Rice blast, caused by the ascomycete fungus Magnaporthe oryzae, is one of the most problematic diseases for rice production, threatening global food security. Genetic resistance to some M. oryzae races can be achieved using major resistance genes that recognize their corresponding fungal avirulence genes. Weedy rice, a close relative of cultivated rice that competes with the crop, has evolved unique genetic mechanisms to resist M. oryzae infections; thus, weedy rice can serve as an excellent resource for blast control. In this study, we assessed disease scores of 183 F5 and F6 recombinant inbred lines (RILs) derived from a weedy rice × crop biparental mapping population and their parental lines, a Black Hull Awn weedy rice strain (PI 653413, RR14) and the aus-196 rice variety, using four distinct common U.S. blast races (IB33, IG1, IE1K, and IC17) under greenhouse conditions. All the parental lines were resistant to all blast races; however, RILs showed a wide degree of variation in resistance. Genotyping-by-sequencing of the RIL population and parents generated 1,498 single-nucleotide polymorphisms, which were used to construct a linkage map, and quantitative trait locus (QTL) mapping of blast resistance was performed using r/qtl. A single major blast resistance QTL on chromosome 12 was mapped to the Pi-ta/Pi39(t)/Ptr locus. Identification of Pi-ta/Pi-39(t)/Ptr as the key contributor to blast resistance in weedy rice provides insight into the evolution and adaptation of weedy rice and can aid in the development of blast-resistant rice varieties through marker-assisted selection.

Lack of seed dormancy (SD) often causes pre-harvest sprouting (PHS) or inadequate germination in cereal crops and seed production. This research aimed to integrate a dormancy (D) allele isolated from weedy rice at qSD12 into the genetic background of a restoration-of-fertility line (RFL) to mitigate the PHS and germination problems. A hybrid F2 population was developed to map quantitative trait loci (QTLs) and model their epistatic and genotype-by-environment interactions. Twelve QTLs for flowering time (FT, 3), plant height (5) or SD (4) were identified. Of the 4 SD loci, qSD12 explained most of the phenotypic variance (R2 = 0.34), and 2 (qSD3 & qSD6) have the D alleles from the RFL. qSD12 interacted with qSD3 or qSD7-2, with the presence of the D allele at qSD12 increasing the effects of the others, as well as the duration of seed storage at 24 or 40 ˚C for dormancy release. The F2 plant-derived F4 to F6 lines were marker-assisted selected. The major effect of qSD12 on seed germination and on-panicle sprouting was confirmed with the F4 and F5 lines, respectively. A sample of F2 plant-derived backcross (BC1F1) plants, which are heterozygous for 2–4 of the SD QTLs, was evaluated for agronomic traits and genotyped with an array of SNP markers. Recurrent backcrossing with the RFL and genomic selection are used to pyramid the D alleles from qSD12 and other locus/loci to develop new varieties and RF lines with improved resistance to PHS.Supplementary InformationThe online version contains supplementary material available at 10.1007/s11032-025-01623-8.

Weedy rice (Oryza sativa L.) presents a formidable challenge in global paddy cultivation due to its morphological similarity to cultivated rice, making its eradication difficult. To address this, an integrated weed management system (IWMS) was developed and collected across various regions in Kaohsiung, Taiwan, from 2018 to 2020. This study evaluated the efficacy of the IWMS in controlling the spread of weedy rice through systematic applications in three distinct agricultural zones: Meinong Contractual (MC), Meinong Public Stock (MP), and Shanlin Public Stock (SP). The data reveal a consistent decline in weedy rice invasion with sustained implementation of the IWMS, alongside improvements in seed purity and corresponding grain quality. These enhancements not only mitigate the adverse effects on seed purity but also elevate grain quality, thereby curtailing yield losses and bolstering economic returns. Further analysis indicates that the patterns of weedy rice invasion correlate strongly with geographical and agronomic variables, such as the source of seedlings, land preparation techniques, field management, and the sharing of agricultural implements. Consequently, raising farmer awareness and providing specialized training on management strategies are crucial for effective prevention of weedy rice.

Whole genome resequencing dataset of weedy rice variants

Although the yield and resistance of cultivated rice have been significantly enhanced since domestication, its genetic basis remains narrow, with many beneficial genes having been lost. Weedy rice is an important source of genetic material for improving rice and provides valuable germplasm resources for identifying excellent genes. In our study, we constructed an F2 genetic population by crossing the weedy rice variety LM8, which has extremely small grains, with cultivated rice. High-density genetic maps were constructed using whole-genome sequencing. Five grain shape traits were observed in the F2 population, including grain length, grain width, grain thickness, length width ratio and thousand grain weight. The phenotype data were found to be consistent with a normal distribution. Through linkage analysis of the phenotype and genetic maps, a total of 14 QTL loci were identified, one of which was associated with grain length. Grain length values ranged from 5.32 to 11.14 mm. The associated locus was located at 18.81–18.87 Mb on chromosome 3, and accounted for 19.88% of the total phenotypic variation. The BC1F2 population was constructed using Bulked Segregant Analysis (BSA) sequencing to locate the grain length gene. The ORUFILM03g000096 gene, which is homologous to the Os03g0427300 gene of Nipponbare, was identified as the grain length gene. According to the annotation of the known genes, the ORUFILM03g000096 gene belongs to the Glutelin (GLU) gene family, which is generally associated with rice quality. A systematic investigation of the expression profile of ORUFILM03g000096 gene using the Rice Expression Profile (RiceXPro) database showed high expression in young panicles. Evolutionary tree analysis revealed a closer evolutionary relationship with the Japanese gene sequence. Hplotype analysis of the gene in the hybrid offspring indicated that a non-synonymous mutation (G-A), located 861 bp downstream of the ATG site in the third exon of the candidate gene, affected the grain length. It is hypothesized that this gene plays a crucial role in grain length growth and enhances rice quality.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12284-025-00858-5.

The interaction between yield and yield components in cultivated rice and weedy rice in the Nile Delta of Egypt

ABSTRACTWeedy rice, a wild relative of cultivated rice, is highly stress‐resistant and proliferates in paddy fields. In this study, 353 weedy rice accessions were analyzed to identify salt‐tolerance genes using population evolution analysis, phenotypic screening, genome‐wide association studies (GWAS), transcriptome analysis, haplotype characterization, gene knockout experiments, and Na+ and K+ ion flux assays. Population structure analysis classified the accessions into six distinct groups. Three salt‐tolerant accessions—HW131, HW136, and HW119—were identified based on leaf rolling degree (LRD), leaf withering degree (LWD), chlorophyll content (ChlC), and nitrogen content (NC) traits. GWAS and transcriptome data pinpointed LOC_Os06g39270 and LOC_Os06g11860 as candidate salt‐tolerance genes. Haplotype analysis and qPCR confirmed two major haplotypes: AHap2 and BHap1. A 2‐bp deletion (TC) at position 818 bp in LOC_Os06g11860 was associated with severe salt sensitivity (phenotypic grade 7), whereas the wild‐type exhibited strong tolerance (grade1). Knockout mutants exhibited significantly increased Na+ and K+ flux across mesophyll cell membranes compared to wild‐type plants, validating LOC_Os06g11860 (OsERFH1) as a crucial salt‐tolerance gene. This study provides novel genetic insights into salt‐stress adaptation in weedy rice, paving the way for breeding enhanced salt‐tolerant varieties.

Weeds pose a significant challenge to agricultural productivity, requiring control strategies that are both effective and environmentally sustainable. Therefore, this study evaluated the inhibitory potential of aqueous extracts from Ricinus communis L. leaves to manage the weeds Oryza sativa L. (weedy rice) and Cyperus ferax. Extracts were obtained through pressurized liquid extraction using water as the solvent. Bioassays were conducted during pre- and post-emergence stages by foliar spraying 15 and 30 days after sowing (DAS). The effect of extraction time (1–30 min) on inhibitory efficacy was also assessed. Chemical profiles of the extracts were characterized using high-performance liquid chromatography. The extracts significantly inhibited seed germination, with suppression rates reaching 92.7%. Plant growth was also diminished, particularly with earlier treatments (at 15 DAS), resulting in reductions of up to 32% and 53% in shoot length, and 69% and 73% in total dry mass for O. sativa L. and C. ferax, respectively. Mortality rates of O. sativa L. and C. ferax reached 64% and 58%, respectively. Phenolic compounds were identified in the extracts, and higher concentrations were observed at shorter extraction times. These findings underscore the potential of R. communis L. leaf extracts as an ecologically sustainable alternative for weed management, providing an effective and natural approach that may reduce reliance on synthetic herbicides and mitigate their environmental impact.

Comparative Analysis of Seed Morphological Traits in Egyptian Cultivated Rice and Weedy Rice

IntroductionBidirectional gene flow via pollen between transgenic rice and weedy rice could occur in natural fields. Gene flow from transgenic rice to weedy rice has been confirmed in many studies, and thus results showed that F1 hybrids could persist in natural agroecosystems due to their unimpaired reproductive ability. However, the reverse gene flow from weedy rice to transgenic rice is rarely reported.MethodWe quantified reverse gene flow from three weedy rice accessions to transgenic rice line T1c-19 with cry1C*/bar. In field trials with alternating layout of cultivating transgenic rice and weedy rice accessions and adjacent layout cultivating them in a close vicinity, the reverse gene flow was detected. And the fitness of reverse F1 (RF1) hybrids obtained by manual pollination using T1c-19 as maternal plants and weedy rice as paternal plants was evaluated in field.ResultNo gene flow from WRTZ was observed, while gene flows from WRMM were observed at 0.0508% and 0.0808%, respectively, and those from WRYY were 0.0692% and 0.1008%, respectively. RF1 plants exhibited significantly higher composite fitness compared to their weedy rice counterparts, due to enhanced fecundity-related traits observed under both insect pressure and no-insect pressure conditions. However, the impact of reverse gene flow may be limited because RF1 hybrid seeds presented lower seed shattering, and therefore most of it would be harvested by combine harvester.DiscussionOur study revealed that gene flow from three weedy rice accessions to T1c-19 could produce RF1 hybrids with greater composite fitness. Any loss of seeds into agroecosystem may result in a greater risk of RF1 hybrids due to their morphological similarity and high fitness.

Seeds are coated with pigments presumably to promote plant adaptation. To understand the adaptive mechanisms of seed pigment traits, allelic variants of the red (Rc/rc) and purple (Pb/pb) pericarp color genes were assembled into the same genetic background to identify the trait development patterns and pleiotropies of the loci on seed flavonoids, dormancy, and germination in rice (Oryza sativa). Nonallelic recombination and epistasis of the loci dictated 4 patterns of the trait development from 5 to 40 d post-anthesis. The Rc- and Pb-controlled pigments were synthesized in the same lower epidermal cells but compartmented in the cells and lignified wall area, respectively, after 10 d. Four flavan-3-ols (catechin, epicatechin, and their dimeric procyanidins) and anthocyanins (AC) were detected in the Pb and Rc systems, respectively, with catechin being most abundant. Both genes affected seed primary dormancy, and imbibition and germination velocities of the dormancy-released seeds. Additive effects of the loci contributed most to the variances for all the pleiotropic traits, the development time and its interaction with the additive components influenced the flavonoid contents, and the additive-by-additive epistasis modified the AC content and dormancy level. Thus, seed pigment traits influence plant adaptation likely through a series of pleiotropies, including the coat structure, enhanced dormancy, and reduced germination speed. The differences between the Rc and Pb loci in the flavonoid type/content and the size of pleiotropic effects could partly explain the predominance of red pericarp-colored genotypes in wild and weedy rice and in pigmented specialty cultivars.

Weedy rice (Oryza sativa f. spontanea) poses considerable challenges to rice production. Benzobicyclon, a 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor, has demonstrated potential for controlling weedy rice. However, weedy rice populations exhibit different sensitivities to benzobicyclon and other HPPD inhibitors. Additionally, the genetic and molecular basis of HPPD herbicide sensitivity remains underexplored. Here, we divided weedy rice populations into indica weedy rice (QPAG) and japonica weedy rice (FXYX) and examined the mechanisms behind their varying sensitivity to HPPD inhibitors. Whole-plant dose-response assays showed that the FXYX and QPAG populations had up to >20 times tolerance to benzobicyclon compared to the relatively sensitive population PDRY. Both populations also showed decreased sensitivity to topramezone and pyraquinate. Sequence comparison demonstrated no amino acid mutations in HPPD in any population. The relative expression levels of HPPD did not differ substantially between the populations. Thus, no target site-based mechanisms were present in the weedy rice populations. HPPD INHIBITOR SENSITIVE 1 (HIS 1) was responsible for the reduced sensitivity to benzobicyclon in the FXYX population. Furthermore, P450- and GST-based metabolic mechanisms contributed to lower sensitivity to benzobicyclon to varying degrees in both FXYX and QPAG populations. The mechanisms of varying sensitivities to benzobicyclon were different and complex in the japonica and indica weedy rice populations. Increased herbicide metabolism by HIS 1, P450, and GST was the primary mechanism, but varied among the different weedy rice types. Our results provide new insights into the chemical control of different weedy rice types using HPPD inhibitors. © 2025 Society of Chemical Industry.

The weedy rice contamination in certified rice seed samples greatly impacts the Malaysian rice seed industry. The existing manual process to identify the weedy rice seed is only based on the physical appearance of the seed. The physical characteristics such as morphology, colour and texture image of the seeds were captured and analysed using image processing and the application of machine vision to understand the physical characteristics of the weedy rice seed. The objective of this study is to understand the physical characteristics of the weedy rice seed using Principal Component Analysis (PCA) transformation. A total of 7350 images of cultivated rice seeds from five major varieties and 895 images of weedy rice seeds were acquired using machine vision setup, and 67 features from the three major parameters (morphology, colour, and texture) were extracted. The test of equality of means based on Wilks' Lambda was performed to assess significant differences among the group parameters. PCA transformed data into principal components. The relationships between weedy rice seed and cultivated rice seed samples were examined through the score and loading plots of the PCA analysis. This newly transformed data visualises the experimental data's underlying structure and helps identify the parameters distinguishing between weedy rice and cultivated rice seed. The results on the PCA score plot have shown overlapping areas between the cultivated and weedy rice seeds, indicating high similarities between the seed samples.

Increasing global temperatures threaten rice production, a vital staple for over half the world’s population, particularly due to the vulnerability of seedlings to heat stress, which can reduce rice growth and yield. Weedy rice (Oryza spp.), an invasive weed in paddy fields, has demonstrated a degree of heat resistance. To better understand the mechanisms behind this tolerance, we analyzed genome-wide gene expression and adaptive strategies during the seedling stage under heat stress. Four weedy rice genotypes and two controls (MR219 and MU201) were subjected to heat treatment at 44 °C for 0, 2 and 4 h, followed by RNA isolation and RNA-Seq analysis. Results showed a decrease in the stress tolerance gene expression in heat-susceptible (HS) genotypes, particularly those associated with the oxidative phosphorylation (OXPHOS) pathway. Conversely, heat tolerant (HT) samples exhibited upregulated genes related to the endoplasmic reticulum pathways. Physiological assessments indicated high sensitivity to heat stress within the first four hours, with HS samples displaying significant cellular damage and increased ion leakage. In contrast, HT samples demonstrated better physiological characteristics and identified genes involved in damage repair. They also show stronger gene network connectivity, highlighting their critical coordination role in stress resilience. These findings reveal diverse mechanisms of heat stress response in weedy rice, providing insights for selecting weedy rice genotypes and targeting heat tolerance genes in rice breeding.

Quizalofop-p-ethyl is used in ProvisiaTM rice for selecive grass weed control. In southern Brazil, other weeds occur, and an herbicide tank mix is needed to achieve a broad spectrum. This study aimed to evaluate the interaction of quizalofop-p-ethyl with other herbicides used to control the main paddy rice weeds occurring in Southern Brazil. Two greenhouse experiments were performed using Aeschynomene denticulata Rudd (jointvetches), Cyperus iria L. (rice flatsedge), Echinochloa crus-galli L. (barnyard grass), and Oryza spp. (weedy rice). The factorial arrangement to each species comprises: Factor A) Doses of quizalo-fop-p-ethyl (g ha-1): 0, 120, and 120 plus 120 (applied 14 days after the initial treatment - DAIT); Factor B) Tank mix partner: bentazon (960 g ha-1), florpyrauxifen-benzyl (30 g ha-1), quinclorac (375 g ha-1), saflufenacil (30 g ha-1), and control. At 42 DAIT, control and shoot dry weight (SDW) were evaluated. Colby’s method compared treatments using Tukey’s HSD and tank mix. No herbicide tank mix reduced or increased the variables evaluated compared to the herbicides applied alone, suggesting a neutral effect. Between the mixtures, in terms of spectrum of weed control, quizalofop-p-ethyl plus florpyrauxifen-benzyl was the best treatment, providing effective control or SDW reduction (≥ 90%) in all tested species.

The continued emergence of weedy rice (Oryza sativa L.) in Taiwan poses serious challenges to seed purity and commercial rice cultivation, particularly under transplanting systems. These off-type individuals, often marked by a red pericarp, reduce varietal integrity and complicate seed propagation. This study evaluated the morphological variation among 117 Taiwan weedy rice (TWR) accessions and 55 control cultivars, which include 24 temperate japonica cultivars (TEJ), 24 indica cultivars, and seven U.S. weedy rice (UWR) types. Principal component analysis (PCA) showed that TWR shares vegetative traits with modern cultivars but exhibits grain morphology resembling indica landraces—indicating weak artificial selection pressure on grain traits during nursery propagation. TWR was also found to possess a suite of adaptive weedy traits, including semi-dwarfism, delayed heading, high shattering, and superior seed storability, facilitating its persistence in field conditions. These findings provide critical insights for integrated weed management and cultivar purity strategies, emphasizing the importance of certified seed use, stringent field hygiene, and disruption of weedy rice reproductive cycles.

Germination represents the first major transition in plants, and seed dormancy influences germination timing. However, the mechanism by which variations in seed dormancy due to genetic variation or the maternal environment influence germination timing has not been studied in depth. In this study, the effects of temperature during seed maturation (maternal temperature) and genetic variation on weedy rice seedling emergence in a field environment were evaluated. The experiments were repeated for 4 years using seeds collected from weedy rice groups, which represented different degrees of seed dormancy. The maternal temperature was evaluated via the yearly variation in the field temperature. Genetic variation had a greater effect on seedling emergence during unfavourable seasons than during favourable seasons. A higher maternal temperature delayed seedling emergence during favourable seasons. The notable impact of global warming on seedling emergence has been confirmed over the past 15 years, and this impact will continue even under the sustainable CO2 emission scenario. Maternal effects have long-term effects on seedling emergence at relatively high maternal temperatures, and these effects may increase under global warming.

Emergence of invasive weedy rice in Southeast Asia. A review

Weed management in rice cultivation faces increasing challenges due to herbicide resistance and environmental concerns, necessitating alternative, eco-friendly strategies. Among plant-based bioherbicides, Cosmos bipinnatus has emerged as a promising candidate due to its allelopathic potential. This study evaluated the efficacy of C. bipinnatus extracts in inhibiting key weed species, namely Echinochloa zcrus-galli, Leptochloa chinensis, Fimbristylis miliacea, and weedy rice (Oryza sativa f. spontanea). Bioassays demonstrated significant inhibition of radicle and coleoptile growth in these weeds, with stronger effects at higher concentrations. At 0.48 g mL⁻¹, inhibition reached 88% for E. crus-galli coleoptiles, 93% for its radicles, and 76% for L. chinensis coleoptiles. Notably, weedy rice, a major competitor in rice fields, was effectively suppressed, suggesting the potential of C. bipinnatus for integrated weed management. However, low extract concentrations (<0.06 g mL⁻¹) induced a hormesis effect, slightly promoting growth in some weeds and rice cultivars (OM380, OM5451, and OM18). Phytochemical analysis identified high phenolic (94.48 mg GAE g-1) and flavonoid (514.61 mg QE g-1) contents, particularly in leaves (45.93 mg GAE/g phenolic, 107.13 mg QE/g flavonoid) and flowers (63.89 mg GAE/g phenolic, 127.74 mg QE/g flavonoid), indicating their role as key inhibitory agents. These findings highlight C. bipinnatus as a viable biological solution for sustainable weed control, particularly against weedy rice. Further research is needed to optimize application strategies and minimize potential crop impacts, ensuring effective field applications while reducing reliance on synthetic herbicides in rice production systems.

Grain volume is a key agronomic trait of rice. It is coordinately determined by grain length, width, thickness, and roundness, which influences the rice yield and quality, yet the molecular mechanism is still not fully understood. In this study, a mapping population of Ludao (weedy rice) and Guangbaixiangzhan (GBXZ) was developed in Lianyungang, Jiangsu province, China, and was employed to construct a high-density genetic map by use of the RICE 1 K mGPS chip in 2021. The mapping of QTLs was carried out with IciMapping software using the inclusive composite interval mapping (ICIM) method. A total of eight QTLs for grain volume, explained 4.22-19.75% of the total phenotypic variation, were detected with LOD scores ranging from 3.33 to 13.25. Among these loci, five are known genes or loci related to grain size, and three loci, qGV4-2, qGV7-1, and qGV7-2, were newly identified. The major QTL, qGV7-2, explained the highest phenotypic variation, was validated using NIL pairs. By combining gene functional annotation, gene expression analysis and sequence comparison within the mapping interval of qGV7-2, a candidate gene (LOC_Os07g15540), encoding an ethylene receptor, OsETR4, was identified. Further haplotype-phenotype analysis revealed this gene to be significantly associated with grain length, width, and thousand-grain weight. Thus we identified LOC_Os07g15540 as the most likely candidate gene. Taken together, our findings provide a basis for functional research on qGV7-2, and broaden our understanding of role of genetic factors in regulating grain volume, thus providing an important resource for yield improvement in rice.