Search Results (1,836)

Background/Objectives: Miscanthus Andersson, a genus of perennial grasses that includes wild relatives of key crop species, remains poorly characterized in terms of genetic diversity and evolutionary relationships. The aim of this study was to elucidate the phylogenetic structure of Miscanthus through comparative genomic analysis of the chloroplast genomes of six Korean species. Methods: Complete chloroplast genomes were assembled and analyzed for six Miscanthus species. Informative nucleotide motifs and their associated gene locations were identified as potential markers, and their phylogenetic relationships with related crops were examined. Results: The chloroplast genomes exhibited a conserved quadripartite structure, with genome sizes and GC contents within typical ranges. Analysis of codon usage showed a preference for A/U-ending codons, consistent with patterns in other angiosperms. Simple sequence repeats and long repeats demonstrated non-random distributions, indicating their value as molecular markers for phylogenetic and population studies. Comparative analyses confirmed structural conservation across Miscanthus species, whereas variation in non-coding regions provided important phylogenetic signals. Phylogenetic reconstruction based on 21 chloroplast genomes revealed four major clades, corroborating previous findings and highlighting complex evolutionary relationships within Miscanthus, including close affinities between African and Himalayan species and the genus Saccharum L. Conclusions: This study provides complete chloroplast genomes of six Miscanthus species, contributing to enhanced understanding of the relationships within the subtribe Saccharinae. The findings support the inclusion of Miscanthus species in the Korea Crop Wild Relatives inventory and highlight their potential as a genetic resource for breeding programs aimed at enhancing crop resilience to environmental stress. Full article

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

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

Lignin, as one of the three primary components of renewable lignocellulosic biomass, can be converted into aromatic platform chemicals and holds significant potential for high-value applications. p-Hydroxybenzaldehyde is a compound derived from lignin. In this study, the mutant Δ60 of the glycosyltransferase UGT_BL1 derived from Bacillus licheniformis was adopted to catalyze the glycosylation reaction of p-hydroxybenzaldehyde, producing a bioactive compound Helicid analogue (p-hydroxybenzaldehyde β-glucoside). Truncation mutations targeting loop regions may reduce local flexibility, thereby facilitating enhanced access of p-hydroxybenzaldehyde to the active site pocket and promoting relative activity. Under optimal conditions (35 °C, pH 7.5, and glucose 200 mM), a high yield of 97.8% for p-hydroxybenzaldehyde β-glucoside was achieved from 2 mM p-hydroxybenzaldehyde within 10 h. The conversion of 3 mM p-hydroxybenzaldehyde (366.4 mg/L) yielded up to 2.7 mM (767.5 mg/L) of p-hydroxybenzaldehyde β-glucoside within 48 h. According to the molecular docking results, the CDOCKER energy value of mutant Δ60 was lower than that of the wild-type, at −16.0 kcal/mol. To our knowledge, this is the first example of an efficient and environmentally sustainable approach for the synthesis of p-hydroxybenzaldehyde β-glucoside, providing a new insight for the valorization of lignin into valuable biobased chemicals. Full article

Coronaviruses (CoVs) were first described in poultry in the early 1930s and formally recognized as pathogens of both animal and human populations in the late 1960s. They are now considered among the most abundant viral families in the world. Though their distribution and diversity remain understudied in wild animals, representatives from 13 orders of wild birds worldwide have tested positive for CoVs of the gamma and delta genera over the last 25 years. Many of these wild bird species are in the orders Charadriiformes (shorebirds and their relatives) and Anseriformes (waterfowl including ducks, geese, and swans). Waterfowl are particularly concerning as potential reservoirs for CoVs because they are globally distributed; often congregate in large, mixed-species flocks; and may exist in close proximity to humans and domesticated animals. This review describes the history and current knowledge of CoVs in birds, provides an updated list of global detections of CoVs in 124 species of wild birds as reported in the peer-reviewed literature since 2000, and highlights topics for future research that would help elucidate the role of waterfowl in CoV transmission. Our review reiterates the need for continuous surveillance to detect and monitor CoVs across all bird species and for standardization in data reporting and analysis of both negative and positive results. Such information is critical to understand the potential role of free-ranging birds in the maintenance, evolution, and transmission of the virus. Further, we believe that research on the potential impacts of coronavirus infections and coinfections on avian demographics, especially reproduction in waterfowl, is warranted given known consequences in domestic poultry. Full article

Inorganic pyrophosphatase (PPase) is an enzyme that catalyzes the hydrolysis of pyrophosphate (PPi) into two phosphates. Ton1914, a thermophilic inorganic pyrophosphatase derived from Thermococcus onnurineus NA1, has good thermal stability and an extremely high optimum temperature and has been shown to reduce pyrophosphate inhibition. In this study, eight sites were selected based on sequence alignment and software calculations, and multiple single mutants were successfully constructed. After saturation and superposition mutations, six superior mutants were obtained. The enzyme activities of E97Y, D101K and L42F were increased 2.57-, 2.47- and 2.15-fold, respectively, while those of L42F/E97Y, L42F/D101K and E97Y/D101K were increased 2.60-, 2.63- and 1.88-fold, respectively, relative to the wild-type enzyme. Compared to Ton1914, all mutants more effectively increased PCR product quantity, reduced the number of qPCR cycles required to reach the threshold, and improved the efficiency of gene amplification. In the UDP-Galactose (UDP-Gal) synthesis reaction, the addition of mutants could further improve yield. When Ton1914 and mutants with the same activity were added, the yield of UDP-Gal was almost identical, effectively reducing the dosage of pyrophosphatase. Overall, the mutants showed greater prospects for industrial application. Full article

Xylanase, an essential enzyme for breaking down xylan, faces limitations in its industrial applications due to the relatively low catalytic activity of the wild type. Directed evolution was used to enhance the catalytic efficiency of xylanase that originated from the Dickeya dadantii DCE-01. A xylanase variant (Xyn-ep) was obtained with improved catalytic activity by random mutant library employing two rounds of error-prone PCR. The results showed that the Xyn-ep demonstrated enzyme activity 1.6 times higher than that of wild-type xylanase. Sequencing analysis pinpointed key mutation sites at S159P, K212N, and N397S, respectively. Homology modeling was used to analyze the location of the mutation sites and to investigate the mechanism of the improved catalytic performance. The mutant Xyn-ep showed improved catalytic performance by error-prone PCR. Additionally, the increased flexibility of the loop of the mutant may contribute to the enhanced activity. These findings indicate that error-prone PCR is an effective method for enhancing enzyme activity and that the mutant Xyn-ep may be a new GH30 xylanase, being a potential candidate for industrial applications such as bast fiber bio-degumming, cotton bio-refinery, paper making, and so on. Full article

The wild yak (Bos mutus) is a flagship species on the Qinghai–Tibet Plateau, possessing significant ecological functions and conservation value. Using single-nucleotide polymorphism markers from whole-genome resequencing, we systematically analyzed golden wild yak (n = 37), common wild yak (n = 106), and domestic yak (Bos grunniens) (n = 20) to characterize the population genetic structure and adaptive selection signals in the golden wild yak. Genetic diversity analyses revealed that the golden wild yak had the lowest nucleotide diversity (π = 0.00148) and the highest inbreeding coefficient (F_Hom = 0.043). Population structure analyses integrating principal component analysis, phylogenetic tree, and ancestral component clustering indicated that the golden wild yak formed a relatively independent evolutionary lineage. However, its genetic differentiation from sympatric common wild yak population was limited (fixation index = 0.031). Selective sweep analysis identified a set of candidate positively selected genes in the golden wild yak genome associated with key traits and physiological functions, including coat color (TYRP1), hypoxia adaptation (MYH11, POLQ), reproductive function (SLC9C1, SPAG16, CFAP97D1), and immune response (CASP8, PGGT1B, BIRC6). Overall, our study reveals a distinct genetic background and selection signatures in the golden wild yak and provides genomic insights to inform the conservation and management of the wild yak. Full article

Natural areas near farmland can provide refuge for birds that contribute to natural pest control. However, birds can endanger food safety by defecating on or near produce. Work in the western US suggests that Campylobacter spp. are the potential foodborne pathogens most commonly associated with wild birds and that pathogen prevalence is higher in landscapes dominated by animal agriculture. However, relatively little is known about other fresh-market-produce growing regions. Working on produce farms in the Southeastern US, we characterized bird communities, tested bird feces deposited on crop foliage for Campylobacter and Salmonella, and searched for landscape features associated with heightened bird-associated food safety risks. We found that bird communities on farms were generally similar across ecoregions. Campylobacter was never detected from bird feces deposited on crop foliage, but Salmonella was detected in 8.6% of fecal samples. Salmonella prevalence in crop-surface-collected bird feces was highest when farms also produced livestock and when wetland cover was prevalent in the landscape. Overall, our results suggest that on-farm livestock production may be an indicator of bird-associated food safety risks in the Southeast, as in the West. We suggest there may be some similarities, but important differences, in food safety risks posed by birds in different US produce growing regions. Full article

To improve the deep processing and utilization of wild blueberries, this study presents a green and highly efficient method for extracting flavonoids from blueberries. The approach combines natural deep eutectic solvents (NADESs) with ultrasound-assisted extraction. Among the 22 tested NADES, Betaine/urea (BU), was the most effective solvent for extracting flavonoids from blueberries. The extraction parameters of ultrasound-assisted betaine/urea (UABU) were optimized using a response surface methodology (RSM). This optimization procedure yielded the optimized conditions outlined below: a molar ratio of urea to betaine of 3.3:1, a water content of 60% (m/v), an ultrasonic power of 330 W, a solid-to-liquid ratio of 1:30, an extraction temperature of 50 °C, and an ultrasonic extraction duration of 30 min. Under these conditions, the total flavonoid content (TFC) extracted using UABU reached 6.06 ± 0.024 mg_RE/g_DW, a 1.44-fold increase compared to ultrasound-assisted 70% (v/v) ethanol (UAE). Liquid Chromatography–Tandem Mass Spectrometry (LC-MS/MS) nontargeted metabolomics analysis revealed that the flavonoids extracted by UABU had highly relative content (RC) of Oenin, 3′-methoxy-4′,5,7-trihydroxyflavonol, Isorhamnetin-3-O-glucoside and Isoquercitrin. Significant disparities exist regarding the types and RC of flavonoids obtained via UAE. Results from in vitro antioxidant assays demonstrated that UABU has superior antioxidant activity relative to UAE. This study demonstrated the feasibility of using NADESs, specifically BU, as an efficient and eco-friendly extraction medium for flavonoids from wild blueberries. The yield of flavonoids was increased by this method, and bioactive compounds were also protected—findings that underscore the potential of green solvents for application in the food industry. Full article

Nitrogen (N) is the primary macronutrient that supports global agriculture. The Haber–Bosch process revolutionized the use of synthetic N fertilizers, enabling significant increases in crop yield. However, N losses from fertilization led to negative impacts on the environment. Improving crops’ N use efficiency (NUE) has been constrained by the limited understanding of N uptake and assimilation mechanisms, and the role of plant–microbe interactions. Among biological approaches, N fixation by cover crops and rhizobia symbioses represents a cornerstone strategy for improving NUE. The adoption of plant growth-promoting bacteria and arbuscular mycorrhizal fungi may enhance N acquisition by increasing root surface, modulating phytohormone levels, and facilitating nutrient transfer. Advances in plant molecular biology have identified key players and regulators of NUE (enzymes, transporters, and N-responsive transcription factors), which enhance N uptake and assimilation. Emerging biotechnological strategies include de novo domestication by genome editing of crop wild relatives to combine NUE traits and stress resilience back into domesticated cultivars. Additionally, novel fertilizers with controlled nutrient release and microbe-mediated nutrient mobilization, hold promise for synchronizing N availability with plant demand, reducing losses, and increasing NUE. Together, these strategies form a multidimensional framework to enhance NUE, mitigate environmental impacts, and facilitate the transition towards more sustainable agricultural systems. Full article

As nutrient allocation trade-offs occur between reproductive and vegetative development in crops, optimizing their partitioning holds promise for improving agricultural productivity and quality. Herein, we characterize the phenotypic diversity of the fruitfulness trait and identify associated genes in tea plants (Camellia sinensis). Over three consecutive years, we monitored the fruitfulness of an F₁ hybrid population (n = 206) derived from crosses of ‘Emei Wenchun’ and ‘Chuanmu 217’. A marked variation was observed in the yield of individual plants, ranging from complete sterility (zero fruits) to exceptionally high fertility (1612 fruits). Using the high-resolution genetic linkage map and the fruitfulness data, we identified a stable major QTL designated as qFN5. To fine-map the underlying gene(s), artificial pollination experiments were conducted with extreme phenotype individuals (with the highest vs. lowest fruit numbers). Bulked segregant RNA sequencing (BSR-Seq) with ovules collected at two and seven days post-pollination (DPP) identified the genomic intervals that exhibit a high degree of overlap with qFN5. Analysis of expression dynamics combined with functional genomics data revealed a prominent candidate gene, CsETR2 (TGY048509), which encodes an ethylene receptor protein. When CsETR2 was overexpressed in Arabidopsis thaliana, the transgenic lines exhibited significantly decreased reproductive performance relative to the wild-type plants. Relative to the wild type, the transgenic lines exhibited a significant decline in several key traits: the number of effective panicles decreased by 72.5%, the seed setting rate dropped by 67.7%, and the silique length shortened by 38%. These findings demonstrate its role in regulating plant fruitfulness. Furthermore, yeast one-hybrid and dual-luciferase assays verified that CsMYB15 (TGY110225) directly binds to the CsETR2 promoter, thus repressing its transcription. In summary, our findings expand the understanding of genetic regulation underlying fruitfulness in tea plants and provide candidate target loci for breeding. Full article

Background/Objectives: Aeromonas veronii is a significant pathogen affecting aquatic animals and has the potential to infect humans. Vaccination remains the most effective strategy for preventing infections caused by this bacterial strain. Methods: This study aimed to validate the efficacy of bacterial ghosts as an oral vaccine by administering them to Cyprinus carpio and evaluating the resultant innate and acquired immune responses. Following immunization, the vaccinated Cyprinus carpio were exposed to a lethal dose of the wild-type bacterial strain to assess survival rates and relative protection efficiency. Results: Oral vaccination with bacterial ghosts led to the significant enhancement of lysozyme (LZM) and myeloperoxidase (MPO) activity in koi serum. It also resulted in the upregulation of cytokines, such as IL-2 and TNF-α, as well as an increase in both systemic (IgM) and mucosal (IgZs) antibody responses. The immunized group demonstrated reduced cumulative mortality following bacterial challenge. The relative percent survival in the vaccinated group reached as high as 87.50%. Conclusions: The oral immunization of Cyprinus carpio with A. veronii-derived bacterial ghosts confers substantial immune protection, providing a foundational basis for the development of novel vaccines against A. veronii. Full article

Mongolia’s rapidly expanding capital is encroaching on Bogd Khan Mountain, a UNESCO Biosphere Reserve and the oldest protected area in Eurasia. Gray wolves (Canis lupus) in this wildland–urban interface are locally near-threatened due to hunting, local beliefs, and human–wildlife conflict. In 2022 and 2023, we deployed 72 camera traps (11,539 trap nights) to investigate how wolves respond to overlapping pressures from free-ranging dogs, livestock, and human activity. Using a random habitat-stratified camera design and abundance modeling, we assessed diel activity and spatial co-occurrence. Wolves exhibited nocturnal and crepuscular activity, with the greatest temporal overlap with wild prey (wapiti: ∆⁴ = 0.73; Siberian roe deer: ∆⁴ = 0.79), moderate overlap with dogs (∆⁴ = 0.60) and horses (∆⁴ = 0.68), and minimal overlap with cattle (∆⁴ = 0.40) and people (∆⁴ = 0.43). Mean wolf abundance estimates ranged from λ = 0.91 (CI 95%, 0.05–1.77) in 2022 to λ = 1.52 (CI 95%, 0.44–3.53) in 2023. Wolves were more abundant at higher relative abundance of wild ungulates and in areas with more people. Wolves co-occurred with dogs at 11 sites and were more abundant in areas with a higher number of dogs. Our findings highlight the complex dynamics between wildlife, livestock, and human-associated disturbances at the wildland–urban interface, underscoring the need for integrated management strategies that address both ecological and human dimensions of conservation. Full article