum, and Potato virus Y infection. The three major pathogens, namely, Phytophthora infestans, Ralstonia solanacearum, and Potato virus Y, can cause late blight, bacterial wilt, and necrotic ringspot, respectively, and thus severely reduce the yield and quality of potatoes (Solanum tuberosum L.). This study was the first to systematically analyze the relationship between transcriptome alterations in potato infected by these pathogens at the early stages. A total of 75,500 unigenes were identified, and 44,008 were annotated into 5 databases, namely, non-redundant (NR), Swiss-Prot protein, clusters of orthologous groups for eukaryotic complete genomes (KOG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. A total of 6945 resistance genes and 11,878 transcription factors (TFs) were identified from all transcriptome data. Differential expression analysis revealed that 13,032 (9490 specifics), 9877 (6423 specifics), and 6661 (4144 specifics) differentially expressed genes (DEGs) were generated from comparisons of the P. infestans/control (Pi vs. Pi-CK), R. solanacearum/control (Rs vs. Rs-CK), and PVY/control (PVY vs. PVY-CK) treatments, respectively. The specific DEGs from the 3 comparisons were assigned to 13 common pathways, such as biosynthesis of amino acids, plant hormone signal transduction, carbon metabolism, and starch and sucrose metabolism. Weighted Gene Co-Expression Network Analysis (WGCNA) identified many hub unigenes, of which several unigenes were reported to regulate plant immune responses, such as FLAGELLIN-SENSITIVE 2 and chitinases. The present study provide crucial systems-level insights into the relationship between transcriptome changes in potato infected with the three pathogens. Moreover, this study presents a theoretical basis for breeding broad-spectrum and specific pathogen-resistant cultivars.

Gene Pyramiding for Sustainable Crop Improvement against Biotic and Abiotic Stresses

Sustainable agricultural production is endangered by several ecological factors, such as drought, extreme temperatures, excessive salts, parasitic ailments, and insect pest infestation. These challenging environmental factors may have adverse effects on future agriculture production in many countries. In modern agriculture, conventional crop-breeding techniques alone are inadequate for achieving the increasing population’s food demand on a sustainable basis. The advancement of molecular genetics and related technologies are promising tools for the selection of new crop species. Gene pyramiding through marker-assisted selection (MAS) and other techniques have accelerated the development of durable resistant/tolerant lines with high accuracy in the shortest period of time for agricultural sustainability. Gene stacking has not been fully utilized for biotic stress resistance development and quality improvement in most of the major cultivated crops. This review emphasizes on gene pyramiding techniques that are being successfully deployed in modern agriculture for improving crop tolerance to biotic and abiotic stresses for sustainable crop improvement.

What natural variation can teach us about resistance durability

Breeding a crop variety to be resistant to a pathogen usually takes years. This is problematic because pathogens, with short generation times and fluid genomes, adapt quickly to overcome resistance. The triumph of the pathogen is not inevitable, however, as there are numerous examples of durable resistance, particularly in wild plants. Which factors then contribute to such resistance stability over millennia? We review current knowledge of wild and agricultural pathosystems, detailing the importance of genetic, species and spatial heterogeneity in the prevention of pathogen outbreaks. We also highlight challenges associated with increasing resistance diversity in crops, both in light of pathogen (co-)evolution and breeding practices. Historically it has been difficult to incorporate heterogeneity into agriculture due to reduced efficiency in harvesting. Recent advances implementing computer vision and automation in agricultural production may improve our ability to harvest mixed genotype and mixed species plantings, thereby increasing resistance durability.

Functional characterization of wheat myo-inositol oxygenase promoter under different abiotic stress conditions in Arabidopsis thaliana

The production of wheat is severely affected by abiotic stresses such as cold, drought, salinity, and high temperature. Although constitutive promoters are frequently used to regulate the expression of alien genes, these may lead to undesirable side-effects in transgenic plants. Therefore, identification and characterization of an inducible promoter that can express transgene only when exposed to stresses are of great importance in the genetic engineering of crop plants. Previous studies have indicated the abiotic stress-responsive behavior of myo-inositol oxygenase (MIOX) gene in different plants. Here, we isolated the MIOX gene promoter from wheat (TaMIOX). The in-silico analysis revealed the presence of various abiotic stress-responsive cis-elements in the promoter region. The TaMIOX promoter was fused with the UidA reporter gene and transformed into Arabidopsis thaliana. The T₃ single-copy homozygous lines were analyzed for GUS activity using histochemical and fluorometric assays. Transcript expression of TaMIOX::UidA was significantly up-regulated by heat (five fold), cold (seven fold), and drought (five fold) stresses as compared to transgenic plants grown without stress-induced conditions. The CaMV35S::UidA plants showed very high GUS activity even in normal conditions. In contrast, the TaMIOX::UidA plants showed prominent GUS activity only in stress treatments (cold, heat, and drought), which suggests the inducible behavior of the TaMIOX promoter. The substrate myo-inositol feeding assay of TaMIOX::UidA plants showed lesser GUS activity as compared to plants treated in abiotic stress conditions. Results support that the TaMIOX promoter could be used as a potential candidate for conditional expression of the transgene in abiotic stress conditions.

Transgene Stacking as Effective Tool for Enhanced Disease Resistance in Plants

Introduction of more than one gene into crop plants simultaneously or sequentially, called transgene stacking, has been a more effective strategy for conferring higher and durable insect and disease resistance in transgenic plants than single-gene technology. Transgenes can be stacked against one or more pathogens or for traits such as herbicide tolerance or anthocyanin pigmentation. Polygenic agronomic traits can be improved by multiple gene transformation. The most widely engineered stacked traits are insect resistance and herbicide tolerance as these traits may lead to lesser use of pesticides, higher yield, and efficient control of weeds. In this review, we summarize transgene stacking of two or more transgenes into crops for different agronomic traits, potential applications of gene stacking, its limitations and future prospects.

Genome Editing in Cereals: Approaches, Applications and Challenges

Over the past decades, numerous efforts were made towards the improvement of cereal crops mostly employing traditional or molecular breeding approaches. The current scenario made it possible to efficiently explore molecular understanding by targeting different genes to achieve desirable plants. To provide guaranteed food security for the rising world population particularly under vulnerable climatic condition, development of high yielding stress tolerant crops is needed. In this regard, technologies upgradation in the field of genome editing looks promising. Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 is a rapidly growing genome editing technique being effectively applied in different organisms, that includes both model and crop plants. In recent times CRISPR/Cas9 is being considered as a technology which revolutionized fundamental as well as applied research in plant breeding. Genome editing using CRISPR/Cas9 system has been successfully demonstrated in many cereal crops including rice, wheat, maize, and barley. Availability of whole genome sequence information for number of crops along with the advancement in genome-editing techniques provides several possibilities to achieve desirable traits. In this review, the options available for crop improvement by implementing CRISPR/Cas9 based genome-editing techniques with special emphasis on cereal crops have been summarized. Recent advances providing opportunities to simultaneously edit many target genes were also discussed. The review also addressed recent advancements enabling precise base editing and gene expression modifications. In addition, the article also highlighted limitations such as transformation efficiency, specific promoters and most importantly the ethical and regulatory issues related to commercial release of novel crop varieties developed through genome editing.

The Histological, Effectoromic, and Transcriptomic Analyses of Solanum pinnatisectum Reveal an Upregulation of Multiple NBS-LRR Genes Suppressing Phytophthora infestans Infection

Utilization of disease resistance components from wild potatoes is a promising and sustainable approach to control Phytophthora blight. Here, we combined avirulence (Avr) genes screen with RNA-seq analysis to discover the potential mechanism of resistance in Mexican wild potato species, Solanum pinnatisectum. Histological characterization displayed that hyphal expansion was significantly restricted in epidermal cells and mesophyll cell death was predominant, indicating that a typical defense response was initiated in S. pinnatisectum. Inoculation of S. pinnatisectum with diverse Phytophthora infestans isolates showed distinct resistance patterns, suggesting that S. pinnatisectum has complex genetic resistance to most of the prevalent races of P. infestans in northwestern China. Further analysis by Avr gene screens and comparative transcriptomic profiling revealed the presence and upregulation of multiple plant NBS-LRR genes corresponding to biotic stresses. Six NBS-LRR alleles of R1, R2, R3a, R3b, R4, and Rpi-smira2 were detected, and over 60% of the 112 detected NLR proteins were significantly induced in S. pinnatisectum. On the contrary, despite the expression of the Rpi-blb1, Rpi-vnt1, and Rpi-smira1 alleles, fewer NLR proteins were expressed in susceptible Solanum cardophyllum. Thus, the enriched NLR genes in S. pinnatisectum make it an ideal genetic resource for the discovery and deployment of resistance genes for potato breeding.

Exploiting Broad-Spectrum Disease Resistance in Crops: From Molecular Dissection to Breeding

Plant diseases reduce crop yields and threaten global food security, making the selection of disease-resistant cultivars a major goal of crop breeding. Broad-spectrum resistance (BSR) is a desirable trait because it confers resistance against more than one pathogen species or against the majority of races or strains of the same pathogen. Many BSR genes have been cloned in plants and have been found to encode pattern recognition receptors, nucleotide-binding and leucine-rich repeat receptors, and defense-signaling and pathogenesis-related proteins. In addition, the BSR genes that underlie quantitative trait loci, loss of susceptibility and nonhost resistance have been characterized. Here, we comprehensively review the advances made in the identification and characterization of BSR genes in various species and examine their application in crop breeding. We also discuss the challenges and their solutions for the use of BSR genes in the breeding of disease-resistant crops.

International Plant Pathology: Past and Future Contributions to Global Food Security

The challenge of feeding the current and future world population is widely recognized, and the management of plant diseases has an important role in overcoming this. This paper explores the ways in which international plant pathology has contributed and continues to support efforts to secure adequate, safe and culturally appropriate nourishment and livelihoods for present and future generations. For the purposes of this paper, "international plant pathology" refers to the work that plant pathologists do when they work across international borders, with a focus on enhancing food security in tropical regions. Significant efforts involve public and philanthropic resources from the global North for addressing plant disease concerns in the global South, where food security is a legitimate and pressing concern. International disease management efforts are also aimed at protecting domestic food security, for example when pathogens of major staples migrate across national borders. In addition, some important crops are largely produced in tropical countries and consumed globally, including in industrialized countries; the diseases of these crops are of international interest, and they are largely managed by the private sector. Finally, host-microbe interactions are fascinating biological systems, and basic research on plant diseases of international relevance has often yielded insights and technologies with both scientific and practical implications.

Plant NLRs: The Whistleblowers of Plant Immunity

The study of plant diseases is almost as old as agriculture itself. Advancements in molecular biology have given us much more insight into the plant immune system and how it detects the many pathogens plants may encounter. Members of the primary family of plant resistance (R) proteins, NLRs, contain three distinct domains, and appear to use several different mechanisms to recognize pathogen effectors and trigger immunity. Understanding the molecular process of NLR recognition and activation has been greatly aided by advancements in structural studies, with ZAR1 recently becoming the first full-length NLR to be visualized. Genetic and biochemical analysis identified many critical components for NLR activation and homeostasis control. The increased study of helper NLRs has also provided insights into the downstream signaling pathways of NLRs. This review summarizes the progress in the last decades on plant NLR research, focusing on the mechanistic understanding that has been achieved.