Search Results (35)

Invasive species pose a growing threat to global biodiversity, agricultural productivity, and ecosystem health, as climate change worsens their spread. This study focused on modelling the current and projected distribution of the Japanese beetle (Popillia japonica Newman), an invasive pest with potentially devastating impacts on crops and natural vegetation across Europe. Using the MaxEnt species distribution model, we integrated beetle occurrence data with bioclimatic variables, analyzing current and future climate scenarios based on Shared Socio-economic Pathways (SSP1-2.6, SSP2-4.5, SSP5-8.5) for near-term (2021–2040) and mid-term (2041–2060) periods. By reclassifying the model results, we identified European regions with negligible, low, medium, and high exposure to this invasive pest under climate change pathways. The results identified regions in central Europe covering an area of 83,807 km² that are currently at medium to high risk of Japanese beetle infestation. Future projections suggest northward expansion with suitable areas potentially increasing to 120,436 km² in the worst-case scenario, particularly in northern Italy, southern Germany, the Western Balkans, and parts of France. These spatially explicit findings can inform targeted monitoring, early detection, and management strategies to mitigate the economic and ecological threats posed by the Japanese beetle. Integrating species distribution modelling with climate change scenarios is imperative for science-based policies to tackle the growing challenge of biological invasions. This research provides a framework for assessing invasion risks at the European scale and guiding adaptive responses in agricultural and natural systems. Full article

Magnolia sieboldii, an important ornamental tree native to East Asia, comprises two subspecies in distinct regions, with wild populations facing suboptimal survival. This study aimed to understand the potential habitat distribution of these subspecies under future climate-change conditions to support climate-adaptive conservation. The maximum entropy (MaxEnt) model was used with occurrence and environmental data to simulate the current and future suitable habitats under various climate scenarios. Precipitation in the warmest quarter played a crucial role in shaping the potential habitats of both subspecies; however, they exhibited different sensitivities to temperature-related variables and altitude. Magnolia sieboldii subsp. sieboldii is more sensitive to temperature seasonality and annual mean temperature, whereas Magnolia sieboldii subsp. japonica is more affected by altitude, mean temperature in the driest quarter, and isothermality. Currently, the subsp. sieboldii is predicted to have larger, more contiguous suitable habitats across northeastern China, the Korean Peninsula, and Japan, whereas the subsp. japonica occupies smaller, more disjunct habitats scattered in central and western Japan and the southern Chinese mountains. These two subspecies will respond differently to future climate change. Potentially suitable habitats for subsp. sieboldii are expected to expand significantly northward over time, especially under the SSP585 scenario compared with the SSP126 scenario. In contrast, moderately and highly suitable habitats for the subsp. japonica are projected to contract southward significantly. Therefore, we recommend prioritizing the conservation of the subsp. japonica over that of the subsp. sieboldii. Strategies include in situ and ex situ protection, introduction and cultivation, regional hybridization, and international cooperation. Our study offers valuable insights for the development of targeted conservation strategies for both subspecies of M. sieboldii to counteract the effects of climate change. Full article

Drought stress poses a significant threat to rice production, necessitating the identification of genes associated with drought tolerance. This study employed a combination of genome-wide association study (GWAS) and linkage mapping to pinpoint seedling drought tolerance genes in Japonica rice. Using the leaf rolling scale (LRS) as the phenotypic index, we assessed rice drought tolerance under polyethylene glycol-induced drought during the seedling stage. A lead SNP C8_28933410 by GWAS was identified, which was located within qLRS-8-1 identified by linkage mapping on chromosome 8. Combing the LD block analyses and QTL interval, a 138.6 kb overlap interval was considered as the candidate region. Haplotype analysis, qRT-PCR, sequence analysis, and mutant phenotype verification led to the speculation that LOC_Os08g05520 is a candidate gene associated with drought tolerance. Our findings provide a valuable reference for breeders aiming to enhance rice drought tolerance. Full article

Salinity stress is one of the major abiotic stresses affecting crop growth and production. Rice is an important food crop in the world, but also a salt-sensitive crop, and the rice seedling stage is the most sensitive to salt stress, which directly affects the final yield formation. In this study, two RIL populations derived from the crosses of CD (salt-sensitive)/WD (salt-tolerant) and KY131 (salt-sensitive)/XBJZ (salt-tolerant) were used as experimental materials, and the score of salinity toxicity (SST), the relative shoot length (RSL), the relative shoot fresh weight (RSFW), and the relative shoot dry weight (RSDW) were used for evaluating the degree of tolerance under salt stress in different lines. The genetic linkage map containing 978 and 527 bin markers were constructed in two RIL populations. A total of 14 QTLs were detected on chromosomes 1, 2, 3, 4, 7, 9, 10, 11, and 12. Among them, qSST12-1, qSST12-2, and qRSL12 were co-localized in a 140-kb overlap interval on chromosome 12, which containing 16 candidate genes. Furthermore, transcriptome sequencing and qRT-PCR were analyzed in CD and WD under normal and 120 mM NaCl stress. LOC_Os12g29330, LOC_Os12g29350, LOC_Os12g29390, and LOC_Os12g29400 were significantly induced by salt stress in both CD and WD. Sequence analysis showed that LOC_Os12g29400 in the salt-sensitive parents CD and KY131 was consistent with the reference sequence (Nipponbare), whereas the salt-tolerant parents WD and XBJZ differed significantly from the reference sequence both in the promoter and exon regions. The salt-tolerant phenotype was identified by using two T₃ homozygous mutant plants of LOC_Os12g29400; the results showed that the score of salinity toxicity (SST) of the mutant plants (CR-3 and CR-5) was significantly lower than that of the wild type, and the seedling survival rate (SSR) was significantly higher than that of the wild type, which indicated that LOC_Os12g29400 could negatively regulate the salinity tolerance of rice at the seedling stage. The results lay a foundation for the analysis of the molecular mechanism of rice salinity tolerance and the cultivation of new rice varieties. Full article

Single segment substitution line (SSSL) libraries are an ideal platform for breeding by design. To develop SSSLs-Xihui18 covering the whole genome, a novel rice chromosome segment substitution line (CSSL), Z783, carrying two substitution segments (average length of 6.55 Mb) on Chr.4 and Chr.9 was identified, which was a gap in the library previously. Z783 was developed from the progeny of recipient “Xihui18” (an indica restorer line) and donor “Huhan3” (a japonica cultivar) by advanced backcross combined molecular marker-assisted selection (MAS). It displayed multiple panicles and less spikelets and wide grains. Then, a F₂ population derived from Xihui18/Z783 was used to map quantitative trait loci (QTLs) for yield-related traits by the mixed linear model method. Nine QTLs were detected (p < 0.05). Furthermore, three SSSLs were constructed by MAS, and all 9 QTLs could be validated, and 15 novel QTLs could be detected by these SSSLs by a one-way ANOVA analysis. The genetic analysis showed that qSSP4 for less spikelets and qGW9 for wide grain all displayed dominant gene action in their SSSLs. Finally, qSSP4 and qGW9 were fine-mapped to intervals of 2.75 Mb and 1.84 Mb, on Chromosomes 4 and 9, respectively. The results lay a solid foundation for their map cloning and molecular breeding by design. Full article

This study investigated novel quantitative traits loci (QTLs) associated with the control of grain shape and size as well as grain weight in rice. We employed a joint-strategy multiple GAPIT (Genome Association and Prediction Integrated Tool) models [(Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK)), Fixed and random model Circulating Probability Uniform (FarmCPU), Settlement of MLM Under Progressive Exclusive Relationship (SUPER), and General Linear Model (GLM)]–High-Density SNP Chip DNA Markers (60,461) to conduct a Genome-Wide Association Study (GWAS). GWAS was performed using genotype and grain-related phenotypes of 143 recombinant inbred lines (RILs). Data show that parental lines (Ilpum and Tung Tin Wan Hein 1, TTWH1, Oryza sativa L., ssp. japonica and indica, respectively) exhibited divergent phenotypes for all analyzed grain traits), which was reflected in their derived population. GWAS results revealed the association between seven SNP Chip makers and QTLs for grain length, co-detected by all GAPIT models on chromosomes (Chr) 1–3, 5, 7, and 11, were qGL1-1^BFSG (AX-95918134, Chr1: 3,820,526 bp) explains 65.2–72.5% of the phenotypic variance explained (PVE). In addition, qGW1-1^BFSG (AX-273945773, Chr1: 5,623,288 bp) for grain width explains 15.5–18.9% of PVE. Furthermore, BLINK or FarmCPU identified three QTLs for grain thickness independently, and explain 74.9% (qGT1^Blink, AX-279261704, Chr1: 18,023,142 bp) and 54.9% (qGT2-1^Farm, AX-154787777, Chr2: 2,118,477 bp) of the observed PVE. For the grain length-to-width ratio (LWR), the qLWR2^BFSG (AX-274833045, Chr2: 10,000,097 bp) explains nearly 15.2–32% of the observed PVE. Likewise, the major QTL for thousand-grain weight (TGW) was detected on Chr6 (qTGW6^BFSG, AX-115737727, 28,484,619 bp) and explains 32.8–54% of PVE. The qTGW6^BFSG QTL coincides with qGW6-1^Blink for grain width and explained 32.8–54% of PVE. Putative candidate genes pooled from major QTLs for each grain trait have interesting annotated functions that require functional studies to elucidate their function in the control of grain size, shape, or weight in rice. Genome selection analysis proposed makers useful for downstream marker-assisted selection based on genetic merit of RILs. 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

According to numerous chamber and free-air CO₂ enrichment (FACE) studies with artificially raised CO₂ concentration and/or temperature, it appears that increasing atmospheric CO₂ concentrations ([CO₂]) stimulates crop yield. However, there is still controversy about the extent of the yield stimulation by elevating [CO₂] and concern regarding the potential adverse effects when temperature rises concomitantly. Here, we tested the effects of natural elevated [CO₂] (ca. 120 ppm above the ambient level in 100 years ago) and warming (ca. 1.7–3.2 °C above the ambient level 100 years ago) on rice growth and yield over three crop seasons via a past reference investigation and current experiment (PRICE) study. In 2020–2022, the rice cultivar Tamanishiki (Oryza sativa, ssp. japonica) was grown in Wagner’s pots (1/2000 a) at the experiment fields of Chonnam National University (35°10′ N, 126°53′ E), Gwangju, Korea, according to the pot trial methodology of the reference experiment conducted in 1920–1922. Elevated [CO₂] and temperature over the last 100 years significantly stimulated plant height (13.4% on average), tiller number (11.5%), and shoot biomass (10.8%). In addition, elevated [CO₂] and warming resulted in a marked acceleration of flowering phenology (6.8% or 5.1 days), potentially leading to adverse effects on tiller number and grain yield. While the harvest index exhibited a dramatic reduction (12.2%), grain yield remained unchanged with elevated [CO₂] and warming over the last century. The response of these crop parameters to elevated [CO₂] and warming was highly sensitive to sunshine duration during the period from transplanting to heading. Despite the pot-based observations, considering a piecewise response pattern of C₃ crop productivity to [CO₂] of <500 ppm, our observations demonstrate realistic responses of rice crops to elevated [CO₂] (+120 ppm) and moderate warming (+1.7–3.2 °C) in the absence of adaptation measures (e.g., cultivars and agronomic management practices). Hence, our results suggest that the PRICE platform may provide a promising way to better understand and forecast the net impact of climate change on major crops that have historical and experimental archived data, like rice, wheat, and soybean. Full article

Saline–alkaline stress is one of the major damages that severely affects rice (Oryza sativa L.) growth and grain yield; however, the mechanism of the tolerance remains largely unknown in rice. Herein, we comparatively investigated the transcriptome and metabolome of two contrasting rice subspecies genotypes, Luohui 9 (abbreviation for Chao2R under study, O. sativa ssp. indica, saline–alkaline-sensitive) and RPY geng (O. sativa ssp. japonica, saline–alkaline-tolerant), to identify the main pathways and important factors related to saline–alkaline tolerance. Transcriptome analysis showed that 68 genes involved in fatty acid, amino acid (such as phenylalanine and tryptophan), phenylpropanoid biosynthesis, energy metabolism (such as Glycolysis and TCA cycle), as well as signal transduction (such as hormone and MAPK signaling) were identified to be specifically upregulated in RPY geng under saline–alkaline conditions, implying that a series of cascade changes from these genes promotes saline–alkaline stress tolerance. The transcriptome changes observed in RPY geng were in high accordance with the specifically accumulation of metabolites, consisting mainly of 14 phenolic acids, 8 alkaloids, and 19 lipids based on the combination analysis of transcriptome and metabolome. Moreover, some genes involved in signal transduction as hub genes, such as PR5, FLS2, BRI1, and NAC, may participate in the saline–alkaline stress response of RPY geng by modulating key genes involved in fatty acid, phenylpropanoid biosynthesis, amino acid metabolism, and glycolysis metabolic pathways based on the gene co-expression network analysis. The present research results not only provide important insights for understanding the mechanism underlying of rice saline–alkaline tolerance at the transcriptome and metabolome levels but also provide key candidate target genes for further enhancing rice saline–alkaline stress tolerance. Full article

The tonoplast monosaccharide transporter (TMT) family plays essential roles in sugar transport and plant growth. However, there is limited knowledge about the evolutionary dynamics of this important gene family in important Gramineae crops and putative function of rice TMT genes under external stresses. Here, the gene structural characteristics, chromosomal location, evolutionary relationship, and expression patterns of TMT genes were analyzed at a genome-wide scale. We identified six, three, six, six, four, six, and four TMT genes, respectively, in Brachypodium distachyon (Bd), Hordeum vulgare (Hv), Oryza rufipogon (Or), Oryza sativa ssp. japonica (Os), Sorghum bicolor (Sb), Setaria italica (Si), and Zea mays (Zm). All TMT proteins were divided into three clades based on the phylogenetic tree, gene structures, and protein motifs. The transcriptome data and qRT-PCR experiments suggested that each clade members had different expression patterns in various tissues and multiple reproductive tissues. In addition, the microarray datasets of rice indicated that different rice subspecies responded differently to the same intensity of salt or heat stress. The Fst value results indicated that the TMT gene family in rice was under different selection pressures in the process of rice subspecies differentiation and later selection breeding. Our findings pave the way for further insights into the evolutionary patterns of the TMT gene family in the important Gramineae crops and provide important references for characterizing the functions of rice TMT genes. 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

Mature and efficient tissue culture systems are already available for most japonica rice varieties (Oryza sativa ssp. geng). However, it remains challenging to regenerate the majority of indica rice varieties (Oryza sativa ssp. xian). In this study, quantitative trait loci (QTLs) associated with rice callus regeneration ability were identified based on the plant regeneration rate (PRR) and total green plant rate (TGPR) of the 93-11 × Nip recombinant inbred line population. Significant positive correlations were found between PRR and TGPR. A total of three QTLs (one for PRR and two for TGPR) were identified. qPRR3 (located on chromosome 3) was detected for both traits, which could explain 13.40% and 17.07% of the phenotypic variations of PRR and TGPR, respectively. Subsequently, the effect of qPRR3 on callus regeneration ability was validated by cryptographically tagged near-isogenic lines (NILs), and the QTL was narrowed to an interval of approximately 160 kb. The anatomical structure observation of the regenerated callus of the NILs revealed that qPRR3 can improve the callus regeneration ability by promoting the regeneration of shoots. Full article

Emerging evidence supports the role of rice bran in cancer prevention. Studies were conducted on multiple rice cultivars. However, limited studies were conducted on rice cultivars in the Middle East. In this study, rice bran growing in Iraq (O. sativa ssp. Japonica, cultivars: Amber Barka) was evaluated for its effect on preventing cancer and stimulating the immune system. Rice bran was collected from local mills in Al-Najaf (south of Iraq). Several solvent extracts (ethanol, methanol, n-hexane, and water) were prepared by maceration. MTT assay was used to measure the antiproliferative effects of extracts against a panel of cancer cell lines. The ability of each extract to induce apoptosis and inhibit angiogenesis was measured using standard ELISA kits. The effect of extracts on the immune system was evaluated using a lymphocyte proliferation assay, a pinocytic activity assay, a phagocytic activity assay, and a Th1/Th2 cytokine detection kit. A microbroth dilution method was used to detect the antimicrobial activity of each extract against different microbial strains. LC–MS analysis was used to detect the phytochemical composition of extracts, while DPPH assay was used to determine the antioxidant activity. For the in vivo study, rice bran was added to mouse fodder at 10% and 20%. Mice were treated for two weeks using mouse fodder supplemented with rice bran. In the third week of the experiment, EMT6/P breast cancer cells (1 × 10⁶ cells/mL) were injected subcutaneously into the abdominal area of each mouse. The dimensions of the grown tumors were measured after 14 days of tumor inoculation. A microbroth dilution method was used to evaluate the antimicrobial activity of rice bran extracts against three bacterial strains. The highest antiproliferative activity was observed in ethanol and n-hexane extracts. Ethanol and methanol extract showed the highest activity to induce apoptosis and inhibit angiogenesis. Both extracts were also effective to enhance immunity by activating lymphocytes and phagocytes proliferation with modulations of cytokine levels. The incorporation of rice bran in mice food caused a 20% regression in tumor development and growth compared with the negative control. All extracts exhibited limited antimicrobial activity against tested microorganisms. Methanol extract showed antioxidant activity with an IC₅₀ value of 114 µg/mL. LC–MS analysis revealed the presence of multiple phytochemicals in rice bran including apiin, ferulic acid, and succinic acid. Rice bran is a rich source of active phytochemicals that may inhibit cancer and stimulate the immune system. Rice bran’s biological activities could be due to the presence of multiple synergistically active phytochemicals. Further studies are needed to understand the exact mechanisms of action of rice bran. Full article

Drought is a misfortune for agriculture and human beings. The annual crop yield reduction caused by drought exceeds the sum of all pathogens. As one of the gatekeepers of China’s “granary”, rice is the most important to reveal the key drought tolerance factors in rice. Rice seedlings of Nipponbare (Oryza sativa L. ssp. Japonica) were subjected to simulated drought stress, and their root systems were analyzed for the non-targeted metabolome and strand-specific transcriptome. We found that both DEGs and metabolites were enriched in purine metabolism, and allantoin accumulated significantly in roots under drought stress. However, few studies on drought tolerance of exogenous allantoin in rice have been reported. We aimed to further determine whether allantoin can improve the drought tolerance of rice. Under the treatment of exogenous allantoin at different concentrations, the drought resistant metabolites of plants accumulated significantly, including proline and soluble sugar, and reactive oxygen species (ROS) decreased and reached a significant level in 100 μmol L⁻¹. To this end, a follow-up study was identified in 100 μmol L⁻¹ exogenous allantoin and found that exogenous allantoin improved the drought resistance of rice. At the gene level, under allantoin drought treatment, we found that genes of scavenge reactive oxygen species were significantly expressed, including peroxidase (POD), catalase (CATA), ascorbate peroxidase 8 (APX8) and respiratory burst oxidase homolog protein F (RbohF). This indicates that plants treated by allantoin have better ability to scavenge reactive oxygen species to resist drought. Alternative splicing analysis revealed a total of 427 differentially expressed alternative splicing events across 320 genes. The analysis of splicing factors showed that gene alternative splicing could be divided into many different subgroups and play a regulatory role in many aspects. Through further analysis, we restated the key genes and enzymes in the allantoin synthesis and catabolism pathway, and found that the expression of synthetase and hydrolase showed a downward trend. The pathway of uric acid to allantoin is completed by uric acid oxidase (UOX). To find out the key transcription factors that regulate the expression of this gene, we identified two highly related transcription factors OsERF059 and ONAC007 through correlation analysis. They may be the key for allantoin to enhance the drought resistance of rice. Full article

The composition and nutritional properties of rice are the product of the expression of genes in the developing seed. RNA-Seq was used to investigate the level of gene expression at different stages of seed development in domesticated rice (Oryza sativa ssp. japonica var. Nipponbare) and two Australian wild taxa from the primary gene pool of rice (Oryza meridionalis and Oryza rufipogon type taxa). Transcriptome profiling of all coding sequences in the genome revealed that genes were significantly differentially expressed at different stages of seed development in both wild and domesticated rice. Differentially expressed genes were associated with metabolism, transcriptional regulation, nucleic acid processing, and signal transduction with the highest number of being linked to protein synthesis and starch/sucrose metabolism. The level of gene expression associated with domestication traits, starch and sucrose metabolism, and seed storage proteins were highest at the early stage (5 days post anthesis (DPA)) to the middle stage (15 DPA) and declined late in seed development in both wild and domesticated rice. However, in contrast, black hull colour (Bh4) gene was significantly expressed throughout seed development. A substantial number of novel transcripts (38) corresponding to domestication genes, starch and sucrose metabolism, and seed storage proteins were identified. The patterns of gene expression revealed in this study define the timing of metabolic processes associated with seed development and may be used to explain differences in rice grain quality and nutritional value. Full article