A receptor-like kinase enhances sunflower resistance to Orobanche cumana

A cluster of putative resistance genes is associated with a dominant resistance to sunflower broomrape

KEY MESSAGE

The HaOr5 resistance gene is located in a large genomic insertion containing putative resistance genes and provides resistance to O. cumana, preventing successful connection to the sunflower root vascular system. Orobanche cumana (sunflower broomrape) is a parasitic plant that is part of the Orobanchaceae family and specifically infests sunflower crops. This weed is an obligate parasitic plant that does not carry out photosynthetic activity or develop roots and is fully dependent on its host for its development. It produces thousands of dust-like seeds per plant. It possesses a high spreading ability and has been shown to quickly overcome resistance genes successively introduced by selection in cultivated sunflower varieties. The first part of its life cycle occurs underground. The connection to the sunflower vascular system is essential for parasitic plant survival and development. The HaOr5 gene provides resistance to sunflower broomrape race E by preventing the connection of O. cumana to the root vascular system. We mapped a single position of the HaOr5 gene by quantitative trait locus mapping using two segregating populations. The same location of the HaOr5 gene was identified by genome-wide association. Using a large population of thousands of F2 plants, we restricted the location of the HaOr5 gene to a genomic region of 193 kb. By sequencing the whole genome of the resistant line harboring the major resistance gene HaOr5, we identified a large insertion of a complex genomic region containing a cluster of putative resistance genes.

Identification and genetic diversity analysis of broomrape in Xinjiang, China

BACKGROUND

As a holoparasitic weed, broomrape has seriously threatened the production of economically important crops, such as melon, watermelon, processed tomato, and sunflower, in Xinjiang in recent years. However, the distribution and genetic diversity of broomrape populations in Xinjiang are not clear at present, which hinders their prevention and control. The purpose of this study was to identify the main species and the genetic differentiation structure of the broomrape population in Xinjiang.

METHODS AND RESULTS

In the present study, 93 samples from different geographic regions of Xinjiang were collected to identify the species based on ITS and plastid rps2 regions, and the samples were also used to analyze the genetic diversity based on ISSR markers. The results showed that broomrape is not monophyletic in Xinjiang and consists of two major clades (Orobanche cf. aegyptiaca and O. cernua) and three subclades (O. cf. aegyptiaca var. tch, O. cf. aegyptiaca var. klz, and O. cernua.var. alt) based on phylogenetic analysis. Furthermore, the results of the genetic diversity analysis indicated that the average polymorphic information content and marker index were high values of 0.58 and 7.38, respectively, showing the efficiency of the ISSR markers in detecting polymorphism among the broomrape population studied. Additionally, the 11 selected primers produced 154 repeatable polymorphic bands, of which 150 were polymorphic. The genetic diversity of the samples was 37.19% within populations and 62.81% among the populations, indicating that the main genetic differentiation occurred among the populations. There was less gene exchange between populations, with a gene flow index (Nm) of 0.2961 (< 1). The UPGMA dendrogram indicated that most populations with similar geographical conditions and hosts were clustered first, and then all samples were separated into two major groups and seven subclusters.

CONCLUSION

The broomrapes are mainly O. cf. aegyptiaca and O. cernua in Xinjiang, which were separated into two major groups and seven subclusters based on ISSR markers. Our results provide a theoretical basis for breeding broomrape-resistant varieties.

Development and characterization of a new sunflower source of resistance to race G of Orobanche cumana Wallr. derived from Helianthus anomalus

KEY MESSAGE

A new OrAnom1 gene introgressed in cultivated sunflower from wild Helianthus anomalus confers late post-attachment resistance to Orobanche cumana race G and maps to a target interval in Chromosome 4 where two receptor-like kinases (RLKs) have been identified in the H. anomalus genome as putative candidates. Sunflower broomrape is a parasitic weed that infects sunflower (Helianthus annuus L.) roots causing severe yield losses. Breeding for resistance is the most effective and sustainable control method. In this study, we report the identification, introgression, and genetic and physiological characterization of a new sunflower source of resistance to race G of broomrape developed from the wild annual sunflower H. anomalus (accession PI 468642). Crosses between PI 468642 and the susceptible line P21 were carried out, and the genetic study was conducted in BC1F1, BC1F2, and its derived BC1F3 populations. A BC1F5 germplasm named ANOM1 was developed through selection for race G resistance and resemblance to cultivated sunflower. The resistant trait showed monogenic and dominant inheritance. The gene, named OrAnom1, was mapped to Chromosome 4 within a 1.2 cM interval and co-segregated with 7 SNP markers. This interval corresponds to a 1.32 Mb region in the sunflower reference genome, housing a cluster of receptor-like kinase and receptor-like protein (RLK-RLP) genes. Notably, the analysis of the H. anomalus genome revealed the absence of RLPs in the OrAnom1 target region but featured two RLKs as possible OrAnom1 candidates. Rhizotron and histological studies showed that OrAnom1 determines a late post-attachment resistance mechanism. Broomrape can establish a vascular connection with the host, but parasite growth is stopped before tubercle development, showing phenolic compounds accumulation and tubercle necrosis. ANOM1 will contribute to broadening the genetic basis of broomrape resistance in the cultivated sunflower pool and to a better understanding of the molecular basis of the sunflower-broomrape interaction.

A novel sunflower broomrape race with unusual virulence potentially caused by a mutation

Introduction

The sunflower broomrape (Orobanche cumana Wallr.) gene pools of the Guadalquivir Valley and Cuenca province in Spain had predominantly race-F virulence. A new race G was observed recently in the Guadalquivir Valley potentially due to the genetic recombination of the avirulence genes of both gene pools.

Methods

In this research, we have studied populations with atypical virulence from Cuenca. These populations parasitize on DEB2 sunflower line, resistant to all race-G populations evaluated. Ten populations collected in Cuenca province were evaluated with sunflower differential lines and genotyped with 67 SNP markers.

Results

Although genetic recombination with individuals of the Guadalquivir Valley gene pool has been observed in most populations, recombination of avirulence genes was discarded as the cause of the new virulence because the population with the highest degree of attack on DEB2 showed no introgression from an external gene pool. Accordingly, a point mutation is proposed as the putative cause of the new virulence.

Discussion

The present study provided a detailed characterization of each population, including the accurate classification of the individuals belonging to each of the classical Spanish gene pools, F1 hybrids, and those that evolved from hybridization between both gene pools. This information is essential to understand how sunflower broomrape populations are evolving in Spain, which in turn may be helpful to understand the dynamics of sunflower broomrape populations in other areas of the world and use this information to develop durable strategies for resistance breeding.

Phylogeny of the plant receptor-like kinase (RLK) gene family and expression analysis of wheat RLK genes in response to biotic and abiotic stresses

BACKGROUND

The receptor-like kinase (RLK) gene families in plants contains a large number of members. They are membrane proteins with an extracellular receptor domain and participate in biotic and abiotic stress responses.

RESULTS

In this study, we identified RLKs in 15 representative plant genomes, including wheat, and classified them into 64 subfamilies by using four types of phylogenetic trees and HMM models. Conserved exon‒intron structures with conserved exon phases in the kinase domain were found in many RLK subfamilies from Physcomitrella patens to Triticum aestivum. Domain distributions of RLKs were also diagrammed. Collinearity events and tandem gene clusters suggested that polyploidization and tandem duplication events contributed to the member expansions of T. aestivum RLKs. Global expression pattern analysis was performed by using public transcriptome data. These analyses were involved in T. aestivum, Aegilops tauschii and Brachypodium distachyon RLKs under biotic and abiotic stresses. We also selected 9 RLKs to validate the transcriptome prediction by using qRT‒PCR under drought treatment and with Fusarium graminearum infection. The expression trends of these 9 wheat RLKs from public transcriptome data were consistent with the results of qRT‒PCR, indicating that they might be stress response genes under drought or F. graminearum treatments.

CONCLUSION

In this study, we identified, classified, evolved, and expressed RLKs in wheat and related plants. Thus, our results will provide insights into the evolutionary history and molecular mechanisms of wheat RLKs.

Host Resistance to Parasitic Plants-Current Knowledge and Future Perspectives

Parasitic flowering plants represent a diverse group of angiosperms, ranging from exotic species with limited distribution to prominent weeds, causing significant yield losses in agricultural crops. The major damage caused by them is related to the extraction of water and nutrients from the host, thus decreasing vegetative growth, flowering, and seed production. Members of the root parasites of the Orobanchaceae family and stem parasites of the genus Cuscuta are among the most aggressive and damaging weeds, affecting both monocotyledonous and dicotyledonous crops worldwide. Their control and eradication are hampered by the extreme seed longevity and persistence in soil, as well as their taxonomic position, which makes it difficult to apply selective herbicides not damaging to the hosts. The selection of resistant cultivars is among the most promising approaches to deal with this matter, although still not widely employed due to limited knowledge of the molecular mechanisms of host resistance and inheritance. The current review aims to summarize the available information on host resistance with a focus on agriculturally important parasitic plants and to outline the future perspectives of resistant crop cultivar selection to battle the global threat of parasitic plants.

Phenotypic and histological analyses on the resistance of melon to Phelipanche aegyptiaca

Melon (Cucumis melo L.) is an economically important crop in Xinjiang, China, but its production is constrained by the parasitic plant Phelipanche aegyptiaca that attaches to the roots of many crops and causes severe stunting and loss of yield. Rhizotron, pot, and field experiments were employed to evaluate the resistance of 27 melon cultivars to P. aegyptiaca. Then, the resistant and susceptible cultivars were inoculated with P. aegyptiaca from six populations to assess their resistance stability and broad spectrum. Further microscopic and histological analyses were used to clarify the resistance phenotypes and histological structure. The results showed that Huangpi 9818 and KR1326 were more resistant to P. aegyptiaca compared to other cultivars in the rhizotron, pot, and field experiments. In addition, compared to the susceptible cultivar K1076, Huangpi 9818 and KR1326 showed broad-spectrum resistance to six P. aegyptiaca populations. These two resistant cultivars had lower P. aegyptiaca biomass and fewer and smaller P. aegyptiaca attachments on their roots compared to susceptible cultivar K1076. KR1326 (resistant) and K1076 (susceptible) were selected to further study resistance phenotypes and mechanisms. Germination-inducing activity of root exudates and microscopic analysis showed that the resistance in KR1326 was not related to low induction of P. aegyptiaca germination. The tubercles of parasite on KR1326 were observed slightly brown at 14 days after inoculation (DAI), the necrosis and arrest of parasite development occurred at 23 DAI. Histological analysis of necrosis tubercles showed that the endophyte of parasite had reached host central cylinder, connected with host xylem, and accumulation of secretions and callose were detected in neighbouring cells. We concluded that KR1326 is an important melon cultivar for P. aegyptiaca resistance that could be used to expand the genetic basis of cultivated muskmelon for resistance to the parasite.

Genomic and Epigenomic Mechanisms of the Interaction between Parasitic and Host Plants

Parasitic plants extract nutrients from the other plants to finish their life cycle and reproduce. The control of parasitic weeds is notoriously difficult due to their tight physical association and their close biological relationship to their hosts. Parasitic plants differ in their susceptible host ranges, and the host species differ in their susceptibility to parasitic plants. Current data show that adaptations of parasitic plants to various hosts are largely genetically determined. However, multiple cases of rapid adaptation in genetically homogenous parasitic weed populations to new hosts strongly suggest the involvement of epigenetic mechanisms. Recent progress in genome-wide analyses of gene expression and epigenetic features revealed many new molecular details of the parasitic plants' interactions with their host plants. The experimental data obtained in the last several years show that multiple common features have independently evolved in different lines of the parasitic plants. In this review we discuss the most interesting new details in the interaction between parasitic and host plants.

Association mapping for broomrape resistance in sunflower

INTRODUCTION

Sunflower breeding for resistance to the parasitic plant sunflower broomrape (Orobanche cumana Wallr.) requires the identification of novel resistance genes. In this research, we conducted a genome-wide association study (GWAS) to identify QTLs associated with broomrape resistance.

METHODS

The marker-trait associations were examined across a germplasm set composed of 104 sunflower accessions. They were genotyped with a 600k AXIOM® genome-wide array and evaluated for resistance to three populations of the parasite with varying levels of virulence (races EFR, FGV, and GTK) in two environments.

RESULTS AND DISCUSSION

The analysis of the genetic structure of the germplasm set revealed the presence of two main groups. The application of optimized treatments based on the general linear model (GLM) and the mixed linear model (MLM) allowed the detection of 14 SNP markers significantly associated with broomrape resistance. The highest number of marker-trait associations were identified on chromosome 3, clustered in two different genomic regions of this chromosome. Other associations were identified on chromosomes 5, 10, 13, and 16. Candidate genes for the main genomic regions associated with broomrape resistance were studied and discussed. Particularly, two significant SNPs on chromosome 3 associated with races EFR and FGV were found at two tightly linked SWEET sugar transporter genes. The results of this study have confirmed the role of some QTL on resistance to sunflower broomrape and have revealed new ones that may play an important role in the development of durable resistance to this parasitic weed in sunflower.

The ecologically relevant genetics of plant-plant interactions

Interactions among plants have been long recognized as a major force driving plant community dynamics and crop yield. Surprisingly, our knowledge of the ecological genetics associated with variation of plant-plant interactions remains limited. In this opinion article by scientists from complementary disciplines, the international PLANTCOM network identified four timely questions to foster a better understanding of the mechanisms mediating plant assemblages. We propose that by identifying the key relationships among phenotypic traits involved in plant-plant interactions and the underlying adaptive genetic and molecular pathways, while considering environmental fluctuations at diverse spatial and time scales, we can improve predictions of genotype-by-genotype-by-environment interactions and modeling of productive and stable plant assemblages in wild habitats and crop fields.

HeliantHOME, a public and centralized database of phenotypic sunflower data

Genomic studies often attempt to link natural genetic variation with important phenotypic variation. To succeed, robust and reliable phenotypic data, as well as curated genomic assemblies, are required. Wild sunflowers, originally from North America, are adapted to diverse and often extreme environments and have historically been a widely used model plant system for the study of population genomics, adaptation, and speciation. Moreover, cultivated sunflower, domesticated from a wild relative (Helianthus annuus) is a global oil crop, ranking fourth in production of vegetable oils worldwide. Public availability of data resources both for the plant research community and for the associated agricultural sector, are extremely valuable. We have created HeliantHOME ( http://www.helianthome.org ), a curated, public, and interactive database of phenotypes including developmental, structural and environmental ones, obtained from a large collection of both wild and cultivated sunflower individuals. Additionally, the database is enriched with external genomic data and results of genome-wide association studies. Finally, being a community open-source platform, HeliantHOME is expected to expand as new knowledge and resources become available.

Root cell types as an interface for biotic interactions

Root responses to environmental stresses show a high level of cell type and developmental stage specificity. Interactions with beneficial and pathogenic organisms - including microbes and parasites - elicit a set of transcriptional responses unique to each root cell type, often dependent on their differentiation state. Localized changes to the cell wall and to the integrity of root cell types can serve as a physical barrier for a range of pests. Conversely, certain microorganisms weaken existing barriers within root cell types. Interactions with microorganisms vary between roots of different developmental origins and cellular architectures. Here we provide an overview of the molecular, architectural, and structural properties of root cell types crucial to both maintaining beneficial interactions and protecting from pathogens.

Wild Helianthus species: A reservoir of resistance genes for sustainable pyramidal resistance to broomrape in sunflower

Orobanche cumana Wall., sunflower broomrape, is one of the major pests for the sunflower crop. Breeding for resistant varieties in sunflower has been the most efficient method to control this parasitic weed. However, more virulent broomrape populations continuously emerge by overcoming genetic resistance. It is thus essential to identify new broomrape resistances acting at various stages of the interaction and combine them to improve resistance durability. In this study, 71 wild sunflowers and wild relatives accessions from 16 Helianthus species were screened in pots for their resistance to broomrape at the late emergence stage. From this initial screen, 18 accessions from 9 species showing resistance, were phenotyped at early stages of the interaction: the induction of broomrape seed germination by sunflower root exudates, the attachment to the host root and the development of tubercles in rhizotron assays. We showed that wild Helianthus accessions are an important source of resistance to the most virulent broomrape races, affecting various stages of the interaction: the inability to induce broomrape seed germination, the development of incompatible attachments or necrotic tubercles, and the arrest of emerged structure growth. Cytological studies of incompatible attachments showed that several cellular mechanisms were shared among resistant Helianthus species.

Phenotypic characterization of the Hordeum bulbosum derived leaf rust resistance genes Rph22 and Rph26 in barley

Aims

Two introgression lines (ILs), 182Q20 and 200A12, which had chromosomal segments introgressed from Hordeum bulbosum in H. vulgare backgrounds, were identified to show seedling resistance against Puccinia hordei, possibly attributed to two resistance genes, Rph22 and Rph26, respectively. This study characterized the phenotypic responses of the two genes against P. hordei over different plant development stages.

Methods and Results

Using visual and fungal biomass assessments, responses of ILs 182Q20, 200A12 and four other barley cultivars against P. hordei were determined at seedling, tillering, stem elongation and booting stages. Plants carrying either Rph22 or Rph26 were found to confer gradually increasing resistance over the course of different development stages, with partial resistant phenotypes (i.e. prolonged rust latency periods, reduced uredinia numbers but with susceptible infection types) observed at seedling stage and adult plant resistance (APR) at booting stage. A definitive switch between the two types of resistance occurred at tillering stage.

Conclusions

Rph22 and Rph26 derived from H. bulbosum were well characterized and had typical APR phenotypes against P. hordei.

Significance and Impact of the Study

This study provides important insights on the effectiveness and expression of Rph22 and Rph26 against P. hordei during plant development and underpins future barley breeding programmes using non‐host as a genetic resource for leaf rust management.

Parasitic Plants: An Overview of Mechanisms by Which Plants Perceive and Respond to Parasites

In contrast to most autotrophic plants, which produce carbohydrates from carbon dioxide using photosynthesis, parasitic plants obtain water and nutrients by parasitizing host plants. Many important crop plants are infested by these heterotrophic plants, leading to severe agricultural loss and reduced food security. Understanding how host plants perceive and resist parasitic plants provides insight into underlying defense mechanisms and the potential for agricultural applications. In this review, we offer a comprehensive overview of the current understanding of host perception of parasitic plants and the pre-attachment and post-attachment defense responses mounted by the host. Since most current research overlooks the role of organ specificity in resistance responses, we also summarize the current understanding and cases of cross-organ parasitism, which indicates nonconventional haustorial connections on other host organs, for example, when stem parasitic plants form haustoria on their host roots. Understanding how different tissue types respond to parasitic plants could provide the potential for developing a universal resistance mechanism in crops against both root and stem parasitic plants.

Heinz-resistant tomato cultivars exhibit a lignin-based resistance to field dodder (Cuscuta campestris) parasitism

Cuscuta species (dodders) are agriculturally destructive, parasitic angiosperms. These parasitic plants use haustoria as physiological bridges to extract nutrients and water from hosts. Cuscuta campestris has a broad host range and wide geographical distribution. While some wild tomato relatives are resistant, cultivated tomatoes are generally susceptible to C. campestris infestations. However, some specific Heinz tomato (Solanum lycopersicum) hybrid cultivars exhibit resistance to dodders in the field, but their defense mechanism was previously unknown. Here, we discovered that the stem cortex in these resistant lines responds with local lignification upon C. campestris attachment, preventing parasite entry into the host. Lignin Induction Factor 1 (LIF1, an AP2-like transcription factor), SlMYB55, and Cuscuta R-gene for Lignin-based Resistance 1, a CC-NBS-LRR (CuRLR1) are identified as factors that confer host resistance by regulating lignification. SlWRKY16 is upregulated upon C. campestris infestation and potentially negatively regulates LIF1 function. Intriguingly, CuRLR1 may play a role in signaling or function as an intracellular receptor for receiving Cuscuta signals or effectors, thereby regulating lignification-based resistance. In summary, these four regulators control the lignin-based resistance response in specific Heinz tomato cultivars, preventing C. campestris from parasitizing resistant tomatoes. This discovery provides a foundation for investigating multilayer resistance against Cuscuta species and has potential for application in other essential crops attacked by parasitic plants.

Knowing me, knowing you: Self and non-self recognition in plant immunity

Perception of non-self molecules known as microbe-associated molecular patterns (MAMPs) by host pattern recognition receptors (PRRs) activates plant pattern-triggered immunity (PTI). Pathogen infections often trigger the release of modified-self molecules, termed damage- or danger-associated molecular patterns (DAMPs), which modulate MAMP-triggered signaling to shape the frontline of plant immune responses against infections. In the context of advances in identifying MAMPs and DAMPs, cognate receptors, and their signaling, here, we focus on the most recent breakthroughs in understanding the perception and role of non-self and modified-self patterns. We highlight the commonalities and differences of MAMPs from diverse microbes, insects, and parasitic plants, as well as the production and perception of DAMPs upon infections. We discuss the interplay between MAMPs and DAMPs for emerging themes of the mutual potentiation and attenuation of PTI signaling upon MAMP and DAMP perception during infections.

Genetic and physiological characterization of sunflower resistance provided by the wild-derived OrDeb2 gene against highly virulent races of Orobanche cumana Wallr

Or_Deb2 confers post-attachment resistance to Orobanche cumana and is located in a 1.38 Mbp genomic interval containing a cluster of receptor-like kinase and receptor-like protein genes with nine high-confidence candidates. Sunflower broomrape is a holoparasitic angiosperm that parasitizes on sunflower roots, severely constraining crop yield. Breeding for resistance is the most effective method of control. Or_Deb2 is a dominant resistance gene introgressed into cultivated sunflower from a wild-related species that confers resistance to highly virulent broomrape races. The objectives of this study were as follows: (i) locate Or_Deb2 into the sunflower genome and determine putative candidate genes and (ii) characterize its underlying resistance mechanism. A segregating population from a cross between the sunflower resistant line DEB2, carrying Or_Deb2, and a susceptible line was phenotyped for broomrape resistance in four experiments, including different environments and two broomrape races (F_GV and G_TK). This population was also densely genotyped with microsatellite and SNP markers, which allowed locating Or_Deb2 within a 0.9 cM interval in the upper half of Chromosome 4. This interval corresponded to a 1.38 Mbp genomic region of the sunflower reference genome that contained a cluster of genes encoding LRR (leucine-rich repeat) receptor-like proteins lacking a cytoplasmic kinase domain and receptor-like kinases with one or two kinase domains and lacking an extracellular LRR region, which were valuable candidates for Or_Deb2. Rhizotron and histological studies showed that Or_Deb2 determines a post-attachment resistance response that blocks O. cumana development mainly at the cortex before the establishment of host-parasite vascular connections. This study will contribute to understand the interaction between crops and parasitic weeds, to establish durable breeding strategies based on genetic resistance and provide useful tools for marker-assisted selection and Or_Deb2 map-based cloning.

Biological and Transcriptomic Characterization of Pre-Haustorial Resistance to Sunflower Broomrape (Orobanche cumana W.) in Sunflowers (Helianthus annuus)

Infestations with sunflower broomrape (Orobanche cumana Wallr.), an obligatory root parasite, constitute a major limitation to sunflower production in many regions around the world. Breeding for resistance is the most effective approach to reduce sunflower broomrape infestation, yet resistance mechanisms are often broken by new races of the pathogen. Elucidating the mechanisms controlling resistance to broomrape at the molecular level is, thus, a desirable way to obtain long-lasting resistance. In this study, we investigated broomrape resistance in a confectionery sunflower cultivar with a robust and long-lasting resistance to sunflower broomrape. Visual screening and histological examination of sunflower roots revealed that penetration of the broomrape haustorium into the sunflower roots was blocked at the cortex, indicating a pre-haustorial mechanism of resistance. A comparative RNA sequencing between broomrape-resistant and -susceptible accessions allowed the identification of genes that were significantly differentially expressed upon broomrape infestation. Among these genes were β-1,3-endoglucanase, β-glucanase, and ethylene-responsive transcription factor 4 (ERF4). These genes were previously reported to be pathogenesis-related in other plant species. This transcriptomic investigation, together with the histological examinations, led us to conclude that the resistance mechanism involves the identification of the broomrape and the consequent formation of a physical barrier that prevents the establishment of the broomrape into the sunflower roots.

How to resist parasitic plants: pre- and post-attachment strategies

The lifecycle of parasitic plants can be divided into pre-attachment and post-attachment phases that equate to free living and parasitic stages. Similarly, plant resistance to parasitic plants can be defined as pre-attachment and post-attachment resistance. Parasitic plants rely on host cues for successful host invasion. During pre-attachment resistance, changes in the composition of host signals can disrupt parasitic plant development and ultimately host invasion. Recent studies have only now begun to elucidate the genetic elements in the host that promote pre-attachment resistance. In comparison, new research points to post-attachment resistance using the common molecular mechanisms utilized by the plant immune system during plant-pathogen interactions. In kind, parasitic plants secrete proteinaceous and RNA-based effectors post-attachment to subvert the host immune system.

Image analysis for the automatic phenotyping of Orobanche cumana tubercles on sunflower roots

BACKGROUND

The parasitic plant Orobanche cumana is one of the most important threats to sunflower crops in Europe. Resistant sunflower varieties have been developed, but new O. cumana races have evolved and have overcome introgressed resistance genes, leading to the recurrent need for new resistance methods. Screening for resistance requires the phenotyping of thousands of sunflower plants to various O. cumana races. Most phenotyping experiments have been performed in fields at the later stage of the interaction, requiring time and space. A rapid phenotyping screening method under controlled conditions would need less space and would allow screening for resistance of many sunflower genotypes. Our study proposes a phenotyping tool for the sunflower/O. cumana interaction under controlled conditions through image analysis for broomrape tubercle analysis at early stages of the interaction.

RESULTS

We optimized the phenotyping of sunflower/O. cumana interactions by using rhizotrons (transparent Plexiglas boxes) in a growth chamber to control culture conditions and Orobanche inoculum. We used a Raspberry Pi computer with a picamera for acquiring images of inoculated sunflower roots 3 weeks post inoculation. We set up a macro using ImageJ free software for the automatic counting of the number of tubercles. This phenotyping tool was named RhizOSun. We evaluated five sunflower genotypes inoculated with two O. cumana races and showed that automatic counting of the number of tubercles using RhizOSun was highly correlated with manual time-consuming counting and could be efficiently used for screening sunflower genotypes at the tubercle stage.

CONCLUSION

This method is rapid, accurate and low-cost. It allows rapid imaging of numerous rhizotrons over time, and it enables image tracking of all the data with time kinetics. This paves the way toward automatization of phenotyping in rhizotrons that could be used for other root phenotyping, such as symbiotic nodules on legumes.

Mechanisms of resistance and virulence in parasitic plant-host interactions

Parasitic plants pose a major biotic threat to plant growth and development and lead to losses in crop productivity of billions of USD annually. By comparison with "normal" autotrophic plants, parasitic plants live a heterotrophic lifestyle and rely on water, solutes and to a greater (holoparasitic plants) or lesser extent (hemiparasitic plants) on sugars from other host plants. Most hosts are unable to detect an infestation by plant parasites or unable to fend off these parasitic invaders. However, a few hosts have evolved defense strategies to avoid infestation or protect themselves actively post-attack often leading to full or partial resistance. Here, we review the current state of our understanding of the defense strategies to plant parasitism used by host plants with emphasis on the active molecular resistance mechanisms. Furthermore, we outline the perspectives and the potential of future studies that will be indispensable to develop and breed resistant crops.

Molecular actors of seed germination and haustoriogenesis in parasitic weeds

One-sentence summary Recent advances provide insight into the molecular mechanisms underlying host-dependent seed germination and haustorium formation in parasitic plants.

Using biotechnological approaches to develop crop resistance to root parasitic weeds

New transgenic and biotechnological approaches may serve as a key component in achieving crop resistance to root parasitic weeds. Root parasitic weeds inflict severe damage to numerous crops, reducing yield quantity and quality. A lack of new sources of resistance limits our ability to manage newly developing, more virulent races. Having no effective means to control the parasites in most crops, innovative biotechnological solutions are needed. Several novel biotechnological strategies using regulatory RNA molecules, the CRISPR/Cas9 system, and T-DNA insertions have been acknowledged for engineering resistance against parasitic weeds. Significant breakthroughs have been made over the years in deciphering the plant genome and its functions, including the genomes of parasitic weeds. However, the basis of biotechnological strategies to generate host resistance to root parasitic weeds needs to be further developed. Gene-silencing and editing tools should be used to target key processes of host-parasite interactions, such as strigolactone biosynthesis and signaling, haustorium development, and degradation and penetration of the host cell wall. In this review, we summarize and discuss the main areas of research leading to the discovery and functional analysis of genes involved in host-induced gene silencing that target key parasite genes, transgenic host modification, and host gene editing to generate sustainable resistance to root parasitic weeds.

Orobanchaceae parasite-host interactions

Parasitic plants in the family Orobanchaceae, such as Striga, Orobanche and Phelipanche, often cause significant damage to agricultural crops. The Orobanchaceae family comprises more than 2000 species in about 100 genera, providing an excellent system for studying the molecular basis of parasitism and its evolution. Notably, the establishment of model Orobanchaceae parasites, such as Triphysaria versicolor and Phtheirospermum japonicum, that can infect the model host Arabidopsis, has greatly facilitated transgenic analyses of genes important for parasitism. In addition, recent genomic and transcriptomic analyses of several Orobanchaceae parasites have revealed fascinating molecular insights into the evolution of parasitism and strategies for adaptation in this family. This review highlights recent progress in understanding how Orobanchaceae parasites attack their hosts and how the hosts mount a defense against the threats.

Host sunflower-induced silencing of parasitism-related genes confers resistance to invading Orobanche cumana

Orobanche cumana is a holoparasitic plant that attaches to host-plant roots and seriously reduces the yield of sunflower (Helianthus annuus L.). Effective control methods are lacking with only a few known sources of genetic resistance. In this study, a seed-soak agroinoculation (SSA) method was established, and recombinant tobacco rattle virus vectors were constructed to express RNA interference (RNAi) inducers to cause virus-induced gene silencing (VIGS) in sunflower. A host target gene HaTubulin was systemically silenced in both leaf and root tissues by the SSA-VIGS approach. Trans-species silencing of O. cumana genes were confirmed for 10 out of 11 target genes with silencing efficiency of 23.43%-92.67%. Knockdown of target OcQR1, OcCKX5, and OcWRI1 genes reduced the haustoria number, and silencing of OcEXPA6 caused further phenotypic abnormalities such as shorter tubercles and necrosis. Overexpression of OcEXPA6 caused retarded root growth in alfalfa (Medicago sativa). The results demonstrate that these genes play an important role in the processes of O. cumana parasitism. High-throughput small RNA (sRNA) sequencing and bioinformatics analyses unveiled the distinct features of target gene-derived siRNAs in O. cumana such as siRNA transitivity, strand polarity, hotspot region, and 21/22-nt siRNA predominance, the latter of which was confirmed by Northern blot experiments. The possible RNAi mechanism is also discussed by analyzing RNAi machinery genes in O. cumana. Taken together, we established an efficient host-induced gene silencing technology for both functional genetics studies and potential control of O. cumana. The ease and effectiveness of this strategy could potentially be useful for other species provided they are amenable to SSA.

Genome-wide investigation and expression analysis of membrane-bound fatty acid desaturase genes under different biotic and abiotic stresses in sunflower (Helianthus annuus L.)

Membrane-bound fatty acid desaturase (FAD) gene family plays crucial roles in regulation of fatty acid (FA) compositions in plants. Sunflower (Helianthus annuus L.) is an important oilseed crop in the world; however, no comprehensive study on exploring the role of FAD family in relation to stress tolerance in sunflower has been performed yet. In this study, we identified 40 putative FAD genes in H. annuus (HaFAD), which were unevenly distributed across 13 of the total 17 chromosomes. Phylogenetic analysis indicated that HaFAD genes were divided into four subfamilies, as supported by highly conserved gene structures and motifs. Collinearity analysis showed that tandem duplication events played a crucial role in the expansion of HaFAD gene family. In addition, tissue-specific expression showed that 32 HaFAD genes were widely expressed in various tissues or organs of sunflower. Furthermore, qRT-PCR results revealed significant expression changes of HaFAD genes in response to abiotic (cadmium, drought) and biotic (Orobanche cumana) stresses, suggesting their important functions in response to different stresses. Therefore, our results provide insights into HaFAD gene family in response to different stresses, and some specific up-regulated genes such as HaFAD3.2, HaADS8, HaFAD2.1, and HaADS9 would be the potential candidate genes for the sunflower tolerance breeding.

Plant plasma membrane-resident receptors: Surveillance for infections and coordination for growth and development

As sessile organisms, plants are exposed to pathogen invasions and environmental fluctuations. To overcome the challenges of their surroundings, plants acquire the potential to sense endogenous and exogenous cues, resulting in their adaptability. Hence, plants have evolved a large collection of plasma membrane-resident receptors, including RECEPTOR-LIKE KINASEs (RLKs) and RECEPTOR-LIKE PROTEINs (RLPs) to perceive those signals and regulate plant growth, development, and immunity. The ability of RLKs and RLPs to recognize distinct ligands relies on diverse categories of extracellular domains evolved. Co-regulatory receptors are often required to associate with RLKs and RLPs to facilitate cellular signal transduction. RECEPTOR-LIKE CYTOPLASMIC KINASEs (RLCKs) also associate with the complex, bifurcating the signal to key signaling hubs, such as MITOGEN-ACTIVATED PROTEIN KINASE (MAPK) cascades, to regulate diverse biological processes. Here, we discuss recent knowledge advances in understanding the roles of RLKs and RLPs in plant growth, development, and immunity, and their connection with co-regulatory receptors, leading to activation of diverse intracellular signaling pathways.

The Effect of Virulence and Resistance Mechanisms on the Interactions between Parasitic Plants and Their Hosts

Parasitic plants have a unique heterotrophic lifestyle based on the extraction of water and nutrients from host plants. Some parasitic plant species, particularly those of the family Orobanchaceae, attack crops and cause substantial yield losses. The breeding of resistant crop varieties is an inexpensive way to control parasitic weeds, but often does not provide a long-lasting solution because the parasites rapidly evolve to overcome resistance. Understanding mechanisms underlying naturally occurring parasitic plant resistance is of great interest and could help to develop methods to control parasitic plants. In this review, we describe the virulence mechanisms of parasitic plants and resistance mechanisms in their hosts, focusing on obligate root parasites of the genera Orobanche and Striga. We noticed that the resistance (R) genes in the host genome often encode proteins with nucleotide-binding and leucine-rich repeat domains (NLR proteins), hence we proposed a mechanism by which host plants use NLR proteins to activate downstream resistance gene expression. We speculated how parasitic plants and their hosts co-evolved and discussed what drives the evolution of virulence effectors in parasitic plants by considering concepts from similar studies of plant-microbe interaction. Most previous studies have focused on the host rather than the parasite, so we also provided an updated summary of genomic resources for parasitic plants and parasitic genes for further research to test our hypotheses. Finally, we discussed new approaches such as CRISPR/Cas9-mediated genome editing and RNAi silencing that can provide deeper insight into the intriguing life cycle of parasitic plants and could potentially contribute to the development of novel strategies for controlling parasitic weeds, thereby enhancing crop productivity and food security globally.

Exploration of resistance to Phelipanche aegyptiaca in tomato

BACKGROUND

Cultivated tomatoes are highly susceptible to the destructive parasite Phelipanche aegyptiaca. Wild relatives show the potential resistance for genetic improvement. However, their genetic and molecular mechanisms are still unknown.

RESULTS

Among 50 wild tomato accessions were evaluated for resistance to P. aegyptiaca, most of the wild relatives exhibited varying degrees of resistance compared to the cultivars. Solanum pennellii LA0716 performed the most promising and solid resistance with very low infection by the broomrape. The resistance involved in LA0716 was further confirmed by cytological analysis, and explored by employing a permanent introgression line (IL) population. Thirteen putative quantitative trait loci (QTLs) conferring the different resistance traits were identified. They are located on chromosomes 1, 2, 3, 4, 6, 8 and 9. The most attractive QTLs are positioned in IL6-2 and overlap with IL6-3. Specially, IL6-2 showed the highest and most consistent resistance for multiple traits and explained the major phenotypic variation of LA0716. Analysis of candidate genes involved in these regions showed that Beta (Solyc06g074240) and P450 (Solyc06g073570, Solyc06g074180 and Solyc06g074420) genes are substantially related to the strigolactone (SL) pathway. Transcript analysis further demonstrated that both Solyc06g073570 and Solyc06g074180 might play an important role in the reduction of P. aegyptiaca infection.

CONCLUSION

Germplasms resistant to P. aegyptiaca were found in wild tomato species. QTLs conferring P. aegyptiaca tolerance in LA0716 were identified. IL6-2 is identified as a prospective line possessing the major QTLs. The candidate genes would provide the availability to assist the introgression of the resistance in future breeding programmes. © 2020 Society of Chemical Industry.

The tomato receptor CuRe1 senses a cell wall protein to identify Cuscuta as a pathogen

Parasitic plants of the genus Cuscuta penetrate shoots of host plants with haustoria and build a connection to the host vasculature to exhaust water, solutes and carbohydrates. Such infections usually stay unrecognized by the host and lead to harmful host plant damage. Here, we show a molecular mechanism of how plants can sense parasitic Cuscuta. We isolated an 11 kDa protein of the parasite cell wall and identified it as a glycine-rich protein (GRP). This GRP, as well as its minimal peptide epitope Crip21, serve as a pathogen-associated molecular pattern and specifically bind and activate a membrane-bound immune receptor of tomato, the Cuscuta Receptor 1 (CuRe1), leading to defense responses in resistant hosts. These findings provide the initial steps to understand the resistance mechanisms against parasitic plants and further offer great potential for protecting crops by engineering resistance against parasitic plants.

Parasitic plants such as Cuscuta penetrate the shoots of susceptible hosts to obtain sugars, solutes and water. Here the authors show that resistant varieties of tomato can trigger an immune response against Cuscuta by perceiving a small glycine rich protein produced by the parasite.

Management of Infection by Parasitic Weeds: A Review

Parasitic plants rely on neighboring host plants to complete their life cycle, forming vascular connections through which they withdraw needed nutritive resources. In natural ecosystems, parasitic plants form one component of the plant community and parasitism contributes to overall community balance. In contrast, when parasitic plants become established in low biodiversified agroecosystems, their persistence causes tremendous yield losses rendering agricultural lands uncultivable. The control of parasitic weeds is challenging because there are few sources of crop resistance and it is difficult to apply controlling methods selective enough to kill the weeds without damaging the crop to which they are physically and biochemically attached. The management of parasitic weeds is also hindered by their high fecundity, dispersal efficiency, persistent seedbank, and rapid responses to changes in agricultural practices, which allow them to adapt to new hosts and manifest increased aggressiveness against new resistant cultivars. New understanding of the physiological and molecular mechanisms behind the processes of germination and haustorium development, and behind the crop resistant response, in addition to the discovery of new targets for herbicides and bioherbicides will guide researchers on the design of modern agricultural strategies for more effective, durable, and health compatible parasitic weed control.

Multiple immunity-related genes control susceptibility of Arabidopsis thaliana to the parasitic weed Phelipanche aegyptiaca

Parasitic weeds represent a major threat to agricultural production across the world. Little is known about which host genetic pathways determine compatibility for any host–parasitic plant interaction. We developed a quantitative assay to characterize the growth of the parasitic weed Phelipanche aegyptiaca on 46 mutant lines of the host plant Arabidopsis thaliana to identify host genes that are essential for susceptibility to the parasite. A. thaliana host plants with mutations in genes involved in jasmonic acid biosynthesis/signaling or the negative regulation of plant immunity were less susceptible to P. aegyptiaca parasitization. In contrast, A. thaliana plants with a mutant allele of the putative immunity hub gene Pfd6 were more susceptible to parasitization. Additionally, quantitative PCR revealed that P. aegyptiaca parasitization leads to transcriptional reprograming of several hormone signaling pathways. While most tested A. thaliana lines were fully susceptible to P. aegyptiaca parasitization, this work revealed several host genes essential for full susceptibility or resistance to parasitism. Altering these pathways may be a viable approach for limiting host plant susceptibility to parasitism.

Genetic and Genomic Tools in Sunflower Breeding for Broomrape Resistance

Broomrape is a root parasitic plant causing yield losses in sunflower production. Since sunflower is an important oil crop, the development of broomrape-resistant hybrids is the prime breeding objective. Using conventional plant breeding methods, breeders have identified resistant genes and developed a number of hybrids resistant to broomrape, adapted to different growing regions worldwide. However, the spread of broomrape into new countries and the development of new and more virulent races have been noted intensively. Recent advances in sunflower genomics provide additional tools for plant breeders to improve resistance and find durable solutions for broomrape spread and virulence. This review describes the structure and distribution of new, virulent physiological broomrape races, sources of resistance for introduction into susceptible cultivated sunflower, qualitative and quantitative resistance genes along with gene pyramiding and marker assisted selection (MAS) strategies applied in the process of increasing sunflower resistance. In addition, it presents an overview of underutilized biotechnological tools, such as phenotyping, -omics, and genome editing techniques, which need to be introduced in the study of sunflower resistance to broomrape in order to achieve durable resistance.