Genetic variation and host-parasite specificity of Striga resistance and tolerance in rice: the need for predictive breeding

Macronutrient application rescues performance of tolerant sorghum genotypes when infected by the parasitic plant striga

BACKGROUND AND AIMS

Infection by the hemi-parasitic plant Striga hermonthica causes severe host plant damage and seed production losses. Increased availability of essential plant nutrients reduces infection. Whether, how and to what extent it also reduces striga-induced host plant damage has not been well studied.

METHODS

The effects of improved macro- and micronutrient supply on host plant performance under striga-free and infected conditions were investigated in glasshouse pot assays. One striga-sensitive and two striga-tolerant genotypes were compared. Plants growing in impoverished soils were supplied with (1) 25 % of optimal macro- and micronutrient quantities, (2) 25 % macro- and 100 % micronutrients, (3) 100 % macro- and 25 % micronutrients, or (4) 100 % macro- and micronutrients.

KEY RESULTS

Photosynthesis rates of striga-infected plants of the sensitive genotype increased with improved nutrition (from 12.2 to 22.1 μmol m-2 s-1) but remained below striga-free levels (34.9-38.8 μmol m-2 s-1). For the tolerant genotypes, increased macronutrient supply offset striga-induced photosynthesis losses. Striga-induced relative grain losses of 100 % for the sensitive genotype were reduced to 74 % by increased macronutrients. Grain losses of 80 % in the tolerant Ochuti genotype, incurred at low nutrient supply, were reduced to 5 % by improved nutrient supply.

CONCLUSIONS

Increasing macronutrient supply reduces the impact of striga on host plants but can only restore losses when applied to genotypes with a tolerant background.

Harnessing plant resistance against Striga spp. parasitism in major cereal crops for enhanced crop production and food security in Sub-Saharan Africa: a review

Given their long-lasting seed viability, 15–20-year lifespan and their high seed production levels, a significant impact of parasitic plant Striga spp. on African food production is inevitable. Over the last decades, climate change has increasingly favoured the adaptability, spread and virulence of major Striga species, S. hermonthica and S. asiatica, across arable land in Sub-Saharan Africa (SSA). These parasitic weeds are causing important yield losses on several staple food crops and endangering food and nutritional security in many SSA countries. Losses caused by Striga spp. are amplified by low soil fertility and recurrent droughts. The impact of Striga parasitism has been characterized through different phenotypic and genotypic traits assessment of their host plants. Among all control strategies, host-plant resistance remains the most pro-poor, easy-to-adopt, sustainable and eco-friendly control strategy against Striga parasitism. This review highlights the impact of Striga parasitism on food security in SSA and reports recent results related to the genetic basis of different agronomic, pheno-physiological and biochemical traits associated with the resistance to Striga in major African cereal food crops.

Bulinus snails in the Lake Victoria Basin in Kenya: Systematics and their role as hosts for schistosomes

The planorbid gastropod genus Bulinus consists of 38 species that vary in their ability to vector Schistosoma haematobium (the causative agent of human urogenital schistosomiasis), other Schistosoma species, and non-schistosome trematodes. Relying on sequence-based identifications of bulinids (partial cox1 and 16S) and Schistosoma (cox1 and ITS), we examined Bulinus species in the Lake Victoria Basin in Kenya for naturally acquired infections with Schistosoma species. We collected 6,133 bulinids from 11 sites between 2014-2021, 226 (3.7%) of which harbored Schistosoma infections. We found 4 Bulinus taxa from Lake Victoria (B. truncatus, B. tropicus, B. ugandae, and B. cf. transversalis), and an additional 4 from other habitats (B. globosus, B. productus, B. forskalii, and B. scalaris). S. haematobium infections were found in B. globosus and B. productus (with infections in the former predominating) whereas S. bovis infections were identified in B. globosus, B. productus, B. forskalii, and B. ugandae. No nuclear/mitochondrial discordance potentially indicative of S. haematobium/S. bovis hybridization was detected. We highlight the presence of Bulinus ugandae as a distinct lake-dwelling taxon closely related to B. globosus yet, unlike all other members of the B. africanus species group, is likely not a vector for S. haematobium, though it does exhibit susceptibility to S. bovis. Other lake-dwelling bulinids also lacked S. haematobium infections, supporting the possibility that they all lack compatibility with local S. haematobium, thereby preventing widespread transmission of urogenital schistosomiasis in the lake's waters. We support B. productus as a distinct species from B. nasutus, B. scalaris as distinct from B. forskalii, and add further evidence for a B. globosus species complex with three lineages represented in Kenya alone. This study serves as an essential prelude for investigating why these patterns in compatibility exist and whether the underlying biological mechanisms may be exploited for the purpose of limiting schistosome transmission.

Mapping quantitative trait loci and predicting candidate genes for Striga resistance in maize using resistance donor line derived from Zea diploperennis

The parasitic weed, Striga is a major biological constraint to cereal production in sub-Saharan Africa (SSA) and threatens food and nutrition security. Two hundred and twenty-three (223) F_2:3 mapping population involving individuals derived from TZdEI 352 x TZEI 916 were phenotyped for four Striga-adaptive traits and genotyped using the Diversity Arrays Technology (DArT) to determine the genomic regions responsible for Striga resistance in maize. After removing distorted SNP markers, a genetic linkage map was constructed using 1,918 DArTseq markers which covered 2092.1 cM. Using the inclusive composite interval mapping method in IciMapping, twenty-three QTLs influencing Striga resistance traits were identified across four Striga-infested environments with five stable QTLs (qGY4, qSC2.1, qSC2.2, qSC5, and qSC6) detected in more than one environment. The variations explained by the QTLs ranged from 4.1% (qSD2.3) to 14.4% (qSC7.1). Six QTLs each with significant additive × environment interactions were also identified for grain yield and Striga damage. Gene annotation revealed candidate genes underlying the QTLs, including the gene models GRMZM2G077002 and GRMZM2G404973 which encode the GATA transcription factors, GRMZM2G178998 and GRMZM2G134073 encoding the NAC transcription factors, GRMZM2G053868 and GRMZM2G157068 which encode the nitrate transporter protein and GRMZM2G371033 encoding the SBP-transcription factor. These candidate genes play crucial roles in plant growth and developmental processes and defense functions. This study provides further insights into the genetic mechanisms of resistance to Striga parasitism in maize. The QTL detected in more than one environment would be useful for further fine-mapping and marker-assisted selection for the development of Striga resistant and high-yielding maize cultivars.

Crop diversification and parasitic weed abundance: a global meta-analysis

Parasitic weeds cause huge annual losses to food production globally. A small number of species from the genera Cuscuta, Orobanche, Phelipanche and Striga have proliferated across many agroecological zones. Their control is compromised due to the lack of efficacy of conventional herbicides and their rapid adaptation to new resistant crop cultivars. A broad range of studies suggest consistent reductions in parasitic weed densities owing to increased spatial (intercropping) and temporal diversity (crop rotation). However, to date, no synthesis of this body of research has been published. Here we report the results of a meta-analysis using 1525 paired observations from 67 studies across 24 countries, comparing parasitic weed density and crop yields from monocrop and more diverse cropping systems. We found both spatial and temporal crop diversification had a significant effect on parasitic weed density reduction. Furthermore, our results show effects of spatial diversification are stronger in suppressing parasitic weeds than temporal effects. Furthermore, the analysis indicates intercrops which alter both microclimate and soil chemistry (e.g. Crotalaria, Stylosanthes, Berseem clover and Desmodium) are most effective in parasitic weed management. This analysis serves to underline the viability of crop diversification as a tool to enhance food security globally.

Genome-enabled discovery of candidate virulence loci in Striga hermonthica, a devastating parasite of African cereal crops

Parasites have evolved proteins, virulence factors (VFs), that facilitate plant colonisation, however VFs mediating parasitic plant-host interactions are poorly understood. Striga hermonthica is an obligate, root-parasitic plant of cereal hosts in sub-Saharan Africa, causing devastating yield losses. Understanding the molecular nature and allelic variation of VFs in S. hermonthica is essential for breeding resistance and delaying the evolution of parasite virulence. We assembled the S. hermonthica genome and identified secreted proteins using in silico prediction. Pooled sequencing of parasites growing on a susceptible and a strongly resistant rice host allowed us to scan for loci where selection imposed by the resistant host had elevated the frequency of alleles contributing to successful colonisation. Thirty-eight putatively secreted VFs had very different allele frequencies with functions including host cell wall modification, protease or protease inhibitor and kinase activities. These candidate loci had significantly higher Tajima's D than the genomic background, consistent with balancing selection. Our results reveal diverse strategies used by S. hermonthica to overcome different layers of host resistance. Understanding the maintenance of variation at virulence loci by balancing selection will be critical to managing the evolution of virulence as part of a sustainable control strategy.

Genetic composition and diversity of Arabica coffee in the crop's center of origin and its impact on four major fungal diseases

Conventional wisdom states that genetic variation reduces disease levels in plant populations. Nevertheless, crop species have been subject to a gradual loss of genetic variation through selection for specific traits during breeding, thereby increasing their vulnerability to biotic stresses such as pathogens. We explored how genetic variation in Arabica coffee sites in southwestern Ethiopia was related to the incidence of four major fungal diseases. Sixty sites were selected along a gradient of management intensity, ranging from nearly wild to intensively managed coffee stands. We used genotyping-by-sequencing of pooled leaf samples (pool-GBS) derived from 16 individual coffee shrubs in each of the sixty sites to assess the variation in genetic composition (multivariate: reference allele frequency) and genetic diversity (univariate: mean expected heterozygosity) between sites. We found that genetic composition had a clear spatial pattern and that genetic diversity was higher in less managed sites. The incidence of the four fungal diseases was related to the genetic composition of the coffee stands, but in a specific way for each disease. In contrast, genetic diversity was only related to the within-site variation of coffee berry disease, but not to the mean incidence of any of the four diseases across sites. Given that fungal diseases are major challenges of Arabica coffee in its native range, our findings that genetic composition of coffee sites impacted the major fungal diseases may serve as baseline information to study the molecular basis of disease resistance in coffee. Overall, our study illustrates the need to consider both host genetic composition and genetic diversity when investigating the genetic basis for variation in disease levels.

Identifying existing management practices in the control of Striga asiatica within rice-maize systems in mid-west Madagascar

Infestations by the parasitic weed genus Striga result in significant losses to cereal crop yields across sub-Saharan Africa. The problem disproportionately affects subsistence farmers who frequently lack access to novel technologies. Effective Striga management therefore requires the development of strategies utilizing existing cultural management practices. We report a multiyear, landscape-scale monitoring project for Striga asiatica in the mid-west of Madagascar, undertaken over 2019-2020 with the aims of examining cultural, climatic, and edaphic factors currently driving abundance and distribution. Long-distance transects were established across the middle-west region of Madagascar, over which S. asiatica abundance in fields was estimated. Analysis of the data highlights the importance of crop variety and legumes in driving Striga density. Moreover, the dataset revealed significant effect of precipitation seasonality, mean temperature, and altitude in determining abundance. A composite management index indicated the effect of a range of cultural practices on changes in Striga abundance. The findings support the assertion that single measures are not sufficient for the effective, long-term management of Striga. Furthermore, the composite score has potential as a significant guide of integrated Striga management beyond the geographic range of this study.

Impact of the facultative parasitic weed Rhamphicarpa fistulosa (Hochst.) Benth. on photosynthesis of its host Oryza sativa L

Rhamphicarpa fistulosa is a facultative root parasitic annual forb, of the family Orobanchaceae that is native to sub-Saharan Africa. Parasitism results in yield reductions by the host plants but it is not known how exactly R. fistulosa affects its host or how the host responds physiologically. In three pot experiments, we investigated whether and when the parasite affects photosynthesis of rice, whether the level of impact was parasite density dependent and explored mechanisms underlying the response of rice photosynthesis to parasitism. Photosynthesis and related parameters were measured at a range of light use intensities. Host photosynthesis was negatively affected while light use efficiency was negatively affected only later on in the growth process. Except for dark respiration rates, which were never affected by parasite infection, suppression of host photosynthesis at light saturation, the initial light-use efficiency, chlorophyll content, specific leaf area and shoot weight were parasite density dependent with a stronger effect for higher parasite densities. Only at 56 days after sowing, the slope of the linear relationship between light adapted quantum efficiency of PSII electron transport (Φ_PSII) and the quantum yield of CO₂ assimilation (Φ_CO2) of infected plants was less than those of un-infected plants. There was a considerable time lag between the parasite's acquisition of benefits from the association, in terms of growth (previously observed around 42 DAS), and the reduction of host photosynthesis (around 56 DAS). Expression of relative reductions in host growth rates started at the same time as the relative suppression of host photosynthesis. This indicated that R. fistulosa affects host growth by first extracting assimilates and making considerable gains in growth, before impacting host photosynthesis and growth.

New pre-attachment Striga resistant sorghum adapted to African agro-ecologies

BACKGROUND

Pre-attachment resistance to the parasitic plants Striga hermonthica and S. asiatica occurs in sorghum mutants designated low germination stimulant 1 (lgs1). However, only a few of these mutants have been identified and their resistance validated. Additionally, pre-attachment resistance in sorghum beyond lgs1 mutants has not been explored. We used lgs1-specific markers to identify new lgs1-like mutants in a diverse global sorghum collection. The sorghum collection was also evaluated for pre-attachment resistance against Striga using an in vitro assay that measured Striga germination activity and radicle growth.

RESULTS

From a total of 177 sorghum accessions, 60 recorded mean germination levels of below 42%, which is comparable with the previously identified lgs1-like sorghum (SRN39 and IS9830) used as controls in this study. Furthermore, 32 of these accessions recorded Striga radicle lengths comparable or lower than the controls (0.42 mm). Thirty-eight accessions contained the lgs1 mutation and although overall, lgs1 mutants had considerably reduced Striga germination, some low inducers of Striga germination were wild-type for lgs1. Germination was positively but weakly correlated with radicle length pointing to additional radicle growth inhibitory activity.

CONCLUSIONS

lgs1 mutations, alongside other mechanisms for low Striga germination stimulation, are prevalent in sorghum, and poor Striga radicle growth is suggestive of host-derived inhibition. As an outcome, our study makes available multiple Striga-resistant sorghum with adaptability to diverse agro-ecological regions in sub-Saharan Africa making immediate deployment possible. © 2021 Society of Chemical Industry.

Combining host plant defence with targeted nutrition: key to durable control of hemiparasitic Striga in cereals in sub-Saharan Africa?

Host plant defence mechanisms (resistance and tolerance) and plant nutrition are two of the most widely proposed components for the control of hemiparasitic weeds of the genus Striga in tropical cereal production systems. Neither of the two components alone is effective enough to prevent parasitism and concomitant crop losses. This review explores the potential of improved plant nutrition, being the chemical constituent of soil fertility, to fortify the expression of plant inherent resistance and tolerance against Striga. Beyond reviewing advances in parasitic plant research, we assess relevant insights from phytopathology and plant physiology in the broader sense to identify opportunities and knowledge gaps and to develop the way forward regarding research and development of combining genetics and plant nutrition for the durable control of Striga.

Current progress in Striga management

The Striga, particularly S. he rmonthica, problem has become a major threat to food security, exacerbating hunger and poverty in many African countries. A number of Striga control strategies have been proposed and tested during the past decade, however, further research efforts are still needed to provide sustainable and effective solutions to the Striga problem. In this paper, we provide an update on the recent progress and the approaches used in Striga management, and highlight emerging opportunities for developing new technologies to control this enigmatic parasite.

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.

Crystal structure and biochemical characterization of Striga hermonthica HYPO-SENSITIVE TO LIGHT 8 (ShHTL8) in strigolactone signaling pathway

Striga is a parasitic weed that disperses easily, and its seeds can persist in the soil for many years, presenting long-term threats to food security. If SLs stimulate the seed germination of root parasitic weeds before planting, weeds will wither due to no host. Therefore, it is necessary to determine the mechanism of strigolactone (SL) signaling in Striga to reduce the impacts of this parasitic weed. Striga has eleven different kinds of HYPO-SENSITIVE to LIGHT (ShHTL) hydrolases. Different ShHTL hydrolases exhibit distinct responses to SLs, despite these ShHTLs exhibiting more than 60% sequence identity. Currently, structural information is available for only five ShHTL proteins, and more structural information is needed to design Striga germination stimulants or inhibitors. In this paper, we report the crystal structure of ShHTL8, which is determined at a resolution of 1.4 Å. Scanning fluorimetry and HPLC assays indicate that L125, M147, M154 and I194 are important binding sites, and of which L125 may act as a key holder involved in the catalytic reaction. Additionally, the corresponding residue, Y124 of ShHTL1 and F135 of ShHTL2 also play a significant role in the substrate recognition.

Immune-Related Transcriptional Responses to Parasitic Infection in a Naturally Inbred Fish: Roles of Genotype and Individual Variation

Parasites are strong drivers of evolutionary change and the genetic variation of both host and parasite populations can co-evolve as a function of parasite virulence and host resistance. The role of transcriptome variation in specific interactions between host and parasite genotypes has been less studied and can be confounded by differences in genetic variation. We employed two naturally inbred lines of a self-fertilizing fish to estimate the role of host genotype in the transcriptome response to parasite infection using RNA-seq. In addition, we targeted several differentially expressed immune-related genes to further investigate the relative role of individual variation in the immune response using RT-qPCR, taking advantage of the genomic uniformity of the self-fertilizing lines. We found significant differences in gene expression between lines in response to infection both in the transcriptome and in individual gene RT-qPCR analyses. Individual RT-qPCR analyses of gene expression identified significant variance differences between lines for six genes but only for three genes between infected and control fish. Our results indicate that although the genetic background plays an important role in the transcriptome response to parasites, it cannot fully explain individual differences within genetically homogeneous lines, which can be important for determining the response to parasites.

Methyl phenlactonoates are efficient strigolactone analogs with simple structure

Strigolactones (SLs) are a new class of phytohormones that also act as germination stimulants for root parasitic plants, such as Striga spp., and as branching factors for symbiotic arbuscular mycorrhizal fungi. Sources for natural SLs are very limited. Hence, efficient and simple SL analogs are needed for elucidating SL-related biological processes as well as for agricultural applications. Based on the structure of the non-canonical SL methyl carlactonoate, we developed a new, easy to synthesize series of analogs, termed methyl phenlactonoates (MPs), evaluated their efficacy in exerting different SL functions, and determined their affinity for SL receptors from rice and Striga hermonthica. Most of the MPs showed considerable activity in regulating plant architecture, triggering leaf senescence, and inducing parasitic seed germination. Moreover, some MPs outperformed GR24, a widely used SL analog with a complex structure, in exerting particular SL functions, such as modulating Arabidopsis roots architecture and inhibiting rice tillering. Thus, MPs will help in elucidating the functions of SLs and are promising candidates for agricultural applications. Moreover, MPs demonstrate that slight structural modifications clearly impact the efficiency in exerting particular SL functions, indicating that structural diversity of natural SLs may mirror a functional specificity.

Plants under stress by parasitic plants

In addition to other biotic stresses, parasitic plants pose an additional threat to plants and cause crop losses, worldwide. Plant parasites directly connect to the vasculature of host plants thereby stealing water, nutrients, and carbohydrates consequently leading to tremendously reduced biomass and losses in seed yields of the infected host plants. Initial steps to understand the molecular resistance mechanisms and the successes in ancient and recent breeding efforts will provide fundamental knowledge to further generate crop plants that will resist attacks by plant parasites.