Search Results (1,936)

Structural variation (SV) serves as a fundamental driver of phenotypic diversity and environmental adaptation in plants and animals, significantly influencing key agronomic traits in crops. Common wheat (Triticum aestivum L.), an allohexaploid species, harbors extensive chromosomal SVs and distant hybridization-induced recombination events that provide critical resources for genetic improvement. This study utilizes non-denaturing fluorescence in situ hybridization (ND-FISH) and oligonucleotide multiplex probe-based FISH (ONPM-FISH) to analyze the karyotypes of 153 BC₁F₄–BC₁F₆ lines derived from the hybrid line Xiaoyan 7430 and common wheat Yannong 1212. The results revealed that Xiaoyan 7430 carries 8 alien chromosome pairs and 20 wheat chromosome pairs (lacking 6B), and Yannong 1212 contains 21 pairs of wheat chromosomes. The parental lines exhibited presence/absence variations (PAVs) on chromosomes 2A, 6A, 5B, 1D, and 2D. Chromosomal variations, including numerical chromosomal variation (NCV), structural chromosomal variation (SCV), and complex chromosomal variation (CCV), were detected in the progeny lines through ONPM-FISH analysis. The tracking of alien chromosomes over three consecutive generations revealed a significant decrease in transmission frequency, declining from 61.82% in BC₁F₄ to 26.83% in BC₁F₆. Telosomes were also lost during transmission, declining from 21.82% in BC₁F₄ to 9.76% in BC₁F₆. Alien chromosome 1J^S, 4J, and 6J exhibited the highest transmission stability and were detected across all three generations. Association analysis showed that YN-PAV.2A significantly affected the length/width ratio (LWR) and grain diameter (GD); YN-PAV.6A, XY-PAV.6A, and PAV.5B increased six grain traits (+2.25%~15.36%); YN-PAV.1D negatively affected grain length (GL) and grain circumference (GC); and XY-PAV.2D exerted positive effects on thousand-grain weight (TGW). Alien chromosomes differentially modulated grain characteristics: 1J^S and 6J both reduced grain length and grain circumference; 1J^S increased LWR; and 4J negatively impacted TGW, grain width (GW), GD, and grain area (GA). Meanwhile, increasing alien chromosome numbers correlated with progressively stronger negative effects on grain traits. These findings elucidate the genetic mechanisms underlying wheat chromosomal variations induced by distant hybridization and their impact on wheat grain traits, and provide critical intermediate materials for genome design breeding and marker-assisted selection in wheat improvement. Full article

Insufficient fruit intake is a major contributor to the development of non-communicable diseases, as the global average of daily fruit consumption remains far below the recommended levels. Apples are among the most widely consumed fruits worldwide, making them an ideal target for nutritional enhancement. Enhancing the content of health-promoting compounds within apples offers a practical way to increase bioactive intake without requiring major dietary changes. This review evaluates which of the 41 biologically active compounds considered in this article can reach physiologically relevant intake levels at the current average daily consumption of cultivated and wild apples. Comparative analysis shows that wild apples consistently contain higher concentrations of phenolic compounds and organic acids than cultivated varieties, in some cases by more than tenfold. At the average daily fruit intake of 121.8 g, wild species provide effective doses of epicatechins, anthocyanins, chlorogenic acid, and malic acid. In contrast, cultivated apples reach this level only for chlorogenic acid. Notably, less than 50 g of wild apple is sufficient to supply physiologically relevant amounts of several polyphenols. These findings highlight the potential of wild apple species as donors of bioactive compounds and provide a framework for breeding future apple cultivars that combine consumer appeal with enhanced health benefits. Full article

Plants have evolved a complex, multilayered immune system that integrates molecular recognition, signaling pathways, epigenetic regulation, and small RNA-mediated control. Recent studies have shown that DNA-level regulatory mechanisms, such as RNA-directed DNA methylation (RdDM), histone modifications, and chromatin remodeling, are critical for modulating immune gene expression, allowing for rapid and accurate pathogen-defense responses. The epigenetic landscape not only maintains immunological homeostasis but also promotes stress-responsive transcription via stable chromatin modifications. These changes contribute to immunological priming, a process in which earlier exposure to pathogens or abiotic stress causes a heightened state of preparedness for future encounters. Small RNAs, including siRNAs, miRNAs, and phasiRNAs, are essential for gene silencing before and after transcription, fine-tuning immune responses, and inhibiting negative regulators. These RNA molecules interact closely with chromatin features, influencing histone acetylation/methylation (e.g., H3K4me3, H3K27me3) and guiding DNA methylation patterns. Epigenetically encoded immune memory can be stable across multiple generations, resulting in the transgenerational inheritance of stress resilience. Such memory effects have been observed in rice, tomato, maize, and Arabidopsis. This review summarizes new findings on short RNA biology, chromatin-level immunological control, and epigenetic memory in plant defense. Emerging technologies, such as ATAC-seq (Assay for Transposase-Accessible Chromatin using Sequencing), ChIP-seq (Chromatin Immunoprecipitation followed by Sequencing), bisulfite sequencing, and CRISPR/dCas9-based epigenome editing, are helping researchers comprehend these pathways. These developments hold an opportunity for establishing epigenetic breeding strategies that target the production of non-GMO, stress-resistant crops for sustainable agriculture. Full article

The size and mass of fish are crucial parameters in aquaculture management. However, existing research primarily focuses on conducting fish size and mass estimation under ideal conditions, which limits its application in actual aquaculture scenarios with complex water quality and fluctuating lighting. A non-contact size and mass measurement framework is proposed for complex underwater environments, which integrates the improved FishKP-YOLOv11 module based on YOLOv11, stereo vision technology, and a Random Forest model. This framework fuses the detected 2D key points with binocular stereo technology to reconstruct the 3D key point coordinates. Fish size is computed based on these 3D key points, and a Random Forest model establishes a mapping relationship between size and mass. For validating the performance of the framework, a self-constructed grass carp dataset for key point detection is established. The experimental results indicate that the mean average precision (mAP) of FishKP-YOLOv11 surpasses that of diverse versions of YOLOv5–YOLOv12. The mean absolute errors (MAEs) for length and width estimations are 0.35 cm and 0.10 cm, respectively. The MAE for mass estimations is 2.7 g. Therefore, the proposed framework is well suited for application in actual breeding environments. Full article

Ensete ventricosum is a morphologically gigantic, monocot, diploid sister to the banana plant species. It is commercially cultivated as a starch source, only in Ethiopia, where it feeds twenty million people. Here, the complete chloroplast (CP) genomes of 15 diverse landraces of E. ventricosum were assembled and annotated, for comparative genomics, genetic diversity analysis, and molecular marker development. The assembled E. ventricosum CP genomes ranged between 168,388 and 168,806 bp. The sampled CP genomes were quadripartite in structure and had two single-copy regions, a large single-copy region (LSC, average length 88,657 bp), and a small single-copy region (SSC, average length 11,098 bp) separated by inverted repeat regions (IR, average length 34,437 bp). The total number of annotated genes varies between 135 and 138, including 89–92 protein-coding genes, 38 tRNA genes, and 4 rRNA genes. All CP genes, including non-functional ones and intergenic regions, were transcribed with the transcriptome, covering almost 92% of the E. ventricosum CP genome. Codon usage, amino acid frequency, GC contents, and repeat nucleotides were similar among the 15 landraces. Mono- and tetranucleotide simple sequence repeats (SSRs) were found more frequently than other SSRs. An average of 71% of these SSRs were located in the LSC region, and the majority of the SSR motifs were composed of A/T nucleotides. A phylogenetic analysis of the 15 Ensete landraces indicated a common evolutionary origin, while the China sample was positioned separately, suggesting notable genetic differences. This study presents a comparative analysis of the chloroplast genomes of 15 E. ventricosum landraces, providing valuable insights into their genetic diversity and evolution. The identified SSR markers and conserved genomic features offer essential resources for future research and an improvement in Ensete conservation and breeding. Full article

Urban soundscapes are increasingly recognized as fundamental for both ecological integrity and human well-being, yet the complex interplay between the vegetation structure, seasonal dynamics, and microclimatic factors in shaping these soundscapes remains poorly understood. This study tests the hypothesis that vegetation structure and seasonally driven biological activity mediate the balance and the quality of the urban acoustic environment. We investigated seasonal and spatial variations in five acoustic indices (NDSI, ACI, AEI, ADI, and BI) within a historical urban garden in Castelfranco Veneto, Italy. Using linear mixed-effects models, we analyzed the effects of season, microclimatic variables, and vegetation characteristics on soundscape composition. Non-parametric tests were used to assess spatial differences in vegetation metrics. Results revealed strong seasonal patterns, with spring showing increased NDSI (+0.17), ADI (+0.22), and BI (+1.15) values relative to winter, likely reflecting bird breeding phenology and enhanced biological productivity. Among microclimatic predictors, temperature (p < 0.001), humidity (p = 0.014), and solar radiation (p = 0.002) showed significant relationships with acoustic indices, confirming their influence on both animal behaviour and sound propagation. Spatial analyses showed significant differences in acoustic patterns across points (Kruskal–Wallis p < 0.01), with vegetation metrics such as tree density and evergreen proportion correlating with elevated biophonic activity. Although the canopy height model did not emerge as a significant predictor in the models, the observed spatial heterogeneity supports the role of vegetation in shaping urban sound environments. By integrating ecoacoustic indices, LiDAR-derived vegetation data, and microclimatic parameters, this study offers novel insights into how vegetational components should be considered to manage urban green areas to support biodiversity and foster acoustically restorative environments, advancing the evidence base for sound-informed urban planning. Full article

A vision-based autonomous system for emasculating okra enhances agriculture by enabling precise flower bud identification, overcoming the labor-intensive, error-prone challenges of traditional manual methods with improved accuracy and efficiency. This study presents a framework for an adaptive, automated bud identification method to assist the emasculation process, hybridized optical coherence tomography (OCT). Three YOLOv8 variants were evaluated for accuracy, detection speed, and frame rate to identify the most efficient model. To strengthen the findings, YOLO was hybridized with OCT, enabling non-invasive sub-surface verification and precise quantification of the emasculated depth of both sepal and petal layers of the flower bud. To establish a solid benchmark, gold standard color histograms and a digital imaging-based method under optimal lighting conditions with confidence scoring were also employed. The results demonstrated that the proposed method significantly outperformed these conventional frameworks, providing superior accuracy and layer differentiation during emasculation. Hence, the developed YOLOv8 hybridized OCT method for flower bud identification and emasculation offers a powerful tool to significantly improve both the precision and efficiency of crop breeding practices. This framework sets the stage for implementing scalable, artificial intelligence (AI)-driven strategies that can modernize and optimize traditional crop breeding workflows. Full article

Excessive abdominal fat deposition accompanying rapid growth in broiler chickens seriously affects production efficiency. Using divergently selected broiler lines from Northeast Agricultural University, we integrated transcriptome sequencing, whole-genome resequencing, and three-dimensional genomic data to identify key SNPs affecting abdominal fat deposition. From 3,850,758 initial SNPs, 22,721 high-quality SNPs were selected (|ΔAF| ≥ 0.9) and validated to obtain 7341 reliable SNPs. GWAS identified 16 SNPs significantly associated with abdominal fat weight, while LD analysis revealed 22 highly linked SNPs, finally determining 2302 candidate SNPs. Transcriptome analysis identified 825 differentially expressed genes (p ≤ 0.05, |FC| ≥ 1.5). Functional annotation revealed 201 SNPs located in differentially expressed gene regions, including 8 coding SNPs and 193 non-coding SNPs, with an additional 15 SNPs potentially regulating through long-range chromatin interactions. Mechanistic analysis showed that coding SNPs regulate gene expression by altering codon translation rates or mRNA stability, while non-coding SNPs regulate transcription by affecting transcription factor binding. Phenotypic association analysis demonstrated that all 213 SNPs can cause ≥2-fold differences in abdominal fat weight, with 182 SNPs causing ≥3-fold differences. This study successfully identified 213 functional SNPs affecting abdominal fat deposition in broilers and revealed their molecular basis for regulating fat metabolism through multiple mechanisms, providing important genetic markers for low-fat breeding in broilers. Full article

The development of hepatic steatosis in geese is a complex, multistage process involving genes related to lipid synthesis, transport, storage, and metabolism. Key genes activated during this process include ME1 (malic enzyme 1), SCD1 (stearoyl-CoA desaturase), ACSL1 (acyl-CoA synthetase long-chain family member 1), and ELOVL6 (elongation of very-long-chain fatty acids protein 6). The expression of these genes varies depending on the tissue, breed, and metabolic context. Geese possess a unique ability to develop hepatic steatosis (fatty liver) without accompanying inflammation or liver damage. This condition typically arises from overfeeding, either through carbohydrates or fats, leading to significant triglyceride accumulation in hepatocytes. Importantly, this state remains reversible and is considered non-pathological. The physiological and molecular changes observed in overfed geese, particularly regarding liver lipid accumulation and serum enzyme activity, closely resemble those found in human non-alcoholic fatty liver disease (NAFLD). This similarity makes geese an excellent biomedical model for studying NAFLD. Overfeeding initiates a cascade of enzymatic reactions that regulate lipid metabolism at the genetic level. These reactions decrease circulating free fatty acids and glucose while promoting triglyceride storage in the liver. The aim of this study is to synthesize current knowledge on the genetic regulation of fatty acid metabolism in geese, highlighting how these genes coordinate the processes of activation, desaturation, synthesis, and elongation during induced steatosis. Moreover, the summarized effects of different diet supplements will enhance goose feeding strategies for foie gras production. Full article

Background: As a key rice breeding resource, aromatic rice is widely cultivated in agriculture due to its unique aroma. Badh2 mutations cause function loss, enabling rice’s characteristic aroma. Methods: In this study, we analyzed several badh2 mutation types across 8 japonica and 16 indica aromatic rice lines. Based on the 7 bp deletion in badh2-E2 identified in japonica aromatic lines, we developed a multiplex-ready PCR assay for badh2 genotyping. Additionally, leveraging the deletion mutation in badh2-E7 from the indica aromatic line Yexiang, we designed a KASP marker. Results: All 8 japonica aromatic lines carried a 7 bp deletion in badh2-E2, while 12 indica aromatic lines harbored an 8 bp deletion in badh2-E7, and 4 additional indica aromatic lines exhibited an 8 bp deletion in badh2-E2. The multiplex-ready PCR assay was used to screen 200 individual plants from the aromatic rice line Jia 58: 199 plants showed the expected results, while the remaining 1 exhibited two fluorescent signal peaks—suggesting that it may be a heterozygous individual. Using the KASP marker, we performed genotyping analysis on F₇ progeny individuals derived from the cross between Yexiang (aromatic line) and Yuenongsimiao (non-aromatic line). Combined with phenotypic observations, we successfully screened out an elite aromatic line named Zhexiangzhenhe, which not only possesses aroma but also maintains superior agronomic traits. Conclusions: The multiplex-ready PCR assay and KASP markers facilitate high-throughput genotyping in large-scale breeding populations, providing breeders with a rapid and efficient selection tool to accelerate aromatic trait improvement in rice. Full article

The absorption, transport, and distribution of antibiotics in animals are influenced by the composition and function of the intestinal microbial community. However, most existing studies have focused on intensive farming systems involving the artificial addition of antibiotics. For free-range local chicken breeds in mountainous areas without antibiotic additives, systematic research on the presence of antibiotic residues in their muscle tissues and their association with the gut microbiota is lacking. Therefore, in this study, mountainous free-range Lueyang black-bone chickens were selected as the research subjects, employing non-targeted metabolomics and microbiomics to analyze the distribution of antibiotics in intestinal tissues (duodenum and caecum) and muscle tissues (breast and leg muscles), and their correlations with the intestinal microbiota. Metabolomics detected 47 antibiotics in intestinal tissues and 22 in muscle tissues, with 9 common to both tissues, including clinically and veterinary relevant antibiotics such as oxacillin, kanamycin, and tobramycin. Microbiomics analysis indicated significant differences in microbial communities between the duodenum and caecum at the genus level. LEfSe analysis identified seven characteristic genera in the duodenum (e.g., Bacteroides, Alistipes) and five in the caecum (e.g., Lactobacillus, Ureaplasma). Pearson correlation analysis further revealed that these shared antibiotics were significantly associated with the differential genera in the intestine. For instance, oxacillin exhibited a positive correlation with both Bacteroides and Alistipes. Kanamycin was positively correlated with Alistipes, whereas tobramycin showed a negative correlation with Bacteroides. These results indicate that antibiotic residues were present in both intestinal and muscle tissues of Lueyang black-bone chickens raised under free-range mountainous conditions. The nine antibiotics common to both tissues are likely absorbed in the intestines and transported to muscles via the bloodstream. It is hypothesized that the gut microbiota may play a potential regulatory role in this process, providing a theoretical basis for understanding microecological mechanisms under environmental antibiotic exposure. Full article

As a major source of high-quality protein in China, duck meat such as the renowned Beijing Duck plays a critical role in the poultry industry. Sansui duck, a prized native breed, is valued for its tender meat and rich flavor, yet molecular mechanisms underlying its meat quality remain poorly studied. This study employed metabolomics and proteomics techniques to conduct a comprehensive comparative analysis of the breast and thigh muscles from 90-day-old (90X, 90T) and 468-day-old (468X, 468T) Sansui ducks. The meat quality traits indicated that the shear force and redness (a*) were significantly higher in the 468T and 468X groups compared to the 90X and 90T groups (p < 0.05). Similarly, the shear force values of the 90T and 468T groups were significantly higher than those of the 90X and 468X groups (p < 0.05). Quantitative proteomics analysis revealed differentially expressed proteins (DEPs) significantly enriched in oxidative phosphorylation and ribosomal biogenesis pathways. Non-targeted metabolomics identified differentially expressed metabolites (DEMs) concentrated in amino acid and lipid metabolism pathways. Correlation analysis indicated that in the comparison between 90X and 468X, 18 DEPs and 10 DEMs were closely associated with fleshiness, whereas in the comparison between 468X and 468T, 23 DEPs and 19 DEMs were closely associated with fleshiness. Integrating proteomics and metabolomics data analysis, proteins such as A0A8B9TTI1, R0JRM6, and A0A8B9SQI5, along with metabolites including L-lysine, L-pyrrolidone, and γ-aminobutyric acid from lysine degradation, butanoate metabolism, and 2-oxocarboxylic acid metabolism pathways, can be proposed as key factors influencing meat quality through pathways including lysine degradation, butanoate metabolism, and 2-oxocarboxylic acid metabolism in older ducks. In contrast, the protein R0JXJ3 and metabolites choline and L-glutamine may determine meat quality differences between anatomical sites through the ABC transporter pathway. These findings provide molecular insights and potential biomarkers for genetic breeding and meat quality improvement in Sansui ducks. Full article

This study investigated the morphometric characteristics of adenohypophyseal thyrotrophs and circulating thyroid hormone profiles in dromedary camels (Camelus dromedarius) in relation to age and lactation status. Clinically healthy Brela breed camels were divided into lactating female, and non-lactating female groups across two age categories (5–10 years and ≥11 years), with fifty animals per group. Blood samples were collected before slaughter and pituitary glands were collected post-slaughter and processed for immunohistochemical detection of thyroid-stimulating hormone (TSH) using anti-porcine TSHβ antibody, while morphometric measurements of thyrotrophs were conducted through image analysis. Plasma concentrations of TSH, triiodothyronine (T₃), and thyroxine (T₄) were quantified using validated ELISA and enzyme immunoassay kits. Group differences were analyzed using one-way ANOVA followed by post hoc comparisons, with statistical significance set at p < 0.05. Morphometric analysis revealed that lactating female camels exhibited significantly higher thyrotroph counts compared with non-lactating counterparts, whereas non-lactating females displayed larger cell and nuclear dimensions. Age influenced these patterns, with older camels showing hypertrophied thyrotrophs but reduced functional plasticity compared to younger animals. Plasma hormone assays demonstrated that non-lactating camels had higher TSH and T₄ concentrations, while lactating camels maintained elevated T₃ levels, suggesting enhanced peripheral conversion of T₄ to T₃ during milk production. Additionally, younger camels exhibited higher T₃ concentrations than older animals, indicating age-related decline in thyroidal activity. These findings highlight the dynamic regulation of the hypothalamic–pituitary–thyroid axis in camels, demonstrating how lactation and age shape thyroidal morphology and function to meet diverse physiological demands. These findings not only broaden the comparative endocrinology of underexplored species but also provide physiopathological insights relevant to farm animal management, lactation efficiency, and adaptive metabolism in harsh environments. Full article

Low temperature severely restricts maize seedling establishment and yield in northern China, but the proteomic basis of low-temperature tolerance in maize remains unclear. This study used TMT-labeled quantitative proteomics combined with data-independent acquisition (DIA) and liquid chromatography–tandem mass spectrometry (LC-MS/MS) to analyze dynamic proteome changes in two maize inbred lines (low-temperature-tolerant B144 and low-temperature-sensitive Q319) at the three-leaf stage under 5 °C treatment. A total of 4367 non-redundant proteins were identified. For differentially expressed proteins (DEPs, fold change >2.0 or <0.5, ANOVA-adjusted p < 0.05, false discovery rate [FDR] < 0.05), B144 showed exclusive upregulation under stress (6 DEPs at 24 h; 16 DEPs at 48 h), while Q319 exhibited mixed regulation (9 DEPs at 24 h: 6 upregulated, 3 downregulated; 21 DEPs at 48 h: 19 upregulated, 2 downregulated). Functional annotation indicated that ribosomal proteins, oxidoreductases, glycerol-3-phosphate permease, and actin were significantly upregulated in both lines. Pathway enrichment analysis revealed associations with carbohydrate metabolism, amino acid biosynthesis, and secondary metabolite synthesis. Weighted gene co-expression network analysis (WGCNA) identified genotype-specific expression patterns: B144 showed differential expression of proteins related to acetyl-CoA synthetase and fatty acid β-oxidation at 24 h and of proteins related to D-3-phosphoglycerate dehydrogenase at 48 h; Q319 showed differential expression of proteasome-related proteins at 24 h and of proteins related to elongation factor 1α (EF-1α) at 48 h. Venn analysis found no shared DEPs between the two lines at 24 h but four overlapping DEPs at 48 h. These results clarify proteomic differences underlying low-temperature tolerance divergence between maize genotypes and provide candidate targets for molecular breeding of low-temperature-tolerant maize. Full article

The production of facility vegetables is of great significance but there are still limitations to this production in terms of yield and quality. Optical sensing technology offers a rapid and non-destructive solution for phenotypic analysis, which is superior to traditional destructive methods. This article reviews and analyzes nine optical sensing technologies, including RGB imaging, and introduces the application of various algorithms in combination with detection principles throughout the entire growth cycle as well as key phenotypic characteristics of facility vegetables. Each technology has its advantages. For example, RGB and multi/high-spectrum technologies are the most frequently used while thermal imaging is particularly suitable for early detection of non-biological and biological stress responses, and these technologies can effectively obtain physiological, biochemical, yield, and quality information about crops. However, current research mainly focuses on laboratory verification and there is still a significant gap when it comes to practical production. Future progress will depend on the integration of multiple sensing technologies, data analysis based on artificial intelligence, and improvements in model interpretability. These developments will be crucial for ultimately achieving precise breeding and intelligent greenhouse management systems, and will gradually transition from basic phenotypic analysis to comprehensive decision support systems. Full article