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Summary: Rice yellow mottle virus (RYMV) causes one of the most devastating rice diseases in Africa. Management of RYMV is challenging. Genetic resistance provides the most effective and environment‐friendly control. The recessive resistance locus rymv2 (OsCPR5.1) had been identified in African rice (Oryza glaberrima), however, introgression into Oryza sativa ssp. japonica and indica remains challenging due to crossing barriers. Here, we evaluated whether CRISPR/Cas9 genome editing of the two rice nucleoporin paralogs OsCPR5.1 (RYMV2) and OsCPR5.2 can be used to introduce RYMV resistance into the japonica variety Kitaake. Both paralogs had been shown to complement the defects of the Arabidopsis atcpr5 mutant, indicating partial redundancy. Despite striking sequence and structural similarities between the two paralogs, only oscpr5.1 loss‐of‐function mutants were fully resistant, while loss‐of‐function oscpr5.2 mutants remained susceptible, intimating that OsCPR5.1 plays a specific role in RYMV susceptibility. Notably, edited lines with short in‐frame deletions or replacements in the N‐terminal domain (predicted to be unstructured) of OsCPR5.1 were hypersusceptible to RYMV. In contrast to mutations in the single Arabidopsis AtCPR5 gene, which caused severely dwarfed plants, oscpr5.1 and oscpr5.2 single and double knockout mutants showed neither substantial growth defects nor symptoms indicative lesion mimic phenotypes, possibly reflecting functional differentiation. The specific editing of OsCPR5.1, while maintaining OsCPR5.2 activity, provides a promising strategy for generating RYMV‐resistance in elite Oryza sativa lines as well as for effective stacking with other RYMV resistance genes or other traits. [ABSTRACT FROM AUTHOR]

The undomesticated rice relative Oryza longistaminata is a valuable genetic resource for the improvement of the domesticated Asian rice, Oryza sativa. To facilitate the conservation, management, and use of O. longistaminata germplasm, we sought to quantify the population structure and diversity of this species across its geographic range, which includes most of sub-Saharan Africa, and to determine phylogenetic relationships to other AA-genome species of rice present in Africa, including the prevalence of interspecific hybridization between O. longistaminata and O. sativa. Though past plant breeding efforts to introgress genes from O. longistaminata have improved biotic stress resistance, ratooning ability, and yield in O. sativa, progress has been limited by substantial breeding barriers. Nevertheless, despite the strong breeding barriers observed by plant breeders who have attempted this interspecific cross, there have been multiple reports of spontaneous hybrids of O. sativa and O. longistaminata (aka "Obake") obtained from natural populations in Africa. However, the frequency and extent of such natural introgressions and their effect on the evolution of O. longistaminata had not been previously investigated. We studied 190 O. longistaminata accessions, primarily from the International Rice Research Institute genebank collection, along with 309 O. sativa, 25 Oryza barthii, and 83 Oryza glaberrima control outgroups, and 17 control interspecific O. sativa/O. longistaminata hybrids. We analyzed the materials using 178,651 singlenucleotide polymorphisms (SNPs) and seven plastid microsatellite markers. This study identified three genetic subpopulations of O. longistaminata, which correspond geographically to Northwestern Africa, Pan-Africa, and Southern Africa. We confirmed that O. longistaminata is, perhaps counterintuitively, more closely related to the Asian species, O. sativa, than the African species O. barthii and O. glaberrima. We identified 19 recent spontaneous interspecific hybrid individuals between O. sativa and O. longistaminata in the germplasm sampled. Notably, the recent introgression between O. sativa and O. longistaminata has been bidirectional. Moreover, low levels of O. sativa alleles admixed in many predominantly O. longistaminata accessions suggest that introgression also occurred in the distant past, but only in Southern Africa. [ABSTRACT FROM AUTHOR]

Global warming poses a threat to rice production. Breeding heat-tolerant rice is an effective and economical approach to address this challenge. African rice is a valuable genetic resource for developing heat-tolerant crops due to its intricate mechanism for adapting to high temperatures. Oryza longistaminata , a widely distributed wild rice species in Africa, may harbor an even richer gene pool for heat tolerance, which remains untapped. In this study, we identified three heat tolerance QTLs from O. longistaminata at the seedling stage, including novel heat tolerance loci qTT4 and qTT5. Our findings demonstrated that the O. longistaminata alleles for these two QTLs can enhance the heat tolerance of rice seedlings. Remarkably, qTT5 was mapped to a region spanning approximately 287.2 kb, which contains 46 expressing genes. Through the analysis of Gene Ontology and expression differences under heat induction, we identified four candidate genes. Our results lay the foundation for discovering heat tolerance genes underlying O. longistaminata and developing new genetic resources for heat-tolerant rice breeding. [ABSTRACT FROM AUTHOR]

Rice yellow mottle virus (RYMV) is a major biotic constraint to rice cultivation in Africa. RYMV shows a high genetic diversity. Viral lineages were defined according to the coat protein (CP) phylogeny. Varietal selection is considered as the most efficient way to manage RYMV. Sources of high resistance were identified mostly in accessions of the African rice species, Oryza glaberrima. Emergence of resistance-breaking (RB) genotypes was observed in controlled conditions. The RB ability was highly contrasted, depending on the resistance sources and on the RYMV lineages. A molecular marker linked to the adaptation to susceptible and resistant O. glaberrima was identified in the viral protein genome-linked (VPg). By contrast, as no molecular method was available to identify the hypervirulent lineage able to overcome all known resistance sources, plant inoculation assays were still required. Here, we designed specific RT-PCR primers to infer the RB abilities of RYMV isolates without greenhouse experiments or sequencing steps. These primers were tested and validated on 52 isolates, representative of RYMV genetic diversity. The molecular tools described in this study will contribute to optimizing the deployment strategy of resistant lines, considering the RYMV lineages identified in fields and their potential adaptability. [ABSTRACT FROM AUTHOR]

Africa has the world's fastest rate of population expansion, making it vulnerable to food shortages. Africa cultivates two types of rice (Asian rice; Oryza sativa and African rice; Oryza glaberrima). Native African rice called O. glaberrima has some intriguing characteristics, including resistance to several biotic and abiotic regional restrictions in Africa. However, O. glaberrima is solely employed as a tool to increase the production of O. sativa, which cannot grow in Africa, due to its low yield, lodging, grain breaking, and poor tissue culture ability. Enhancing breeding efforts for O. glaberrima is therefore critically important. The protocols for transformation and regeneration, however, are mostly for O. sativa and not O. glaberrima. This study examines the present problems with transformation and regeneration for African rice species as well as potential solutions for using modern breeding methods in O. glaberrima. [ABSTRACT FROM AUTHOR]

For breeding of salinity tolerant rice, halophytic species Oryza coarctata is considered as a valuable resource. Non-availability of molecular markers in the species is a major limitation and identification of markers applicable with wider gene pool will be resource-saving. Even after the recent advancement in high throughput genotyping techniques, sequence-tagged microsatellite sites (STMS) markers are considered as valuable resource for pre-breeding, especially when usable for a large number of species. Using a novel bioinformatics pipeline for cross transferable marker identification, whole genome sequences of nine Oryza species were surveyed with 23,499 STMS markers of rice. With this highly reproducible strategy, band sizes or polymorphism prediction among different species is possible before in-vitro validation. Only 359 STMS markers were cross-transferable to O. coarctata and 77 of those were common with O. sativa complex. These core markers were distributed over 11 chromosomes and nearly 76% were located within various genes of Oryza. The markers also showed unique genome specific polymorphism pattern with high levels of inter- and intraspecific variations in "AA" genome and complete absence of intra- or inter-population variations in O. coarctata (KKLL). The numbers of microsatellite motifs and the repeat numbers in different motifs were much lesser in O. coarctata leading to the exceptionally high level of polymorphism with all "AA" genome species. Two markers are also useful for species identification. The hyper-variable markers are effective resource for pre-breeding of O. sativa, O. glaberrima and new rice for Africa involving O. coarctata or any other species of O. sativa complex. [ABSTRACT FROM AUTHOR]

The ultraviolet B (UVB) sensitivity of rice cultivated in Asia and Africa varies greatly, with African rice cultivars (Oryza glaberrima Steud. and O. barthii A. Chev.) being more sensitive to UVB because of their low cyclobutane pyrimidine dimer (CPD) photolyase activity, which is a CPD repair enzyme, relative to Asian rice cultivars (O. sativa L.). Hence, the production of UVB-resistant African rice with augmented CPD photolyase activity is of great importance, although difficulty in transforming the African rice cultivars to this end has been reported. Here, we successfully produced overexpressing transgenic African rice with higher CPD photolyase activity by modifying media conditions for callus induction and regeneration using the parental line (PL), UVB-sensitive African rice TOG12380 (O. glaberrima). The overexpressing transgenic African rice carried a single copy of the CPD photolyase enzyme, with a 4.4-fold higher level of CPD photolyase transcripts and 2.6-fold higher activity than its PL counterpart. When the plants were grown for 21 days in a growth chamber under visible radiation or with supplementary various UVB radiation, the overexpressing transgenic plants have a significantly increased UVB resistance index compared to PL plants. These results strongly suggest that CPD photolyase remains an essential factor for tolerating UVB radiation stress in African rice. As a result, African rice cultivars with overexpressed CPD photolyase may survive better in tropical areas more prone to UVB radiation stress, including Africa. Collectively, our results provide strong evidence that CPD photolyase is a useful biotechnological tool for reducing UVB-induced growth inhibition in African rice crops of O. glaberrima. [ABSTRACT FROM AUTHOR]

Africa produces around 60% of the rice the continent consumes, relying heavily on rice imports to fulfill the rest of the domestic demand. Over the past 10 years, the rice-agricultural area increased nearly 40%, while average yield remained stagnant. Here we used a process-based crop simulation modelling approach combined with local weather, soil, and management datasets to evaluate the potential to increase rice production on existing cropland area in Africa and assess cropland expansion and rice imports by year 2050 for different scenarios of yield intensification. We find that Africa can avoid further increases in rice imports, and even reduce them, through a combination of cropland expansion following the historical trend together with closure of the current exploitable yield gap by half or more. Without substantial increase in rice yields, meeting future rice demand will require larger rice imports and/or land conversion than now., (© 2024. The Author(s).)

African Oryza glaberrima and Oryza sativa landraces are considered valuable resources for breeding traits due to their adaptation to local environmental and soil conditions. They often possess superior resistance to endemic pests and tolerance to drought and nutrient deficiencies when compared to the "imported" high production Asian rice varieties. In contrast, "domestication traits" such as seed shattering, lodging, and seed yield are not well established in these African landraces. Therefore, the use of these African varieties for high production agriculture is limited by unpredictable yield and grain quality. We are addressing this shortcoming by developing protocols for genetically transforming African landraces to allow the use of CRISPR-Cas mediated breeding approaches. Here we use as proof of concept the cultivated African landrace Kabre to target selected known "domestication loci" and improve the agronomic potential of Kabre rice. Stable genetic transformation with CRISPR-Cas9-based vectors generated single and simultaneous multiple gene knockouts. Plants with reduced stature to diminish lodging were generated by disrupting the HTD1 gene. Furthermore, three loci shown to control seed size and/or yield (GS3, GW2 and GN1A) were targeted using a multiplex CRISPR-Cas9 construct. This resulted in mutants with significantly improved seed yield. Our study provides an example of how new breeding technologies can accelerate the development of highly productive African landrace rice varieties, an important advancement considering that Africa is a hotspot for worldwide population growth and therefore prone to food shortage. [ABSTRACT FROM AUTHOR]

To understand variation in the root development traits (total root length (TRL), maximum root length (MRL) and root number) of 18 New Rice for Africa (NERICA) varieties, seedlings w-ere hydroponically grown under deficient and sufficient concentrations of two forms of nitrogen, NH4+ and N03". The donor African rice variety, 'CGI 4' (Oryza glaberrima Steud.), showed greater TRL and MRL than three background Asian rice varieties (Oryza sativa L.). Wide distribution was observed in all traits of the 18 NERICAs. The 18 NERJCAs and parental varieties were classified into three cluster groups by cluster analysis. Cluster la included only 'CG14'. Comparative analysis characterized cluster lb (including 'NERICA7') as an active root elongation group, and cluster II (including 'WAB56-104') as an active primordia development group. QTL analysis of F2 plants developed from a cross between 'WAB56-104' and 'NERICA7' detected two putative quantitative trait loci (QTLs) for root elongation on chromosome 1. Of these, a major QTL, designated as qRLl, 4-NERICA 7, was an NH4+-responsive QTL, which was narrowed dowm to a 0.7-Mbp region through progeny testing using F7 lines. qRL1.4-NER!CA 7 should help us understand genetic control in NERICAs, and improve root elongation in rice breeding programs. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

As Africa is facing multiple challenges related to food security, frameworks integrating production and availability are urgent for policymaking. Attention should be given not only to gradual socio-economic and climatic changes but also to their temporal variability. Here we present an integrated framework that allows one to assess the impacts of socio-economic development, gradual climate change and climate anomalies. We apply this framework to rice production and consumption in Africa whereby we explicitly account for the continent's dependency on imported rice. We show that socio-economic development dictates rice availability, whereas climate change has only minor effects in the long term and is predicted not to amplify supply shocks. Still, rainfed-dominated or self-producing regions are sensitive to local climatic anomalies, while trade dominates stability in import-dependent regions. Our study suggests that facilitating agricultural development and limiting trade barriers are key in relieving future challenges to rice availability and stability., (© 2023. The Author(s).)

Rice ( Oryza sativa L.) is one of the major staple foods for global consumption. A major roadblock to global rice production is persistent loss of crops caused by plant diseases, including rice blast, sheath blight, bacterial blight, and particularly various vector-borne rice viral diseases. Since the late 19th century, 19 species of rice viruses have been recorded in rice-producing areas worldwide and cause varying degrees of damage on the rice production. Among them, southern rice black-streaked dwarf virus (SRBSDV) and rice black-streaked dwarf virus (RBSDV) in Asia, rice yellow mottle virus (RYMV) in Africa, and rice stripe necrosis virus (RSNV) in America currently pose serious threats to rice yields. This review systematizes the emergence and damage of rice viral diseases, the symptomatology and transmission biology of rice viruses, the arm races between viruses and rice plants as well as their insect vectors, and the strategies for the prevention and control of rice viral diseases.

While agroforestry is a well-established approach for agroecological intensification, rice is less often integrated with trees than other annual staple crops. The benefits and risks from rice agroforestry practices have not been systematically explored. Considering the need for strategies that may address low fertility and high degradation of arable soils and contribute to smallholder farm productivity, livelihoods and climate resilience, such exploration would both be timely and relevant. This study, therefore, reviews the published literature on integrating trees in rice production worldwide and provides perspectives for future research, with special attention to Africa, where the potential for sustainable productivity enhancement is deemed highest. Worldwide, six improved rice agroforestry practices are distinguished: hedgerow alley-cropping, short-term (0.5–4 years) improved fallows, pre-rice green manuring, biomass transfer, systematically arranged rice – tree intercropping and irregularly dispersed trees in fields. The rice agroforestry practices in the 87 publications reviewed were associated with 204 woody perennial species world-wide. Rice agroforestry practices provide a range of products and services to farmers but rice yield is the only quantitative performance indicator reported widely enough to enable meta-analysis. Frequently reported comparative or additional effects of fertilizer application, made it possible to include this aspect in the analyses. Across all types of agroforestry practices enumerated, the average effect of adding trees compared to a no-fertilizer and no-tree control is + 38%. The most beneficial practices in terms of enhancing rice yield were biomass transfer, pre-rice green manuring (100% of data points showing positive responses for both practices) and hedgerow alley-cropping (21% positive cases overall but 64% where fertilizer was not applied). Yield reductions occurred with fertilized intercropping compared to a fertilized mono-crop (in 95% of cases) and with the unfertilized short fallow practice (50% of data points showed yield reduction due to competition in the relay intercropping stage). Tree species that combined rice yield enhancements (alongside other products and services) with wide environmental adaptability across the African continent, include Sesbania rostrata, Aeschynomene afraspera , Acacia auriculiformis , Gliricidia sepium and Gmelia arborea. Yield benefits and risks from integrating trees with smallholder rice cropping depend on the type of agroforestry practice used and how each practice interacts with fertilizer application. Further research is needed to investigate the impact of different ways of integrating trees with rice cropping on wider environmental, social and economic sustainability aspects, that are driving increasing interest in rice agroforestry. • World-wide, 204 woody perennial species were used in 6 types of rice agroforestry. • Pre-rice green manure, biomass transfer and hedgerows increased rice yield most. • Sesbania rostrata and Aeschynomene afraspera are effective as pre-rice green manure. • A broad range of tree species are useful for biomass transfer. • Gliricidia sepium and Gmelia arborea benefit rice yield in hedgerow alley-cropping. [ABSTRACT FROM AUTHOR]

Summary [ABSTRACT FROM AUTHOR]

Here we present the genomic sequence of the African cultivated rice, Oryza glaberrima, and compare these data with the genome sequence of Asian cultivated rice, Oryza sativa. We obtained gene-enriched sequences of O. glaberrima that correspond to about 25% of the gene regions of the O. sativa ( japonica) genome by methylation filtration and subtractive hybridization of repetitive sequences. While patterns of amino acid changes did not differ between the two species in terms of the biochemical properties, genes of O. glaberrima generally showed a larger synonymous-nonsynonymous substitution ratio, suggesting that O. glaberrima has undergone a genome-wide relaxation of purifying selection. We further investigated nucleotide substitutions around splice sites and found that eight genes of O. sativa experienced changes at splice sites after the divergence from O. glaberrima. These changes produced novel introns that partially truncated functional domains, suggesting that these newly emerged introns affect gene function. We also identified 2451 simple sequence repeats (SSRs) from the genomes of O. glaberrima and O. sativa. Although tri-nucleotide repeats were most common among the SSRs and were overrepresented in the protein-coding sequences, we found that selection against indels of tri-nucleotide repeats was relatively weak in both African and Asian rice. Our genome-wide sequencing of O. glaberrima and in-depth analyses provide rice researchers not only with useful genomic resources for future breeding but also with new insights into the genomic evolution of the African and Asian rice species. [ABSTRACT FROM AUTHOR]

Nucleotide variation in 14 unlinked nuclear genes was investigated in species-wide samples of African rice ( Oryza glaberrima) and its wild progenitor ( O. barthii). Average estimates of nucleotide diversity were extremely low in both species ( θ = 0.0007 for O. glaberrima; θ = 0.0024 for O. barthii). About 70% less diversity was found in O. glaberrima than in its progenitor O. barthii. Coalescent simulation indicated that such dramatic reduction of nucleotide diversity in African rice could be explained mainly by a severe bottleneck during its domestication. The progenitor of African rice maintained also low genetic diversity, which may be attributed to small effective population size in O. barthii. Self-pollinating would be another factor leading to the unusually low diversity in both species. Genealogical analyses showed that all O. glaberrima accessions formed a strongly supported cluster with seven O. barthii individuals that were sampled exclusively from the proposed domestication centers of African rice. Population structure and principal component analyses found that the O. glaberrima group was homogeneous with no obvious genetic subdivision, in contrast to the heterogeneous O. barthii cluster. These findings support a single domestication origin of African rice in areas of the Upper Niger and Sahelian Rivers. [ABSTRACT FROM AUTHOR]

Background: Oryza longistaminata, an AA genome type (2 n = 24), originates from Africa and is closely related to Asian cultivated rice (O. sativa L.). It contains various valuable traits with respect to tolerance to biotic and abiotic stress, QTLs with agronomically important traits and high ability to use nitrogen efficiently (NUE). However, only limited genomic or transcriptomic data of O. longistaminata are currently available. Results: In this study we present the first comprehensive characterization of the O. longistaminata root transcriptome using 454 pyrosequencing. One sequencing run using a normalized cDNA library from O. longistaminata roots adapted to low N conditions generated 337,830 reads, which assembled into 41,189 contigs and 30,178 singletons. By similarity search against protein databases, putative functions were assigned to over 34,510 uni-ESTs. Comparison with ESTs derived from cultivated rice collections revealed expressed genes across different plant species, however 16.7% of the O. longistaminata ESTs had not been detected as expressed in O. sativa. Additionally, 15.7% had no significant similarity to known sequences. RT-PCR and Southern blot analyses confirmed the expression of selected novel transcripts in O. longistaminata. Conclusion: Our results show that one run using a Genome Sequencer FLX from 454 Life Science/Roche generates sufficient genomic information for adequate de novo assembly of a large number of transcripts in a wild rice species, O. longistaminata. The generated sequence data are publicly available and will facilitate gene discovery in O. longistaminata and rice functional genomic studies. The large number of abundant of novel ESTs suggests different metabolic activity in O. longistaminata roots in comparison to O. sativa roots. [ABSTRACT FROM AUTHOR]

Background and Aims Oryza glaberrima: is widely grown in flood-prone areas of African river basins and is subject to prolonged periods of annual submergence. The effects of submergence on shoot elongation, shoot biomass, leaf area and CO2 uptake were studied and compared with those of O. sativa. [ABSTRACT FROM PUBLISHER]

Weeds cause considerable yield losses in irrigated rice in West Africa, particularly where sub-optimal crop management or limited resources hamper production. Because of the recent focus of regional breeding programs in West Africa on a wide diversity of interspecific (O. sativa indica×O. glaberrima) and intraspecific (O. sativa×O. sativa) crosses for lowland systems, new genotypes with promising yield potential and putatively improved weed competitiveness are now available. Our study intended to establish a screening methodology for weed competitiveness in irrigated lowlands, to evaluate weed competitive abilities of diverse rice genotypes, and to relate several morphological plant characteristics with competitive abilities. A selection of 25 cultivars and advanced breeding lines was grown under irrigated conditions during the 2000 wet season (WS) and the 2001 dry season (DS) at Ndiaye (Senegal), and their reaction to four different competition levels was assessed. Competition was greatest where the test lines were grown with a mixture of an improved O. sativa indica cultivar and natural weed growth. Average yield losses across rice lines were 36% in the WS and 31% in the DS, but differences between lines were highly significant in both seasons and yield losses ranged from 0 to 84%. Competitive abilities were not related to yields without competition. In the DS, several of the new lines combined high yield with good competitiveness and outperformed the currently widely used check variety. Height, tiller density, specific leaf area (SLA), leaf area index (LAI), and growth duration were mostly negatively related to yield loss. Plant characteristics measured in monoculture had no explanatory value for the competitive ability of tested lines, indicating that screening under conditions of competition with weeds is preferable. Competitive abilities of several lines were stable across sites, years, and seasons; in others, they were strongly influenced by season. The simplified experimental layout can be used to screen advanced breeding lines or established cultivars with moderate resources (e.g., space, seed, labour). Including such a screening in the breeding process would enable more weed competitive cultivars to be identified and would be likely to contribute to increased resource-use efficiency, reduced yield losses, lower costs, and less reliance on herbicides in rice-based lowland systems. [Copyright &y& Elsevier]

The African rice Oryza glaberrima, traditionally cultivated since more than 3.500 years, is of poor agronomic performance but resistant/tolerant to various stresses and diseases. The introduction of these characters into O. sativa cultivars is difficult since crossing barriers cause spikelet sterility in F1. Backcrossing can restore fertility and recently facilitated the development of fertile O. glaberrima × O. sativa ssp. japonica hybrid progenies for rainfed systems. With the objective to gain access to African rice germplasm for improvement of irrigated rice, crosses were performed with eighteen O. glaberrima and twenty O. sativa ssp. indica accessions. In total about one hundred F1-hybrid grains were obtained. The F1 plants were all completely sterile and backcrossing (BC) to O. sativa was performed in order to restore spikelet fertility. Monitoring of Tog5681 × IR64 hybrid progenies under field conditions revealed a broad genetic diversity within the BC1 and BC2 populations. Some BC1 and BC2 progeny plants outperformed the O. sativa parent, indicating that the heterozygocity level and complementary gene action after two backcrosses are still sufficient to positively influence plant vigor. Spikelet fertility of progenies was highly variable, but almost complete fertility was already observed within the BC1F2 population. High spikelet fertility was preserved in one out of two analyzed BC1F3 families and in most of the BC2F3 families. The ability to restore spikelet fertility within few generations and the potential of the genetic diversity present in interspecific progenies facilitates the development of plant types specifically designed for the African irrigated and lowland environment. [ABSTRACT FROM AUTHOR]

The African species of rice (Oryza glaberrima) was cultivated long before Europeans arrived in the continent. At present, O. glaberrima is being replaced by the introduced Asian species of rice, Oryza sativa. Some West African farmers, including the Jola of southern Senegal, still grow African rice for use in ritual contexts. The two species of rice have recently been crossed, producing a promising hybrid. [ABSTRACT FROM AUTHOR]

Accessions of Oryza longistaminata and O. glaberrima, two rice species from Africa, and O. sativa were screened to identify sources of resistance to Meloidogyne graminicola. An initial population of 6000 J2/plant was inoculated to cuttings of the African rice species and 5-day-old seedlings of O. sativa. Root nematode densities were estimated 60 days after the last inoculation. O. sativa entries were all susceptible to the rice root-knot nematode. One accession of O. longistaminata represented by two individuals (WL02-2 and WL02-15) and three accessions of O. glaberrima (TOG7235, TOG5674 and TOG5675) were resistant to M. graminicola. DL01-1, an O. longistaminata accession, was susceptible to the rice root-knot nematode. Identification de sources de resistance a Meloidogyne graminicola chez Oryza longistaminata et O. glaberrima - Plusieurs accessions d'Oryza longistaminata et d'O. glaberrima, deux riz africains, et d'O. sativa ont ete criblees pour trouver des sources de resistance a Meloidogyne graminicola. Des inoculums de 6000 J2 par plante ont ete inocules sur des boutures des deux riz africains et sur des plantules de 5 jours d'O. sativa. Les populations presentes dans les racines ont ete evaluees 60 jours apres l'inoculation. Toutes les varietes testees d'O. sativa etaient sensibles. Une accession d'O. longistaminata, representee par deux individus (WLO2-2 et WLO2-15), et trois accessions d'O. glaberrima (TOG7235, TOG5674 et TOG5675) etaient resistantes. [ABSTRACT FROM AUTHOR]

Life histories and breeding systems strongly affect the genetic diversity of seed plants, but the genetic architectures that promote outcrossing in Oryza longistaminata, a perennial wild species in Africa, are not understood. We conducted a genetic analysis of the anther length of O. longistaminata accession W1508 using advanced backcross quantitative trait locus (QTL) analysis and chromosomal segment substitution lines (CSSLs) in the genetic background of O. sativa Taichung 65 (T65), with simple sequence repeat markers. QTL analysis of the BC3F1 population (n = 100) revealed that four main QTL regions on chromosomes 3, 5, and 6 were associated to anther length. We selected a minimum set of BC3F2 plants for the development of CSSLs to cover as much of the W1508 genome as possible. The additional minor QTLs were suggested in the regional QTL analysis, using 21 to 24 plants in each of the selected BC3F2 population. The main QTLs found on chromosomes 3, 5, and 6 were validated and designated qATL3, qATL5, qATL6.1, and qATL6.2, as novel QTLs identified in O. longistaminata in the mapping populations of 94, 88, 70, and 95 BC3F4 plants. qATL3, qATL5, and qATL6.1 likely contributed to anther length by cell elongation, whereas qATL6.2 likely contributed by cell multiplication. The QTLs were confirmed again in an evaluation of the W1508ILs. In several chromosome segment substitution lines without the four validated QTLs, the anthers were also longer than those of T65, suggesting that other QTLs also increase anther length in W1508. The cloning and diversity analyses of genes conferring anther length QTLs promotes utilization of the genetic resources of wild species, and the understanding of haplotype evolution on the differentiation of annuality and perenniality in the genus Oryza. [ABSTRACT FROM AUTHOR]

To enhance breeding efficiency for iron (Fe) toxicity tolerance and boost lowland rice production in sub-Saharan Africa, we have characterised the morphological, physiological and biochemical responses of contrasting rice varieties to excess iron. Here, we report the capacity of four varieties (CK801 and Suakoko8 (tolerant), Supa and IR64 (sensitive)) to oxidise iron in the rhizosphere and control iron-induced oxidative stress. The experiments were conducted in hydroponic conditions using modified Magnavaca nutrient solution and 300 ppm of ferrous iron (Fe2+) supplied in the form of FeSO4. Severe oxidative stress was observed in sensitive varieties as revealed by their high levels of lipid peroxidation. Histochemical and biochemical analyses showed that tolerant varieties exhibited a better development of the aerenchyma and greater oxygen release than the sensitive varieties in response to excess Fe. Both suberin and lignin deposits were observed in the root, stem and leaf tissues but with varying intensities depending on the variety. Under iron toxic conditions, tolerant varieties displayed increased superoxide dismutase (SOD), glutathione reductase (GR), peroxidase (POX) and ascorbate peroxidase (APX) activities in both the roots and shoots, whereas sensitive varieties showed increased APX and catalase (CAT) activities in the roots. This study had revealed also that Suakoko8 mainly uses root oxidation to exclude Fe2+ from its rhizosphere, and CK801 possesses a strong reactive oxygen species scavenging system, in addition to root oxidation ability. Key traits associated with these tolerance mechanisms such as a well-developed aerenchyma, radial oxygen loss restricted to the root cap as well as strong activation of antioxidative enzymes (SOD, GR, POX and APX) could be useful selection criteria in rice varietal improvement programs for enhanced Fe toxicity tolerance.

The article reports on a project to increase the production of rice in Africa. A partnership was formed between the Alliance for a Green Revolution in Africa, The New Partnership for Africa's Development, and the Japan International Cooperation Agency to launch the Coalition for African Rice Development. The project aims to improve the rice varieties in Africa, reduce its dependence on imported rice, and fund agricultural research. The article also discusses the increasing demand for rice along with the growth of Africa's population.

Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm.

Rice cultivation has drastically increased in Africa over the last decade. During this time, the region has also seen a rise in the incidence of rice bacterial blight caused by the pathogen Xanthomonas oryzae pv. oryzae. The disease is expanding to new rice production areas and threatens food security in the region. Yield losses caused by X. oryzae pv. oryzae range from 20 to 30% and can be as high as 50% in some areas. Employing resistant cultivars is the most economical and effective way to control this disease. To facilitate development and strategic deployment of rice cultivars with resistance to bacterial blight, biotechnology tools and approaches, including marker-assisted breeding, gene combinations for disease control, and multiplex-PCR for pathogen diagnosis, have been developed. Although these technologies are routinely used elsewhere, their application in Africa remains limited, usually due to high cost and advanced technical skills required. To combat this problem, developers of the technologies at research institutions need to work with farmers from an early stage to create and promote the integration of successful, low cost applications of research biotech products. Here, we review the current knowledge and biotechnologies available to improve bacterial blight control. We will also discuss how to facilitate their application in Africa and delivery to the field., (Copyright © 2011 Elsevier B.V. All rights reserved.)

The rate of evolution of an RNA plant virus has never been estimated using temporally spaced sequence data, by contrast to the information available on an increasing range of animal viruses. Accordingly, the evolution rate of Rice yellow mottle virus (RYMV) was calculated from sequences of the coat protein gene of isolates collected from rice over a 40-year period in different parts of Africa. The evolution rate of RYMV was estimated by pairwise distance linear regression on five phylogeographically defined groups comprising a total of 135 isolates. It was further assessed from 253 isolates collected all over Africa by Bayesian coalescent methods under strict and relaxed molecular clock models and under constant size and skyline population genetic models. Consistent estimates of the evolution rate between 4 x 10(-4) and 8 x 10(-4) nucleotides (nt)/site/year were obtained whatever method and model were applied. The synonymous evolution rate was between 8 x 10(-4) and 11 x 10(-4) nt/site/year. The overall and synonymous evolution rates of RYMV were within the range of the rates of 50 RNA animal viruses, below the average but above the distribution median. Experimentally, in host change studies, substitutions accumulated at an even higher rate. The results show that an RNA plant virus such as RYMV evolves as rapidly as most RNA animal viruses. Knowledge of the molecular clock of plant viruses provides methods for testing a wide range of biological hypotheses.