Do NERICA rice cultivars express resistance to Striga hermonthica (Del.) Benth. and Striga asiatica (L.) Kuntze under field conditions?

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.

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.

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.

A Personal History in Parasitic Weeds and Their Control

This invited paper summarises a career in which I became increasingly involved in research and related activities on Striga and other parasitic weeds. It also presents a personal view of the present status of parasitic weed problems and their control.

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.

Genotypic Variation in Cultivated and Wild Sorghum Genotypes in Response to Striga hermonthica Infestation

Striga hermonthica is the most important parasitic weed in sub-Saharan Africa and remains one of the most devastating biotic factors affecting sorghum production in the western regions of Kenya. Farmers have traditionally managed Striga using cultural methods, but the most effective and practical solution to poor smallholder farmers is to develop Striga-resistant varieties. This study was undertaken with the aim of identifying new sources of resistance to Striga in comparison with the conventional sources as standard checks. We evaluated 64 sorghum genotypes consisting of wild relatives, landraces, improved varieties, and fourth filial generation (F₄) progenies in both a field trial and a pot trial. Data were collected for days to 50% flowering (DTF), dry panicle weight (DPW, g), plant height (PH, cm), yield (YLD, t ha^-1), 100-grain weight (HGW, g), overall disease score (ODS), overall pest score (OPS), area under Striga number progress curve (ASNPC), maximum above-ground Striga (NS_max), and number of Striga-forming capsules (NSFC) at relevant stages. Genetic diversity and hybridity confirmation was determined using Diversity Arrays Technology sequencing (DArT-seq). Residual heterosis for HGW and NS_max was calculated as the percent increase or decrease in performance of F₄ crossover midparent (MP). The top 10 best yielding genotypes were predominantly F₄ crosses in both experiments, all of which yielded better than resistant checks, except FRAMIDA in the field trial and HAKIKA in the pot trial. Five F₄ progenies (ICSVIII IN × E36-1, LANDIWHITE × B35, B35 × E36-1, F6YQ212 × B35, and ICSVIII IN × LODOKA) recorded some of the highest HGW in both trials revealing their stability in good performance. Three genotypes (F6YQ212, GBK045827, and F6YQ212xB35) and one check (SRN39) were among the most resistant to Striga in both trials. SNPs generated from DArT-seq grouped the genotypes into three major clusters, with all resistant checks grouping in the same cluster except N13. We identified more resistant and high-yielding genotypes than the conventional checks, especially among the F₄ crosses, which should be promoted for adoption by farmers. Future studies will need to look for more diverse sources of Striga resistance and pyramid different mechanisms of resistance into farmer-preferred varieties to enhance the durability of Striga resistance in the fields of farmers.

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.

Breeding maize (Zea mays) for Striga resistance: Past, current and prospects in sub-saharan africa

Striga hermonthica, causes up to 100% yield loss in maize production in Sub-Saharan Africa. Developing Striga-resistant maize cultivars could be a major component of integrated Striga management strategies. This paper presents a comprehensive overview of maize breeding activities related to Striga resistance and its management. Scientific surveys have revealed that conventional breeding strategies have been used more than molecular breeding strategies in maize improvement for Striga resistance. Striga resistance genes are still under study in the International Institute for Tropical Agriculture (IITA) maize breeding programme. There is also a need to discover QTL and molecular markers associated with such genes to improve Striga resistance in maize. Marker Assistance Breeding is expected to increase maize breeding efficiency with complex traits such as resistance towards Striga because of the complex nature of the host-parasite relationship and its intersection with other environmental factors. Conventional alongside molecular tools and technical controls are promising methods to effectively assess Striga in Sub-Saharan Africa.

Molecular Dialog Between Parasitic Plants and Their Hosts

Parasitic plants steal sugars, water, and other nutrients from host plants through a haustorial connection. Several species of parasitic plants such as witchweeds (Striga spp.) and broomrapes (Orobanche and Phelipanche spp.) are major biotic constraints to agricultural production. Parasitic plants are understudied compared with other major classes of plant pathogens, but the recent availability of genomic and transcriptomic data has accelerated the rate of discovery of the molecular mechanisms underpinning plant parasitism. Here, we review the current body of knowledge of how parasitic plants sense host plants, germinate, form parasitic haustorial connections, and suppress host plant immune responses. Additionally, we assess whether parasitic plants fit within the current paradigms used to understand the molecular mechanisms of microbial plant-pathogen interactions. Finally, we discuss challenges facing parasitic plant research and propose the most urgent questions that need to be answered to advance our understanding of plant parasitism.

The Structural Integrity of Lignin Is Crucial for Resistance against Striga hermonthica Parasitism in Rice

Striga species are parasitic weeds that seriously constrain the productivity of food staples, including cereals and legumes, in Sub-Saharan Africa and Asia. In eastern and central Africa, Striga spp. infest as much as 40 million hectares of smallholder farmland causing total crop failure during severe infestation. As the molecular mechanisms underlying resistance are yet to be elucidated, we undertook a comparative metabolome study using the Striga-resistant rice (Oryza sativa) cultivar 'Nipponbare' and the susceptible cultivar 'Koshihikari'. We found that a number of metabolites accumulated preferentially in the Striga-resistant cultivar upon Striga hermonthica infection. Most apparent was increased deposition of lignin, a phenylpropanoid polymer mainly composed of p-hydroxyphenyl (H), guaiacyl (G), and syringyl (S) aromatic units, around the site of interaction in Nipponbare. The increased deposition of lignin was accompanied by induction of the expression of corresponding enzyme-encoding genes in the phenylpropanoid pathway. In addition, perturbing normal lignin composition by knocking down or overexpressing the genes that regulate lignin composition, i.e. p-COUMARATE 3-HYDROXYLASE or FERULATE 5-HYDROXYLASE, enhanced susceptibility of Nipponbare to S hermonthica infection. These results demonstrate that enhanced lignin deposition and maintenance of the structural integrity of lignin polymers deposited at the infection site are crucial for postattachment resistance against S hermonthica.

Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions

BACKGROUND

Increasing rice demand is one of the consequences of the steadily improving socio-economic status of the African countries. New Rice for Africa (NERICA), which are interspecific hybrids between Asian and African rice varieties, are one of successful breeding products utilizing biodiversity across the two different rice crop species. Upland NERICA varieties (NU) exhibit agronomic traits of value for the harsh eco-geography, including shorter duration, higher yield and stress tolerance, compared to local African varieties. However, the molecular basis of the traits in NU varieties is largely unknown.

RESULTS

Whole genome re-sequencing was performed of four NU lines (3, 4, 5, and 7) and for the parental Oryza sativa WAB56-104 and Oryza glaberrima CG14. The k-mer analysis predicted large genomes for the four NU lines, most likely inherited from WAB56-104. Approximately 3.1, 0.10, and 0.40 million single nucleotide polymorphisms, multi nucleotide polymorphisms, and short insertions/deletions were mined between the parental lines, respectively. Integrated analysis with another four NU lines (1, 2, 8, and 9) showed that the ratios of the donor CG14 allelic sites in the NU lines ranged from 1.3 to 9.8%. High resolution graphical genotype indicated genome-level similarities and common genetic events during the breeding process: five xyloglucan fucosyltransferase from O. glaberrima were introgressed in common. Segregation of genic segments revealed potential causal genes for some agronomic traits including grain shattering, awnness, susceptibility to bacterial leaf bright, and salt tolerance. Analysis of unmapped sequences against the reference cultivar Nipponbare indicated existence of unique genes for pathogen and abiotic stress resistance in the NU varieties.

CONCLUSIONS

The results provide understanding of NU genomes for rice improvement for Africa reinforcing local capacity for food security and insights into molecular events in breeding of interspecific hybrid crops.

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

The parasitic weeds Striga asiatica and Striga hermonthica cause devastating yield losses to upland rice in Africa. Little is known about genetic variation in host resistance and tolerance across rice genotypes, in relation to virulence differences across Striga species and ecotypes. Diverse rice genotypes were phenotyped for the above traits in S. asiatica- (Tanzania) and S. hermonthica-infested fields (Kenya and Uganda) and under controlled conditions. New rice genotypes with either ecotype-specific or broad-spectrum resistance were identified. Resistance identified in the field was confirmed under controlled conditions, providing evidence that resistance was largely genetically determined. Striga-resistant genotypes contributed to yield security under Striga-infested conditions, although grain yield was also determined by the genotype-specific yield potential and tolerance. Tolerance, the physiological mechanism mitigating Striga effects on host growth and physiology, was unrelated to resistance, implying that any combination of high, medium or low levels of these traits can be found across rice genotypes. Striga virulence varies across species and ecotypes. The extent of Striga-induced host damage results from the interaction between parasite virulence and genetically determined levels of host-plant resistance and tolerance. These novel findings support the need for predictive breeding strategies based on knowledge of host resistance and parasite virulence.

Identification of Striga hermonthica-Resistant Upland Rice Varieties in Sudan and Their Resistance Phenotypes

Rice has become a major staple cereal in sub-Saharan Africa. Currently, upland rice cultivation is expanding particularly in rainfed areas where the root parasitic weed Striga hermonthica, a major constraint to cereal production, is endemic. Laboratory, pot, and semi-controlled open air experiments were performed to evaluate resistance of selected rice varieties in Sudan to a resident S. hermonthica population. In the laboratory, 27 varieties were screened for post-attachment resistance using the rhizotron technique. Varieties displaying high post-attachment resistance, Umgar, NERICA5, and NERICA13 together with NERICA4, NERICA18, and Nipponbare, a lowland rice variety, were further evaluated for performance and Striga resistance in pot and semi-controlled open air experiments and for germination inducing activity in a laboratory. In addition, comparative studies on reaction of Umgar, Kosti1 and Kosti2, released varieties for commercial production in Sudan, to the parasite were performed in two pot experiments. In the pot experiments Umgar and NERICA5, consistently, sustained the lowest Striga emergence (<2.2 Striga plants per pot), while NERICA13 and NERICA4 supported 1.8-5.7 and 8.7-16.4 Striga plants per pot, respectively. In an artificially Striga-infested field, number of emergent Striga plants per 10 rice hills, at harvest, was 2.0, 2.0, 4.8, 13.5, 13.3, and 18.3 on Umgar, NERICA5, NERICA13, NERICA4, NERICA18, and Nipponbare, respectively. Striga had no adverse effects on total above-ground parts and panicle dry weight in Umgar and NERICA5. Germination-inducing activity of root exudates, at 14 days after sowing onward, was markedly lower for Umgar than for NERICA5, NERICA13, NERICA4, and NERICA18. Based on these findings, Umgar has both pre and post-attachment resistance to a resident Striga population in Sudan. Kosti1 and Kosti2 did not exhibit Striga-resistance at the same level as Umgar. Further the resistance of NERICA5, a variety reported to be endowed with a broad spectrum resistance to Striga species and ecotypes, at least to one resident Striga population in Sudan was clearly indicated.