Search Results (28)

Introduction: Rice, a cornerstone of global food security, faces escalating demands for enhanced yield and disease resistance. We collected 300 high-quality genomes, representing both cultivated (Oryza sativa indica, O. sativa japonica, and O. sativa aus) and wild species (O. rufipogon, O. glaberrima, and O. barthii). Methods: Leveraging HMMER, NLR-Annotator, and OrthoFinder, we systematically identified 148,077 leucine-rich repeat (LRR) and 143,459 nucleotide-binding leucine-rich repeat (NLR) genes, with LRR receptor-like kinases (LRR-RLKs) dominating immune receptor proportions, followed by coiled-coil domain containing (CNL)-type NLRs and LRR receptor-like proteins (LRR-RLPs). Results: Benchmarking Universal Single-Copy Orthologs (BUSCO) assessments confirmed robust genome quality (average score: 94.78). Strikingly, 454 TIR-NB-LRR (TNL) genes—typically rare in monocots—were detected, challenging prior assumptions. Phylogenetic analysis with Arabidopsis TNLs highlighted five O. glaberrima genes clustering with dicot TNLs; these genes featured truncated PLN03210 motifs fused to nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 (NB-ARC) and LRR domains. Conclusions: By bridging structural genomics, evolutionary dynamics, and domestication-driven adaptation, this work provides a foundation for targeted breeding strategies and advances functional studies of plant immunity in rice. Full article

Rice is a vital staple crop for global food security, yet a worldwide comprehensive assessment of pests and diseases remains lacking. This study aims to (1) identify globally reported pests and diseases, (2) analyze their distribution patterns, and (3) assess their impact on rice productivity. A literature-based assessment with an initial pool of 15,969 articles from three online databases (PubMed, WOS, and CAB Abstract) resulted in 871 articles for analysis. The findings highlight a regional focus on Africa and Asia, where rice is predominantly produced. Pest occurrence varies across continents, with Diopsis, Maliarpha, and Chilo being prevalent in Africa, while Nilaparvata, Scirpophaga, Sogatella, and Chilo dominate in Asia. Key pathogens differ across regions, with Pyricularia, Xanthomonas, and Sobemovirus in Africa, while Fusarium and Bipolaris are common in Asia. Major yield losses are attributed to Pyricularia (Blast disease), Bipolaris (Brown Spot), Fusarium (Bakanae), and Sobemovirus (Rice Yellow Mottle Virus). The lack of data from major rice producers like Myanmar highlights reporting gaps, urging future research. This study enhances the global understanding of rice pest and disease distribution and their impacts on productivity. It could also support early warning systems and assess the effectiveness of control methods in the context of climate change. Full article

Mangrove swamp rice (MSR) production is critical for the diet of small farmers of coastal Guinea-Bissau. In mangrove swamp agroecosystems, rice is grown during the rainy season when freshwater and nutrients are abundant. However, small-scale farmers face challenges like unpredictable rainfall and rising sea levels, which increase soil salinity and acidity. This study aims to assess soil physical–chemical properties, paired with farmers’ local practices, to evaluate fertility constraints, and to support sustainable soil–plant management practices. This co-designed research contributes to filling a gap concerning the adoption of sustainable agricultural practices adapted to specific contexts in West Africa. In two regions, Oio (center) and Tombali (south), rice yields were measured in semi-controlled trials both in two agroecological settings: Tidal Mangrove (TM) and Associated Mangrove (AM) fields. 380 soil samples were collected, and rice growing parameters were assessed during the 2021 and 2022 rice sowing, transplanting, and flowering periods. Principal Component Analyses (PCA) and Multivariate Regression Analysis (MRA) were applied to understand trends and build fertility proxies in predicting yields. Significant spatial and temporal variability in the soil properties between agroecologies was found. Salinity constraints in Oio TMs limit production to an average of 110 g/m², compared to 250 g/m² in Tombali. Yield predictions account for 81% and 56.9% of the variance in TMs and AMs, respectively. Variables such as organic matter (OM), nitrogen (N), potassium (K), and precipitation positively influence yields, whereas sand content, pH, and iron oxides show a negative effect. This study advances the understanding of MSR production in Guinea-Bissau and underscores the importance of incorporating farmers’ knowledge of their diverse and complex production systems to effectively address these challenges. Full article

Rice is a staple crop in sub-Saharan Africa, and it is mostly produced by Asian cultivars of Oryza sativa that were introduced to the continent around the fifteenth or sixteenth century. O. glaberrima, the native African rice, has also been planted due to its valuable traits of insect and drought tolerance. Due to competition and resistance evolution, weedy rice has evolved from O. sativa and O. glaberrima, posing an increasing threat to rice production. This paper provides an overview of current knowledge on the introduction and domestication history of cultivated rice in Africa, as well as the genetic properties of African weedy rice that invades paddy fields. Recent developments in genome sequencing have made it possible to uncover findings about O. glaberrima’s population structure, stress resilience genes, and domestication bottleneck. Future rice genomic research in Africa should prioritize producing more high-quality reference genomes, quantifying the impact of crop–wild hybridization, elucidating weed adaptation mechanisms through resequencing, and establishing a connection between genomic variation and stress tolerance phenotypes to accelerate breeding efforts. Full article

Rice cultivation is one of the most important agro-economic activities in many countries, and the correct seed storage between production cycles is essential for crop success. In Guinea-Bissau, mangrove swamp rice (MSR) is a highly productive rice cropping system, thus providing surplus for sale. Depending on storage conditions, rice grains may present moisture, insects, or the development of fungi that might affect crop productivity. Considering different rice varieties and storage conditions, samples were collected from 30 farmers within 13 villages across the main MSR-producing regions. Stored rice was used to isolate and identify seed-borne fungi through DNA barcoding, to test aflatoxin content, and to evaluate seed germination rates. Polyethylene bags (the container), raised wooden platforms, and storage rooms (the structures) are the most used facilities. Hermetic containers were recorded mainly in Oio. A total fungal richness of 18 genera was found, and 16 different species were identified. The most represented fungal genera are Aspergillus, Curvularia, and Bipolaris. Despite the presence of aflatoxin-producing fungal samples, they did not present concerning levels for human consumption, and the germination rate was not affected regardless of storage structures. These results provide a baseline on fungi occurrence in stored MSR seeds from traditional facilities in Guinea-Bissau. Full article

Seed shattering is an adaptive feature of seed dispersal in wild rice, and it is also an important agronomic trait affecting yield. Reduced seed shattering was a significant progress during rice domestication. However, the evolutionary pathway and molecular mechanism of hybrid seed shattering remain largely unknown. In order to gain a deeper understanding of the regulation of hybrid seed shattering, HS4, a locus conferring hybrid seed shattering between Oryza sativa and Oryza glaberrima, was identified and fine mapped to a 13.5-kb genomic region containing two putative genes during the development of chromosomal segment substitution lines (CSSLs). Expression analysis indicated that the hybrid seed shattering was not related to the expression of HS4. Preliminary research on the molecular mechanism of HS4-mediated hybrid seed shattering indicated that HS4^HJX74 and HS4^HP61 may form a multimer in heterozygotes, achieving the original function of a trihelix transcription factor through protein interaction. The identification and characterization of HS4 in this study not only provides new insights into the molecular mechanisms underlying hybrid seed shattering, but also provides a potential target for genome editing to reduce the difficulty of hybridization between the two species, facilitating hybrid breeding and increasing yield in rice. Full article

The WD40 superfamily is widely found in eukaryotes and has essential subunits that serve as scaffolds for protein complexes. WD40 proteins play important regulatory roles in plant development and physiological processes, such as transcription regulation and signal transduction; it is also involved in anthocyanin biosynthesis. In rice, only OsTTG1 was found to be associated with anthocyanin biosynthesis, and evolutionary analysis of the WD40 gene family in multiple species is less studied. Here, a genome-wide analysis of the subfamily belonging to WD40-TTG1 was performed in nine AA genome species: Oryza sativa ssp. japonica, Oryza sativa ssp. indica, Oryza rufipogon, Oryza glaberrima, Oryza meridionalis, Oryza barthii, Oryza glumaepatula, Oryza nivara, and Oryza longistaminata. In this study, 383 WD40 genes in the Oryza genus were identified, and they were classified into four groups by phylogenetic analysis, with most members in group C and group D. They were found to be unevenly distributed across 12 chromosomes. A total of 39 collinear gene pairs were identified in the Oryza genus, and all were segmental duplications. WD40s had similar expansion patterns in the Oryza genus. Ka/Ks analyses indicated that they had undergone mainly purifying selection during evolution. Furthermore, WD40s in the Oryza genus have similar evolutionary patterns, so Oryza sativa ssp. indica was used as a model species for further analysis. The cis-acting elements analysis showed that many genes were related to jasmonic acid and light response. Among them, OsiWD40-26/37/42 contained elements of flavonoid synthesis, and OsiWD40-15 had MYB binding sites, indicating that they might be related to anthocyanin synthesis. The expression profile analysis at different stages revealed that most OsiWD40s were expressed in leaves, roots, and panicles. The expression of OsiWD40s was further analyzed by qRT-PCR in 9311 (indica) under various hormone treatments and abiotic stresses. OsiWD40-24 was found to be responsive to both phytohormones and abiotic stresses, suggesting that it might play an important role in plant stress resistance. And many OsiWD40s might be more involved in cold stress tolerance. These findings contribute to a better understanding of the evolution of the WD40 subfamily. The analyzed candidate genes can be used for the exploration of practical applications in rice, such as cultivar culture for colored rice, stress tolerance varieties, and morphological marker development. Full article

The CYP76 subfamily, a member of the CYP superfamily, plays crucial roles in the biosynthesis of phytohormones in plants, involving biosynthesis of secondary metabolites, hormone signaling, and response to environmental stresses. Here, we conducted a genome-wide analysis of the CYP76 subfamily in seven AA genome species: Oryza sativa ssp. japonica, Oryza sativa ssp. indica, Oryza rufipogon, Oryza glaberrima, Oryza meridionalis, Oryza barthii, and Oryza glumaepatula. These were identified and classified into three groups, and it was found that Group 1 contained the largest number of members. Analysis of cis-acting elements revealed a large number of elements related to jasmonic acid and light response. The gene duplication analysis revealed that the CYP76 subfamily expanded mainly in SD/WGD and tandem forms and underwent strong purifying selection during evolution. Expression pattern analysis of OsCYP76s in various developmental stages revealed that the majority of OsCYP76s exhibit relatively restricted expression patterns in leaves and roots. We further analyzed the expression of CYP76s in O. sativa, japonica, and O. sativa, indica under cold, flooding, drought, and salt abiotic stresses by qRT-PCR. We found that OsCYP76-11 showed a huge increase in relative expression after drought and salt stresses. After flooding stress, OsiCYP76-4 showed a greater increase in expression compared to other genes. CYP76 in japonica and indica showed different response patterns to the same abiotic stresses, revealing functional divergence in the gene family during evolution; these may be the key genes responsible for the differences in tolerance to indica japonica. Our results provide valuable insights into the functional diversity and evolutionary history of the CYP76 subfamily and pave the way for the development of new strategies for improving stress tolerance and agronomic traits in rice. Full article

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. Full article

Water-limiting conditions can severely affect rice yield. Therefore, increasing plant tolerance to water stress is a priority for many rice breeding programs. However, improving rice tolerance to this abiotic stress comes with several complications related to the seeding practices, the adopted water management system and the growth stage where water stress occurs. For this reason, it is challenging to outline single ideotypes showing traits suitable for overcoming drought at different times during the life cycle of rice in diverse cropping ecosystems. The current knowledge of genomics and biochemicals can contribute to drawing rice ideotypes flexible towards diverse water availability conditions. Traits identified in accessions of the wild ancestor of cultivated rice, as well as other wild rice species, in Oryza glaberrima and weedy rice were demonstrated to confer enhanced tolerance to water stress, while screenings of cultivated rice germplasms identified several genes/loci improving water stress resistance. New frontiers are represented by the dissection of the epigenetic control of stress tolerance and the implementation of the contribution of favorable microbiota. Innovative breeding technologies, whose feasibility is related to advancements in genomic analyses, are contributing to enhancing the knowledge-based development of water stress-tolerant rice varieties. Full article

Rice landraces, including Asian rice (Oryza sativa L.) and African rice (Oryza glaberrima Steud.), provide important genetic resources for rice breeding to address challenges related to food security. Due to climate change and farm destruction, rice landraces require urgent conservation action. Recognition of the geographical distributions of rice landraces will promote further collecting efforts. Here we modelled the potential distributions of eight rice landrace subgroups using 8351 occurrence records combined with environmental predictors with Maximum Entropy (MaxEnt) algorithm. The results showed they were predicted in eight sub-regions, including the Indus, Ganges, Meghna, Mekong, Yangtze, Pearl, Niger, and Senegal river basins. We then further revealed the changes in suitable areas of rice landraces under future climate change. Suitable areas showed an upward trend in most of study areas, while sub-regions of North and Central China and West Coast of West Africa displayed an unsuitable trend indicating rice landraces are more likely to disappear from fields in these areas. The above changes were mainly determined by changing global temperature and precipitation. Those increasingly unsuitable areas should receive high priority in further collections. Overall, these results provide valuable references for further collecting efforts of rice landraces, while shedding light on global biodiversity conservation. Full article

The cAMP-dependent protein kinase A, cGMP-dependent protein kinase G and phospholipid-dependent protein kinase C (AGC) perform various functions in plants, involving growth, immunity, apoptosis and stress response. AGC gene family is well described in Arabidopsis, however, limited information is provided about AGC genes in rice, an important cereal crop. This research studied the AGC gene family in the AA genome species: Oryza sativa ssp. japonica, Oryza sativa ssp. indica, Oryza nivara, Oryza rufipogon, Oryza glaberrima, Oryza meridionalis, Oryza barthii, Oryza glumaepatula and Oryza longistaminata were searched and classified into six subfamilies, and it was found that these species have similar numbers of members. The analysis of gene duplication and selection pressure indicated that the AGC gene family expanded mainly by segmental or whole genome duplication (WGD), with purifying selection during the long evolutionary period. RNA-seq analysis revealed that OsAGCs of subfamily V were specifically highly expressed in leaves, and the expression patterns of these genes were compared with that of photosynthesis-related genes using qRT-PCR, discovered that OsAGC9, OsAGC20, and OsAGC22 might participate in photosynthesis. These results provide an informative perspective for exploring the evolutionary of AGC gene family and its practical application in rice. Full article

Single nucleotide polymorphisms (SNPs) that are located in the promoter regions of genes and affect the binding of transcription factors (TFs) are called regulatory SNPs (rSNPs). Their identification can be highly valuable for the interpretation of genome-wide association studies (GWAS), since rSNPs can reveal the biologically causative variant and decipher the regulatory mechanisms behind a phenotype. In our previous work, we presented agReg-SNPdb, a database of regulatory SNPs for agriculturally important animal species. To complement this previous work, in this study we present the extension agReg-SNPdb-Plants storing rSNPs and their predicted effects on TF-binding for 13 agriculturally important plant species and subspecies (Brassica napus, Helianthus annuus, Hordeum vulgare, Oryza glaberrima, Oryza glumipatula, Oryza sativa Indica, Oryza sativa Japonica, Solanum lycopersicum, Sorghum bicolor, Triticum aestivum, Triticum turgidum, Vitis vinifera, and Zea mays). agReg-SNPdb-Plants can be queried via a web interface that allows users to search for SNP IDs, chromosomal regions, or genes. For a comprehensive interpretation of GWAS results or larger SNP-sets, it is possible to download the whole list of SNPs and their impact on transcription factor binding sites (TFBSs) from the website chromosome-wise. Full article

Crop Wild Relatives (CWRs) form a comprehensive gene pool that can answer the queries related to plant domestication, speciation, and ecological adaptation. The genus ‘Oryza’ comprises about 27 species, of which two are cultivated, while the remaining are wild. Here, we have attempted to understand the conservation and diversification of the genes encoding Cystathionine β-synthase (CBS) domain-containing proteins (CDCPs) in domesticated and CWRs of rice. Few members of CDCPs were previously identified to be stress-responsive and associated with multiple stress tolerance in rice. Through genome-wide analysis of eleven rice genomes, we identified a total of 36 genes encoding CDCPs in O. longistaminata, 38 in O. glaberrima, 39 each in O. rufipogon, O. glumaepatula, O. brachyantha, O. punctata, and O. sativa subsp. japonica, 40 each in O. barthii and O. meridionalis, 41 in O. nivara, and 42 in O. sativa subsp. indica. Gene duplication analysis as well as non-synonymous and synonymous substitutions in the duplicated gene pairs indicated that this family is shaped majorly by the negative or purifying selection pressure through the long-term evolution process. We identified the presence of two additional hetero-domains, namely TerCH and CoatomerE (specifically in O. sativa subsp. indica), which were not reported previously in plant CDCPs. The in silico expression analysis revealed some of the members to be responsive to various abiotic stresses. Furthermore, the qRT-PCR based analysis identified some members to be highly inducive specifically in salt-tolerant genotype in response to salinity. The cis-regulatory element analysis predicted the presence of numerous stress as well as a few phytohormone-responsive elements in their promoter region. The data presented in this study would be helpful in the characterization of these CDCPs from rice, particularly in relation to abiotic stress tolerance. Full article

Various kinds of reproductive barriers have been reported in intraspecific and interspecific crosses between the AA genome Oryza species, to which Asian rice (O. sativa) and African rice (O. glaberrima) belong. A hybrid seed sterility phenomenon was found in the progeny of the cross between O. sativa and O. meridionalis, which is found in Northern Australia and Indonesia and has diverged from the other AA genome species. This phenomenon could be explained by an egg-killer model. Linkage analysis using DNA markers showed that the causal gene was located on the distal end of chromosome 1. Because no known egg-killer gene was located in that chromosomal region, this gene was named HYBRID SPIKELET STERILITY 57 (abbreviated form, S57). In heterozygotes, the eggs carrying the sativa allele are killed, causing semi-sterility. This killer system works incompletely: some eggs carrying the sativa allele survive and can be fertilized. The distribution of alleles in wild populations of O. meridionalis was discussed from the perspective of genetic differentiation of populations. Full article