A novel form of resistance in rice to the angiosperm parasite Striga hermonthica

The root hemiparasitic weed Striga hermonthica is a serious constraint to grain production of economically important cereals in sub-Saharan Africa. Breeding for parasite resistance in cereals is widely recognized as the most sustainable form of long-term control; however, advances have been limited owing to a lack of cereal germplasm demonstrating postattachment resistance to Striga. Here, we identify a cultivar of rice (Nipponbare) that exhibits strong postattachment resistance to S. hermonthica; the parasite penetrates the host root cortex but does not form parasite-host xylem-xylem connections. In order to identify the genomic regions contributing to this resistance, a mapping population of backcross inbred lines between the resistant (Nipponbare) and susceptible (Kasalath) parents were evaluated for resistance to S. hermonthica. Composite interval mapping located seven putative quantitative trait loci (QTL) explaining 31% of the overall phenotypic variance; a second, independent, screen confirmed four of these QTL. Relative to the parental lines, allelic substitutions at these QTL altered the phenotype by at least 0.5 of a phenotypic standard deviation. Thus, they should be regarded as major genes and are likely to be useful in breeding programmes to enhance host resistance.     

Variation for host range within and among populations of the parasitic plant Striga hermonthica

Striga hermonthica is an angiosperm parasite that causes substantial damage to a wide variety of cereal crop species, and to the livelihoods of subsistence farmers in sub-Saharan Africa. The broad host range of this parasite makes it a fascinating model for the study of host-parasite interactions, and suggests that effective long-term control strategies for the parasite will require an understanding of the potential for host range adaptation in parasite populations. We used a controlled experiment to test the extent to which the success or failure of S. hermonthica parasites to develop on a particular host cultivar (host resistance/compatibility) depends upon the identity of interacting host genotypes and parasite populations. We also tested the hypothesis that there is a genetic component to host range within individual S. hermonthica populations, using three rice cultivars with known, contrasting abilities to resist infection. The developmental success of S. hermonthica parasites growing on different rice-host cultivars (genotypes) depended significantly on a parasite population by host-genotype interaction. Genetic analysis using amplified fragment length polymorphism (AFLP) markers revealed that a small subset of AFLP markers showed 'outlier' genetic differentiation among sub-populations of S. hermonthica attached to different host cultivars. We suggest that, this indicates a genetic component to host range within populations of S. hermonthica, and that a detailed understanding of the genomic loci involved will be crucial in understanding host-parasite specificity and in breeding crop cultivars with broad spectrum resistance to S. hermonthica.     

New Rice for Africa (NERICA) cultivars exhibit different levels of post-attachment resistance against the parasitic weeds Striga hermonthica and Striga asiatica

Striga hermonthica and S. asiatica are root parasitic weeds that infect the major cereal crops of sub-Saharan Africa causing severe losses in yield. The interspecific upland NEw RICe for Africa (NERICA) cultivars are popular amongst subsistence farmers, but little is known about their post-attachment resistance against Striga. Here, we evaluate the post-attachment resistance levels of the NERICA cultivars and their parents against ecotypes of S. hermonthica and S.asiatica, characterize the phenotype of the resistance mechanisms and determine the effect of Striga on host biomass. Some NERICA cultivars showed good broad-spectrum resistance against several Striga ecotypes, whereas others showed intermediate resistance or were very susceptible. The phenotype of a resistant interaction was often characterized by an inability of the parasite to penetrate the endodermis. Moreover, some parasites formed only a few connections to the host xylem, grew slowly and remained small. The most resistant NERICA cultivars were least damaged by Striga, although even a small number of parasites caused a reduction in above-ground host biomass. The elucidation of the molecular genetic basis of the resistance mechanisms and tolerance would allow the development of cultivars with multiple, durable resistance for use in farmers' fields.     

Physiological and genetic mapping study of tolerance to root-knot nematode in rice

The root-knot nematode Meloidogyne graminicola is an obligate biotrophic parasite and a major pest of rice (Oryza sativa) for which resistant varieties are not currently available. Quantitative trait loci (QTLs) for partial resistance to M. graminicola were identified using a mapping population based on two rice varieties, Bala x Azucena. Experiments were carried out to investigate the interactions between M. graminicola and these two varieties in terms of nematode establishment, reproduction and effect on rice yield. Nematode establishment was also assessed in the mapping population. Meloidogyne graminicola consistently caused more galling and had higher reproductive success in Azucena than in Bala. M. graminicola did not significantly reduce yield in Bala, but caused a yield reduction of almost half in Azucena, suggesting that the partial resistance to nematode establishment was related to nematode tolerance. A total of six significant or putative QTLs for nematode tolerance were detected. For two of the QTLs detected, Azucena was the donor of the tolerance alleles, suggesting it may be possible to breed plants with greater tolerance than Bala.     

Pre-attachment Striga hermonthica resistance of New Rice for Africa (NERICA) cultivars based on low strigolactone production

Striga hermonthica (Striga) is an obligate hemiparasitic weed, causing severe yield losses in cereals, including rice, throughout sub-Saharan Africa. Striga germination depends on strigolactones (germination stimulants) exuded by the host roots. The interspecific New Rice for Africa (NERICA) cultivars offer a potentially interesting gene pool for a screen for low germination-inducing rice cultivars. Exudates were collected from all NERICA cultivars and their parents (Oryza sativa and Oryza glaberrima) for the analysis of strigolactones. In vitro and in situ Striga germination, attachment and emergence rates were recorded for each cultivar. NERICA 1 and CG14 produced significantly less strigolactones and showed less Striga infection than the other cultivars. NERICAs 7, 8, 11 and 14 produced the largest amounts of strigolactones and showed the most severe Striga infection. Across all the cultivars and parents, there was a positive relationship between the amount of strigolactones in the exudate and Striga germination, attachment and emergence rates. This study shows that there is genetic variation in Striga pre-attachment resistance in NERICA rice. Cultivars combining this pre-attachment resistance with post-attachment resistance (already identified) can provide a key component for durable integrated management of this noxious weed in cereal production systems in sub-Saharan Africa.     

Effects of phosphate on arsenate and arsenite sensitivity in two rice (Oryza sativa L.) cultivars of different sensitivity

Arsenate and arsenite sensitivity and arsenate influx tests were conducted for two rice cultivars of different arsenic sensitivity, Azucena and Bala. These were to establish if the mechanism of reduced arsenic sensitivity is achieved through an altered phosphate uptake system, as shown for Holcus lanatus. High phosphate treatments (≥50 μM) provided protection against both arsenate and arsenite. Unlike the H. lanatus tolerance mechanism, in the less sensitive cultivar Bala, arsenate influx did not decrease with phosphate treatment and phosphate transporters appeared to be constitutively upregulated; V_max for arsenate influx remain similar when Bala was grown in the presence or absence of phosphate (V_max - 0.90 and 0.63 nmol g⁻¹ f.wt min⁻¹ respectively). Although mean K_m appear different, Bala did not show lower affinity to arsenate than Azucena in the absence of phosphate (K_m - Azucena, 0.30 mM and Bala, 0.18), while in phosphate treatment, Bala arsenate affinity was half that observed for Azucena (K_m - Azucena, 0.14 and Bala, 0.36 mM). These were low compared to a 4 and 6 fold decrease seen for similar studies on H. lanatus in the absence and presence of phosphate. Phosphate-induced arsenic protection was observed but the mechanism does not resemble that of H. lanatus. Alternative mechanisms were discussed.     

Isolation of Fusarium oxysporum with Potential for Biocontrol of the Witchweed (Striga hermonthica) in the Nigerian Savanna

A fungus isolated from wilted Striga hermonthica plants was identified as Fusarium oxysporum. A comparison of this isolate (PSM-197) with four other Fusarium spp. for control of S. hermonthica using conidial foliar sprays, showed that it was the most pathogenic and virulent. The isolate, grown on sorghum grain and incorporated into soil, completely inhibited the emergence of S. hermonthica compared with other substrates.     

Mapping QTLs associated with drought avoidance in upland rice grown in the Philippines and West Africa

Localizing genes that contribute to drought avoidance in a quantitative way should enable the exploitation of these genes in breeding through marker-assisted selection, and may lead to the discovery of gene identity and function. Between 110 and 176 F₆ recombinant inbred lines from a mapping population derived from a cross of upland rice varieties Bala and Azucena have been evaluated for indicators of drought avoidance in sites in the Philippines and West Africa over two dry seasons. A molecular map with 102 RFLP, 34 AFLP and six microsatellite markers has been used to map (by composite interval mapping) quantitative trait loci (QTLs) for the visual scores of leaf rolling and leaf drying and leaf relative water content. QTLs were mapped for each site and across sites. A total of 17 regions were identified which contained QTLs with a LOD score greater than 3.2. For leaf rolling, Bala was the parent contributing the majority of positive alleles whilst for the other traits, Bala and Azucena contributed more evenly. Six of the 17 regions influenced more than one trait, explaining the phenotypic correlations between traits that were observed. Three QTLs appeared to be specific to the Philippines experiments. One QTL had opposing effects in the Philippines and West Africa. QTLs for relative water content were detected on chromosome 8, congruent with an osmotic adjustment QTL identified in another population. Only three of the QTLs identified here have not been reliably identified in the two other populations that have been screened for drought avoidance. By using several populations assessed for drought avoidance in different sites, the distribution and utility of QTLs for drought avoidance in rice is being elucidated.     

Infection time and density influence the response of sorghum to the parasitic angiosperm Striga hermonthica

Two cultivars of sorghum (CSH-1 and Ochuti) were grown in the presence and absence of the root hemiparasite Striga hermonthica in uniform conditions in the field in Kenya, Africa. S. hermonthica had a marked influence on growth and photosynthesis of 'CSH-1'; however, 'Ochuti' showed a less severe response to infection and tolerance of the parasite. The variation in genotype response might be partly explained by later attachment of the parasite and a lower level of infection. Laboratory studies were used to determine the importance of both variables in determining host response to infection. Early infection by S. hermonthica had a more negative effect on the host than late infection. The level of parasite biomass supported by the host also influenced host productivity but the relationship was nonlinear. Low degrees of parasite infection had a proportionately much greater effect on host grain weight than at greater parasite loading. Early infection of 'Ochuti' in laboratory conditions resulted in lower stem dry weight than in uninfected plants but not in smaller total plant biomass or lower rates of photosynthesis. In conclusion, the time of parasite attachment affected host performance and might explain much of the variation in host sensitivity both within and between studies. The level of parasite infection affected host performance to a lesser extent. In addition, late attachment and low levels of infection might have implications for control management strategies.     

Inhibition of Striga seed germination associated with sorghum growth promotion by soil bacteria

Striga spp. are obligate parasitic weeds of tropical cereals and generally have the same host range as rhizospheric bacteria of the genus Azospirillum. Four strains of Azospirillum brasilense, isolated from soil where sorghum is grown, have been tested for their effect on germination of Striga hermonthica seeds and on cereal (Sorghum vulgare) growth. Two out of four strains assayed significantly inhibited germination of the parasite. Moreover, one of the two strains showed a plant growth promoting (PGPR) effect.     

Photosynthesis and stomatal characteristics of Striga hermonthica in relation to its parasitic habit

Photosynthesis and stomatal characteristics of the angiosperm parasite Striga her-monthica (Del.) Benth. have been compared with those of Antirrhinum majus L. cv. Suttons Yellow Rust Resistant, a related, non-parasitic species. The concentration of photosynthetic pigments in S. hermonthica leaves was less than 40% of those of A. majus leaves. Light saturated CO₂ assimilation rate of S. hermonthica was less than 40% that of A. majus on a chlorophyll basis and under 20% than of A. majus on a leaf area basis.
Stomata of Striga showed only partial closure in darkness, remained open in water stressed leaves and showed little response to exogenously applied abscisic acid. Stomatal conductance and transpiration were considerably higher in Striga compared with Antirrhinum . The high transpiration and low photosynthetic rates of S. hermonthica resulted in a low water use efficiency. The water relations of Striga leaves, while seemingly inappropriate for growth in drought prone environments, do appear to maximise nutrient and water acquisition from the host and as such may be an adaptation to the parasitic habit.     

Biochemical composition and photosynthetic activity of chloroplasts from Striga hermonthica and Striga aspera, root parasites of field-grown cereals

Striga hermonthica (Del.) Benth. and Striga aspera (Willd.) Benth. are root parasites causing dramatic losses in field-grown cereals in semi-and tropics. Being achlorophyllous and obligate parasites during their underground development, upon emergence from the soil, they become green leafy plants; but, despite the presence of chlorophyll, they exhibit only low rates of photosynthesis. To investigate if deficiency in the photosynthetic apparatus could account for the low rates of photosynthesis, chloroplasts were isolated from S. hermonthica parasitizing sorghum [Sorghum bicolor (L.) Moench cv. Tiemarifing] and from S. aspera parasitizing maize ( Zea mays L. cv. Tiémantié ) grown under greenhouse conditions or in their natural surroundings. Isolated chloroplasts exhibited the characteristics of chloroplasts from C₃ plants but displayed low levels of chlorophyll and polar lipids, while the protein content was less reduced. Main changes occurred in polar lipid composition, with decreases in monogalactosyldiacylglycerol and digalactosyldiacylglycerol. All polar lipids showed a decrease in the degree of unsaturation of fatly acids. All these changes were particularly pronounced in chloroplasts from plants that experienced heavy drought in Africa. On a chlorophyll basis, chloroplasts did not display a dramatic decrease in photosynthetic activities. These results are discussed in relation to parasitism and drought adaptation.     

Comparison of QTLs for rice seedling morphology under different water supply conditions

The variation of seedling characteristics under different water supply conditions is strongly associated with drought resistance in rice (Oryza sativa L.) and a better elucidation of its genetics is helpful for improving rice drought resistance. Ninety-six doubled-haploid (DH)rice lines of an indica and japonica cross were grown in both flooding and upland conditions and QTLs for morphological traits at seedling stage were examined using 208 restriction fragment length polymorphism (RFLP) and 76 microsatellite (SSR) markers. A total of 32 putative QTLs were associated with the four seedling traits: average of three adventitious root lengths (ARL), shoot height (SH), shoot biomass (SW), and root to shoot dry weight ratio (RSR). Five QTLs detected were the same under control and upland conditions. The ratio between the mean value of the seedling trait under upland and flooding conditions was used for assessing drought tolerance. A total of six QTLs for drought tolerance were detected. Comparative analysis was performed for the QTLs detected in this case and those reported from two other populations with the same upland rice variety Azucena as parent. Several identical QTLs for seedling elongation across the three populations with the positive alleles from the upland rice Azucena were detected, which suggests that the alleles of Azucena might be involved in water stress-accelerated elongation of rice under different genetic backgrounds. Five cell wall-related candidate genes for OsEXP1, OsEXP2, OsEXP4, EXT, and EGase were mapped on the intervals carrying the QTLs for seedling traits.     

Impact of nitrate supply in C and N assimilation in the parasitic plant Striga hermonthica (Del.) Benth (Scrophulariaceae) and its host Sorghum bicolor L

The threshold of tolerance for nitrate of the parasitic weed Striga hermonthica (Del.) Benth and the host plant Sorghum bicolor L. was determined by estimating the impact of increasing nitrate loads on plant growth and various parameters of C and N assimilation. Nitrate supply improved chlorophyll (Chl) content and photosystem II (PSII) photochemistry of infected S. bicolor that, in comparison to S. hermonthica, displayed a low imbalance between C and N assimilation when nitrate was supplied up to 1500 mg N per plant. Indeed, nitrate supplies increased strongly the leaf N:C ratio of the parasite. The higher nitrate load induced strong accumulation of nitrate, nitrite and ammonium, and consequently the death of S. hermonthica. Nevertheless, lower nitrate loads (up to 500 mg N per S. bicolor in this study) promoted leaf expansion, PSII photochemistry and N metabolism of S. hermonthica mature (M) plants, as attested by the significant rise in soluble protein and free amino-acid contents. Following these N supplies, the nitrate tolerance of S. hermonthica was correlated with an increase in PSII activity and a high incorporation of N excess into asparagine. This confirmed the central role of asparagine in the N metabolism of S. hermonthica, although this detoxification pathway was insufficient to limit ammonium accumulation under higher nitrate loads.     

Genetic mapping of the rice ionome in leaves and grain: identification of QTLs for 17 elements including arsenic, cadmium, iron and selenium

Research into the composition of cereal grains is motivated by increased interest in food quality. Here multi-element analysis is conducted on leaves and grain of the Bala x Azucena rice mapping population grown in the field. Quantitative trait loci (QTLs) for the concentration of 17 elements were detected, revealing 36 QTLs for leaves and 41 for grains. Epistasis was detected for most elements. There was very little correlation between leaf and grain element concentrations. For selenium, lead, phosphorus and magnesium QTLs were detected in the same location for both tissues. In general, there were no major QTL clusters, suggesting separate regulation of each element. QTLs for grain iron, zinc, molybdenum and selenium are potential targets for marker assisted selection to improve seed nutritional quality. An epistatic interaction for grain arsenic also looks promising to decrease the concentration of this carcinogenic element.     

Microorganisms of Striga hermonthica in Northern Ghana with Potential as Biocontrol Agents

A survey of microorganisms of Striga hermonthica Del. Benth., a root parasite of graminaceous crops, was conducted in northern Ghana in 1992. Thirteen fungal species were isolated from infected S. hermonthica plants. Fusarium spp. were the most prevalent, and were isolated from more than 90% of the S. hermonthica samples collected. Other fungi isolated were Alternaria alternata, Bipolaris specifera, Cladosporium oxysporum, Curvularia falax, Macrophomina phaseolina, Nodulisporium gregarium, Phoma sorghina and Sclerotium rolfsii.     

Genetic dissection of root growth in rice (Oryza sativa L.). II: mapping quantitative trait loci using molecular markers

Drought is a major abiotic stress of upland rice, and good root growth has been associated with drought avoidance. We report on the genetic mapping of root growth traits in an F₂ population derived from two drought-resistant rice varieties, ‘Bala’ and ‘Azucena’. Restriction fragment length polymorphism (RFLP) between the parents was 32%, and a molecular map with 71 marker loci and 17 linkage groups covering 1280 cM was produced. Quantitative trait loci (QTLs) for eight root growth characteristics were mapped using phenotype data obtained in a hydroponic screen previously described in a companion paper. Using a significance threshold of LOD 2.4, we observed one QTL for maximum root length after 28 days growth on chromosome 11. It had a LOD score of 6.9, explained nearly 30% of the variation and appeared to be largely additive in effect. QTLs for maximum root length after 3, 7, 14 and 21 days of growth were also revealed. Some root-length QTLs, including that on chromosome 11, varied greatly with developmental stage. One QTL for root volume and two QTLs for adventitious root thickness were detected. No QTLs were detected for the length of cells in the mature (fully expanded) zone of adventitious root tips. The results obtained are discussed in the context of previous reports on mapping root growth parameters in rice.     

QTLs and epistasis for aluminum tolerance in rice (Oryza sativa L.) at different seedling stages

To investigate the genetic background for aluminum (Al) tolerance in rice, a recombinant inbred (RI) population, derived from a cross between an Al-sensitive lowland indica rice variety IR1552 and an Al-tolerant upland japonica rice variety Azucena, was used in culture solution. A molecular linkage map, together with 104 amplified fragment length polymorphism (AFLP) markers and 103 restriction fragment length polymorphism (RFLP) markers, was constructed to map quantitative trait loci (QTLs) and epistatic loci for Al tolerance based on the segregation for relative root length (RRL) in the population. RRL was measured after stress for 2 and 4 weeks at a concentration of 1mM of Al³⁺ and a control with a pH 4.0, respectively. Two QTLs were detected at both the 2nd and the 4th weeks on chromosomes 1 and 12 from unconditional mapping, while the QTL on chromosome 1 was only detected at the 2nd stress week from conditional mapping. The effect of the QTL on chromosome 12 was increased with an increase of the stress period from 2 to 4 weeks. The QTL on chromosome 1 was expressed only at the earlier stress, but its contribution to tolerance was prolonged during growth. At least one different QTL was detected at the different stress periods. Mean comparisons between marker genotypic classes indicated that the positive alleles at the QTLs were from the Al-tolerant upland rice Azucena. An important heterozygous non-allelic interaction on Al tolerance was found. The results indicated that tolerance in the younger seedlings was predominantly controlled by an additive effect, while an epistatic effect was more important to the tolerance in older seedlings; additionally the detected QTLs may be multiple allelic loci for Al tolerance and phosphorus-uptake efficiency, or for Al and Fe²⁺ tolerance. Received: 29 July 1999 / Accepted: 13 October 1999