Search Results (2,914)

Dongxiang wild rice (DXWR, Oryza rufipogon Griff.), the northernmost known wild rice species, exhibits exceptional tolerance to combined low-temperature and anaerobic stress during seed germination, providing a unique model for understanding plant adaptation to complex environmental constraints. Here, we employed an integrated multi-omics approach combining genomic, transcriptomic, and metabolomic analyses to unravel the synergistic regulatory mechanisms underlying this tolerance. Genomic comparative analysis categorized DXWR genes into three evolutionary groups: 18,480 core genes, 15,880 accessory genes, and 6822 unique genes. Transcriptomic profiling identified 10,593 differentially expressed genes (DEGs) relative to the control, with combined stress triggering the most profound changes, specifically inducing the upregulation of 5573 genes and downregulation of 5809 genes. Functional characterization revealed that core genes, including DREB transcription factors, coordinate energy metabolism and antioxidant pathways; accessory genes, such as glycoside hydrolase GH18 family members, optimize energy supply via adaptive evolution; and unique genes, including specific UDP-glycosyltransferases (UDPGTs), confer specialized stress resilience. Widely targeted metabolomics identified 889 differentially accumulated metabolites (DAMs), highlighting significant accumulations of oligosaccharides (e.g., raffinose) to support glycolytic energy production and a marked increase in flavonoids (153 compounds identified, e.g., procyanidins) enhancing antioxidant defense. Hormonal signals, including jasmonic acid and auxin, were reconfigured to balance growth and defense responses. We propose a multi-level regulatory network based on a “core-unique-adaptive” genetic framework, centered on ERF family transcriptional hubs and coordinated through a metabolic adaptation strategy of “energy optimization, redox homeostasis, and growth inhibition relief”. These findings offer innovative strategies for improving rice stress tolerance, particularly for enhancing germination of direct-seeded rice under early spring low-temperature and anaerobic conditions, by utilizing key genes such as GH18s and UDPGTs, thereby providing crucial theoretical and technological support for addressing food security challenges under climate change. Full article

Salinity is a major abiotic stress that limits plant growth and survival. Colobanthus quitensis, the only native dicotyledon in the Antarctic Peninsula and southern South America, naturally inhabits environments with contrasting salinity regimes. This study compared the salt stress responses of three geographically distinct populations—Antarctic (pA), Magellanic coastal (pPA), and Andean inland (pC)—exposed to 0, 50, and 150 mM NaCl under controlled conditions. Morpho-physiological traits, photosynthetic parameters, osmolyte accumulation, oxidative damage markers, and antioxidant responses were evaluated. Population-specific strategies were observed. In pA, salinity reduced shoot biomass by 58% and doubled lipid peroxidation levels at 50 mM, indicating high oxidative stress. In pPA, shoot growth was maintained even at 150 mM, although chlorophyll and carotenoid contents decreased by approximately 20%, along with a reduction in total antioxidant capacity. In contrast, pC showed a coordinated tolerance response, maintaining biomass while accumulating the highest proline levels (742 µmol g⁻¹ FW at 150 mM) and enhancing total antioxidant capacity by 35% compared to the control. Multivariate analyses supported the contrasting strategies among populations. These results provide novel evidence of local adaptation and ecological plasticity in C. quitensis, particularly highlighting the hidden resilience of non-coastal populations. The findings support the potential of this extremophile species as a model system for investigating salinity tolerance and as a promising genetic resource for developing biotechnological strategies aimed at improving crop resilience under saline conditions. Full article

The ability of common carp to withstand both short-term and long-term oxygen deprivation has been well documented; however, the potential genetic mechanisms behind common carp’s hypoxia response remain unclear. Therefore, to understand the possible genetic foundation of their response to hypoxia, comparative genomic analyses were conducted among six common carp varieties: Color, Songpu, European, Yellow, Mirror, and Hebao common carps. We identified 118 single-copy orthologous positively selected genes (PSGs) (dN/dS > 1) in all common carps under study, with GO functions directly related to the cellular responses to hypoxia in Color and European common carp PSGs, such as oxygen transport activity, oxygen binding activity, respiratory burst activity, and superoxide anion production. The Bayes Empirical Bayes (BEB) technique identified possible amino acid substitutions in mitochondrial and hypoxic genes under positive selection. Exonic and intronic structural variations (SVs) were discovered in the CYGB2 hypoxia-related gene of Color and European common carps, as well as in several mitochondrial genes, including MRPL20, MRPL32, NSUN3, GUF1, TMEM17B, PDE12, ACAD6, and COX10 of Color, European, Songpu, Yellow, and Hebao common carps. Moreover, Color common carp and Songpu common carp were found to share the greatest percentage of collinear genes (49.8%), with seven Songpu common carp chromosomes (chr A2, chr A9, chr A13, chr B13, chr B15, chr B2, and chr B12) showing distinct translocation events with the corresponding chromosomes of Color common carp. Additionally, we found 570 translocation sites that contained 3572 translocation-related genes in Color common carp, some of which are directly relevant to mitochondrial and hypoxic GO functions and KEGG pathways. Our results offer strong genome-wide evidence of the possible evolutionary response of Cyprinus carpio to hypoxia, providing important insights into the potential molecular mechanisms that explain their survival in hypoxic environments and guiding future research into carp hypoxia tolerance. Full article

The Auxin-Regulated Gene Involved in Organ Size (ARGOS) proteins have crucial regulatory effects on organ size and responses to environmental stresses. Despite their importance, Brassica oleracea ARGOS gene members and their functions in response to abiotic stresses have not been thoroughly investigated. In this study, we identified 40 ARGOS genes via a genome wide analysis of cauliflower and two other B. oleracea morphotypes as well as Brassica rapa, Brassica nigra, and Raphanus sativus. Expression pattern analyses indicated that these genes are responsive to multiple abiotic stresses, including salinity, heat, cold, and diverse hormones. Notably, the expression of an ARGOS-like gene (BobARL2) was upregulated in cauliflower treated with 1-aminocyclopropane-1-carboxylic acid (ACC). Moreover, the overexpression of BobARL2 decreased ethylene sensitivity, resulting in less inhibition of root elongation compared to the wild-type. Additionally, the overexpression lines exhibited enhanced salt tolerance. A yeast two-hybrid assay and luciferase complementation imaging (LCI) assay confirmed that BobARL2 can interact with Reversion-to-ethylene sensitivity Like4 (BobRTL4), which negatively regulates ethylene signal transduction. These findings advance our understanding of the evolution and functional roles of ARGOS genes in cauliflower and other Brassicaceae species, particularly in relation to abiotic stress responses, while also offering valuable insights relevant to the genetic improvement and breeding of novel varieties. Full article

Shanlan rice, a unique drought-resistant rice germplasm resource in Hainan Province, China, holds significant potential for rice genetic improvement and breeding innovation. However, its genetic diversity and significance in rice breeding remain inadequately explored. This study conducted a comprehensive analysis of phenolic acid profiles and antioxidant properties in the brown rice of 84 Shanlan rice accessions. It was revealed that colored Shanlan rice accessions exhibited significantly higher total phenolic content (249.00–2408.33 mg gallic acid equivalents per 100 g of rice flour (mg GAE/100 g)) and antioxidant capacity (DPPH: 680.39–809.63 micromoles of Trolox equivalent per 100 g (μmol TE/100 g); ABTS: 529.93–1917.77 μmol TE/100 g) compared to white-grained varieties. High-performance liquid chromatography (HPLC) analysis identified eight phenolic acids in the bound fractions, among which the sinapic acid (55.08 μg/g) and vanillic acid (11.72 μg/g) were predominant, accounting for over 60% of total bound phenolic acid content. A genome-wide association study (GWAS) identified 84 significant loci associated with these phenolic-related traits. A major quantitative trait locus (QTL) on chromosome 7 for free phenolic content, total phenolic content, flavonoids, and DPPH activity was co-located at the Rc gene locus, a key regulator of red pericarp pigmentation and proanthocyanidin biosynthesis. Haplotype analysis identified ten haplotypes in Rc, with the haplotype H002 showing the highest antioxidant capacity. Another QTL on chromosome 11 was associated with p-coumaric, vanillic, and sinapic acids, although no significant difference was observed in haplotype analysis. These results highlight Rc as a key genetic factor underlying antioxidant properties in rice, while other loci require further validation. This research provides a foundation for breeding health-benefit, drought-tolerant rice cultivars using Hainan’s unique germplasm. Full article

Miscanthus, a perennial grass, is renowned for its remarkable tolerance to abiotic stress. Excessive levels of drought severely impair plant growth and yield. Plant nuclear factor Y (NF-Y) transcription factors (TFs) play pivotal roles in regulating responses to drought stress in species such as Arabidopsis and maize. However, their functional roles in conferring drought tolerance in Miscanthus remain largely unexplored. This study’s genome-wide analysis and gene expression profiling of Miscanthus under dehydration/osmotic stress identified a transcription factors gene, MsNF-YA4, which was significantly upregulated under dehydration/osmotic stress. MsNF-YA4 overexpression in Arabidopsis significantly enhanced drought tolerance, leading to increased transcription of stress- and antioxidant enzyme-related genes. Compared with the wild type (WT), the transgenic lines exhibited markedly higher relative water content (RWC), chlorophyll content, proline level, and antioxidant enzyme activity. Furthermore, the MsNF-YA4/MsNF-YB3/MsNF-YC2 improved the transactivation of the Miscanthus P5CS1, SOD (Cu/Zn) and CAT1 promoters in the transient system. These results offer fresh perspectives on the role of Miscanthus NF-YAs in drought tolerance and offer promising genetic resources for developing drought-tolerant crops through breeding programs. Full article

Wild potato relatives are vital for breeding programs to tackle rising temperatures. This study proposes a methodological approach based on the examination of genetic variation among 19 accessions belonging to Solanum chacoense and Solanum commersonii from the Embrapa Potato Genebank under heat stress (HS). Heat tolerance coefficient (HTC) was calculated using genotypic values predicted through mixed models. After 15 days of heat stress (DHS), a significant variation in gas exchange and chlorophyll fluorescence indicates strong breeding potential and photosystem resilience. By 35 DHS, increased pigment variation suggests acclimation. Based on predicted genotypic values, S. chacoense outperforms S. commersonii in tuber production and gas exchange under HS, and principal component analysis (PCA) performed using the HTC shows early resistance driven by photosynthesis, mid-term by tuber yield, and long-term by gas exchange and tuber production. Genotypes BRA00167017-3, BRA00167023-1, BRA00167025-6, and BRA00167028-0 excel in heat comprehensive evaluation values (HCEVs)/comprehensive principal component value (F) rankings, demonstrating robust photosynthesis, thermoregulation, and tuber yield. Cluster analysis identifies these as highly tolerant, ideal for breeding heat-resilient potatoes. These PCA-derived weights and genotype clustering system provide a precise tool for selecting heat-tolerant wild potato germplasm, categorizing them into highly tolerant, moderately tolerant, sensitive with late recovery, and highly sensitive groups acquired for specific objectives of the breeding programs to climate change. Full article

In Uganda, rain-fed crops frequently encounter cycles of drought stress followed by rewatering. Thus, with escalating fluctuations in water supply, drought recovery has become a critical focus for future sorghum drought phenotyping, genetics, and breeding research. However, there is currently a low knowledge of the drought recovery potential of prospective genotypes in Uganda’s National Sorghum Improvement Program. The present study aimed to assess the response of selected genotypes to rewatering after drought. Sixteen sorghum genotypes and two check varieties were evaluated under two contrasting moisture regimes: well-watered and drought stress-rewatering in a split-plot layout using a randomized complete block design (RCBD). Watering regimes were assigned to whole plots, while sorghum genotypes were assigned to subplots, with three replications. The results showed highly significant effects (p < 0.05) of drought stress on key agronomic traits, decreased dry weight, grain weight, and biomass yield by 39%, 43% and 37%, respectively, and delayed flowering by an average of 11 days. Key genotype-specific traits associated with drought recovery included rapid rehydration, compensatory growth, and maintenance of high relative chlorophyll content, all of which were essential for optimizing yields after stress. Leveraging drought tolerance indices, genotypes were ranked by their recovery potential and further classified into four distinct groups (A–D) based on their yield performance and stability under the two watering regimes. Genotypes in category A demonstrated high yield stability and strong recovery potential. Conversely, genotypes in category D exhibited the poorest recovery response. Overall, the information generated from this study will support future sorghum breeding efforts for drought resilience. Full article

The BRI1-EMS suppressor/Brassinazole-resistant (BES/BZR) transcription factors (TFs) act as regulators of the Brassinosteroid (BR) signaling pathway and play key roles in modulating plant growth, development, and abiotic stress tolerance. However, the function of BES/BZR TFs remains unknown in warm-season turfgrass species. In this study, ZjBZR2, a BES/BZR TF in Zoysia japonica was identified and shared the closest evolutionary relationship with OsBZR2 from Oryza sativa. ZjBZR2 was a nuclear-localized protein and had transcriptional activation activity. ZjBZR2 was predominantly expressed in roots, stems, and lamina joints, and could be significantly induced by BR treatment and osmotic stresses including PEG and salinity. ZjBZR2-overexpressing rice lines increased leaf angle compared with wild-type plants. Furthermore, overexpression of ZjBZR2 enhanced osmotic stress (PEG and salt) tolerance which is associated with the upregulation of stress-responsive and ROS-scavenging genes. These findings provide the first functional characterization of ZjBZR2 in rice and offer excellent genetic resources for the improvement of turfgrass cultivars. Full article

Acetolactate synthase (ALS) is an important enzyme in plant branched-chain amino acid biosynthesis and the target of several major herbicide classes. Despite its agronomic importance, the role of ALS genes in stress adaptation in the invasive weed Amaranthus palmeri remains unstudied. In this study, four ApALS genes with high motif conservation were identified and analyzed in A. palmeri. Phylogenetic analysis classified ApALS and other plant ALS proteins into two distinct clades, and the ApALS proteins were predicted to localize to the chloroplast. Gene expression analysis demonstrated that ApALS genes are responsive to multiple stresses, including salt, heat, osmotic stress, glufosinate ammonium, and the ALS-inhibiting herbicide imazethapyr, suggesting roles in both early and late stress responses. Herbicide response analysis using an Arabidopsis thaliana ALS mutant (AT3G48560) revealed enhanced imazethapyr resistance, associated with higher chlorophyll retention. Furthermore, high sequence homology between AT3G48560 and ApALS1 suggests a conserved role in protecting photosynthetic function during herbicide stress. This study provides the first comprehensive analysis of the ALS gene family in A. palmeri and offers important insights into its contribution to stress resilience. These findings establish a vital foundation for developing novel strategies to control this pervasive agricultural weed and present potential genetic targets for engineering herbicide tolerance in crops. Full article

This study evaluated genetic parameters for test-day egg production in four Thai native synthetic chicken lines—Soi Nin, Soi Pet, Kaen Thong, and Kaimook e-san—under heat stress in Thailand. A total of 11,887 monthly test-day egg records from 1134 hens, collected between January 2023 and July 2025, were analyzed using a repeatability test-day model with the temperature–humidity index (THI) as an environmental covariate. THI thresholds from 70 to 80 were evaluated, and the THI1 equation provided the best model fit with the highest coefficient of determination (R²) and the lowest mean squared error (MSE). With increasing THI, heritability estimates declined from 0.255–0.323 at THI 70 to 0.173–0.236 at THI 80, a 26.9–32.2% decrease reflecting reduced additive genetic variance and consequent lower genetic expression under heat stress. Genetic correlations between egg production and heat stress were positive at low THI (0.250–0.600) but became negative at THI ≥ 73, suggesting antagonism between productivity and thermotolerance under severe stress. The rate of decline in egg production increased with increasing THI, from −0.35 to −0.45 eggs/bird/THI at THI 73, −0.80 to −1.22 at THI 76, and −1.76 to −2.35 at THI 80. The ranges of heritability and decline rates reflect the variation observed among the four Thai native synthetic chicken lines examined in this study. Kaimook e-san consistently showed the steepest decline in egg production, whereas Soi Nin exhibited the smallest, indicating greater resilience. These findings reveal significant genetic variation in heat tolerance among Thai native synthetic lines and underscore the need to consider both productivity and environmental sensitivity in breeding programs to sustain egg production under future climate change. Full article

Sphagneticola trilobata (L.) Pruski has been introduced to many countries due to its ornamental and economic value. However, it has been listed in the world’s 100 worst alien invasive species due to its invasive nature. This species easily escapes cultivation and forms dense ground covers. It reproduces asexually through ramet formation from stem fragments. It also produces a large number of viable seeds that establish extensive seed banks. The movement of stem fragments and the dispersal of seeds, coupled with human activity, contribute to its short- and long-distance distribution. S. trilobata grows rapidly due to its high nutrient absorption and photosynthetic abilities. It exhibits high genetic and epigenetic variation. It can adapt to the different habitats and tolerate various adverse environmental conditions, including cold and high temperatures, low and high light irradiation, low nutrient levels, waterlogging, drought, salinity and global warming. S. trilobata has powerful defense systems against herbivory and pathogen infection. These systems activate the jasmonic acid signaling pathway, producing several defensive compounds. This species may also acquire more resources through allelopathy, which suppresses the germination and growth of neighboring plants. These life history traits and defensive abilities likely contribute to its invasive nature. This is the first review to focus on the mechanisms of its invasiveness in terms of growth, and reproduction, as well as its ability to adapt to different environmental conditions and defend itself. Full article

Fusarium wilt, caused by Fusarium oxysporum f. sp. phaseoli (Fop), is a major constraint to global common bean (Phaseolus vulgaris L.) production. Thiamine (vitamin B1), an essential coenzyme in plant metabolism, has recently emerged as a potential regulatory factor in plant defense. Here, we performed a comprehensive genome-wide analysis of thiamine biosynthesis-related genes in common bean and elucidated their roles in resistance to Fusarium wilt. Five key thiamine biosynthetic genes were identified and characterized, showing conserved functional domains and evolutionary conservation across species. Expression profiling revealed tissue-specific patterns, with PvTHI1-1 and PvTHIC being highly expressed in reproductive and photosynthetic organs, with their relative expression levels 0.28–0.57 higher than other members in the same tissue, while PvTPK maintained a basal expression level in the roots. Upon Fop infection, resistant genotypes exhibited significantly higher expression of thiamine biosynthetic genes and greater accumulation of endogenous thiamine and its derivatives than susceptible ones. Functional analysis using Agrobacterium rhizogenes-mediated transformation demonstrated that overexpression of PvTPK enhanced thiamine metabolism and conferred resistance in susceptible genotypes. Similarly, exogenous application of thiamine upregulated biosynthetic genes and improved disease resistance. Together, these results reveal that thiamine biosynthesis is intricately linked to Fusarium wilt resistance and that both genetic and biochemical manipulation of thiamine pathways can enhance disease tolerance. This study provides new insights into thiamine-mediated plant immunity and establishes a foundation for its application in the control of Fusarium wilt in common bean. Full article

A novel species of the genus Methylocystis is proposed based on polyphasic evidence from strain SC2^T, isolated from the heavily polluted Saale River near Wichmar, Germany. Digital DNA–DNA hybridization and phylogenomic analyses demonstrate that strain SC2^T represents a distinct species within the genus, clearly separated from its closest relatives, namely Methylocystis suflitae NLS-7^T, Methylocystis rosea SV97^T, Methylocystis silviterrae FS^T, and Methylocystis hirsuta CSC1^T. As is typical of the family Methylocystaceae, cells possess intracytoplasmic membranes arranged parallel to the cytoplasmic membrane, and the dominant fatty acids are C18:1ω8c and C18:1ω7c. The strain grows aerobically on methane as the primary carbon and energy source and expresses both low- and high-affinity particulate methane monooxygenase (pMMO), but lacks the soluble form. The species epithet reflects the strain’s ability to utilize hydrogen as an alternative energy source. A further feature is its use of asparagine as an osmoprotectant, enhancing salt tolerance. Genomic analysis reveals complete pathways for nitrogen fixation, denitrification, and hydrogen oxidation. These genetic and physiological characteristics support the designation of a novel species, for which the name Methylocystis hydrogenophila sp. nov. is proposed. The type strain is SC2^T (=DSM 114506 = NCIMB 15437). Full article

Blue fescue (Festuca glauca) is a widely used ornamental grass worldwide. Drought is an important limiting factor for the growth and development of blue fescue; therefore, cultivating new strains of blue fescue with a strong drought tolerance is of great significance for its production practice. To investigate the drought tolerance mechanism of ds-1, this study subjected both ds-1 and “Festina” to a natural drought treatment and measured their physiological and biochemical indicators. A transcriptomic analysis was also conducted to explore the underlying molecular mechanisms. The results showed that, after the drought treatment, the relative water content (RWC), water use efficiency (WUE), and photosynthetic rate (Pn) of ds-1 leaves were significantly higher than those of “Festina”; in addition, the contents of H₂O₂ and O₂⁻, the relative electrical conductivity (REC), the malondialdehyde (MDA) content, the gas conductance (Gs), and the transpiration rate (Tr) were significantly lower than those of “Festina”. The peroxidase (POD) activity of ds-1 was significantly higher than that of “Festina”, while the superoxide dismutase (SOD) activity of ds-1 was significantly lower than that of “Festina”. The transcriptome data analysis showed that there were a total of 9475 differentially expressed genes (DEGs) between ds-1 and “Festina”. A Venn plot analysis showed 692 DEGs between ds-1—8d vs. “Festina”—8d and ds-1—16d vs. “Festina”—16d. A KEGG enrichment analysis showed that these 692 genes were mainly enriched in 86 pathways, including those related to the photosynthesis antenna protein, plant hormone signal transduction, MAPK signaling, starch and sucrose metabolism, and arginine and proline metabolism. Further screening identified genes that may be associated with drought stress, including PYL, PP2C, SnRK2, ABF, BRI1, JAZ, MYC2, Lhc, and MPK6. The qRT-PCR results indicated that the expression trends of the DEGs were consistent with the transcriptome sequencing results. Our research results can provide a basis for exploring candidate genes for drought tolerance in blue fescue. In addition, our research results provide valuable genetic resources for the development of drought-resistant ornamental grass varieties, which can help reduce water consumption in cities and decrease labor and capital investment. Full article