Search Results (1,650)

Nuclear Factor Y C (NF-YC) transcription factors (TFs) are central regulators of plant development and stress adaptation. However, there remains a gap in identifying NF-YC gene family members in blueberry (Vaccinium corymbosum), a globally significant fruit crop renowned for its nutritional value and good adaptability. In this study, a total of 31 NF-YC genes (designated VcNF-YC1–31) were identified in the blueberry genome, and their basic physicochemical properties, gene structures, motif patterns, and conserved domains were investigated using bioinformatic methods. The cis-acting elements in the promoters of VcNF-YCs were mainly enriched in phytohormone signaling, metabolism, and stress response. qRT-PCR analysis showed that VcNF-YCs were expressed at higher levels in leaves than in roots and stems. Transcriptional profiling revealed rapid upregulation of 24, 25, and 16 VcNF-YC genes upon ABA, salt, and cold treatments, respectively, indicating stress-specific induction patterns. The results of the yeast transformation assay revealed that VcNF-YC10 and VcNF-YC15 lacked transcription-activating activity. The results of tobacco leaf injection revealed that these two TFs were localized in the nucleus. These findings indicate the potentially important roles in abiotic stress responses of blueberry, offering potential targets for molecular breeding to enhance plant resilience. Full article

The common bean (Phaseolus vulgaris L.) is a staple legume crop for the Balkan Peninsula, mainly used for food. A large range of landraces well adapted to the local climate are maintained by farmers. The aim of this study was to estimate in field conditions the variability in morphology and seed biochemical composition of fourteen local common bean genotypes. Sixteen morphological and three biological characteristics were evaluated. Considerable morphological variation was found among genotypes. Thirteen genotypes possessed a determinate growth habit, and one of them an indeterminate one. Plant weight without pods, total weight, and the number and weight of pods per plant displayed the highest variation coefficient (CV%) with 54.5, 44.2, 45, and 37.6%, respectively. According to the seed shape, the variation was among kidney, cuboid, and oval. Seed energy value varied from 339 to 347 kcal/100 g, the amount of protein from 21.8 to 27%, lipids content from 1.6 to 2.5%, carbohydrates from 54 to 60%, ash from 4.6 to 5.4%, dietary fibers from 3.3 to 5.9%, tannins from 14 to 21%, phenols from 1.3 to 17.2 mg/g, and antitrypsin activity from 1.2 to 3.1 units/mg FW. Genotypes were classified according to the earliness, plant and seed characteristics, and yield. Genetic material was discerned useful for future research and breeding purposes. Full article

South African cattle comprise diverse breeds with distinct evolutionary histories, potentially reflecting differences in recombination landscapes. This study assessed genome-wide recombination rates and hotspots in Bonsmara (n = 190) and Nguni (n = 119) cattle using three-generation half-sib pedigrees genotyped with the Illumina Bovine SNP50 BeadChip. Phasing across 29 autosomes was conducted using SHAPEIT v2, and crossover events were inferred using the DuoHMM algorithm. The total number of crossover events detected was higher in Nguni (n = 8982) than in Bonsmara (n = 7462); however, the average recombination rate per 1 Mb window was significantly higher in Bonsmara (0.31) compared to Nguni (0.18) (p < 0.01). This apparent discrepancy reflects differences in genomic distribution and crossover clustering across breeds, rather than overall recombination frequency. A critical limitation of the study is the reliance on half-sib families with small family sizes, which may underestimate recombination rates due to limited meiotic sampling and increased variance in crossover detection. We identified 407 recombination hotspots in Bonsmara and 179 in Nguni, defined as intervals exceeding 2.5 standard deviations above the mean recombination rate. Genes such as PDE1B and FP which are associated with productions traits were located within hotspot-enriched regions. However, functional causality between these genes and local recombination activity remains unverified. Our results provide statistically supported evidence for breed-specific recombination patterns and hotspot distributions, underscoring the importance of incorporating recombination architecture into genetic improvement strategies for South African cattle. Full article

In this study, 944 Subo Merino sheep, a high-quality fine wool breed, were selected as research subjects. The SNP typing of the FAT3 gene was performed using the Fluidigm BiomarkTM HD system, and 11 missense mutation sites were identified. The analysis of population polymorphism of single-nucleotide polymorphisms was conducted. It is noteworthy that a substantial strong linkage disequilibrium was identified between SNP 5 and SNP 6 (r² > 0.8). The association between SNPs of the FAT3 gene and wool traits showed that multiple SNPs were significantly correlated with several different wool traits (p < 0.05). Furthermore, the investigation delved into the impact of the FAT3 gene on wool fiber through the utilization of quantitative polymerase chain reaction (qPCR), which yielded findings that this gene was notably expressed in fine wool fiber (FW) (p < 0.001). To predict the subcellular localization and protein transmembrane structure of FAT3, we employed the PSORT II Prediction and TMHMM online software. It was determined that the protein contains a transmembrane domain. This study provides molecular markers for the improvement of the selection and breeding of ultrafine-wool sheep and offers experimental evidence for accelerating the genetic breeding of sheep. Full article

Individual cow identification is a prerequisite for automatically monitoring behavior patterns, health status, and growth data of each cow, and can provide the assistance in selecting excellent cow individuals for breeding. Despite high recognition accuracy, traditional implantable electronic devices such as RFID (i.e., Radio Frequency Identification) can cause some degree of harm or stress reactions to cows. Image-based methods are widely used due to their non-invasive advantages, but these methods have poor adaptability to different environments and target size, and low detection accuracy in complex scenes. To solve these issues, this study designs a Dy_Conv (i.e., dynamic convolution) module and innovatively constructs a Dynamic_Bottleneck module based on the Dy_Conv and S2Attention (Sparse-shift Attention) mechanism. On this basis, we replaces the first and fourth bottleneck layers of Resnet50 with the Dynamic_Bottleneck to achieve accurate extraction of local features and global information of cows. Furthermore, the QAConv (i.e., query adaptive convolution) module is introduced into the front end of the backbone network, and can adjust the parameters and sizes of convolution kernels to adapt to the scale changes in cow targets and input images. At the same time, NAM (i.e., normalization-based attention module) attention is embedded into the backend of the network to achieve the feature fusion in the channels and spatial dimensions, which contributes to better distinguish visually similar individual cows. The experiments are conducted on the public datasets collected from different cowsheds. The experimental results showed that the Rank-1, Rank-5, and mAP metrics reached 96.8%, 98.9%, and 95.3%, respectively. Therefore, the proposed model can effectively capture and integrate multi-scale features of cow body appearance, enhancing the accuracy of individual cow identification in complex scenes. Full article

Background: Primordial germ cells (PGC) are the progenitor cells of sperm and eggs during the embryonic stage. The maternal gene vasa has been widely studied for its role in PGC origin, and other genes like dead end (dnd) have also been identified. Objectives: Spotted sea bass is an important economic marine fish, and the study of its germ cell characteristics provides important basic data for future population breeding and protection. Methods: In this study, we cloned the full-length sequences of Lmvasa (2384 bp, encoding 1905 aa) and Lmdnd (1523 bp, encoding 386 aa) using RACE. Temporal and spatial expression patterns of Lmvasa and Lmdnd in embryos and gonads were analyzed by PCR, immunohistochemistry, and in situ hybridization. We also used microinjections of chimeric RNA containing GFP and Lmvasa 3′ UTR to visualize PGCs. Results: Our results showed that Lmvasa and Lmdnd are expressed primarily in early embryonic development (pre-blastula stage) and were expressed only in the gonads. Immunohistochemistry revealed abundant expression of Lmvasa and Lmdnd proteins in spermatogonia, weak expression in spermatocytes, and no expression in spermatozoa. In ovaries, both genes were expressed throughout oogenesis. Furthermore, PGCs in spotted sea bass belonged to an early localization pattern. Microinjection experiments demonstrated that Lmvasa 3′ UTR effectively labeled PGCs in embryos of spotted sea bass, zebrafish, and medaka. Conclusions: These findings may contribute to understanding PGC development in spotted sea bass and other Percidae. Full article

Livestock plays a crucial role in the global food system, not only as an important source of nutrients but also as a means of economic and social well-being. It constitutes a critical parameter of agricultural production in Mediterranean countries, with the majority of farms still having a relatively small herd size and depending largely on family labor. The purpose of this study is to record and evaluate the perceptions of livestock farmers in the Region of Western Macedonia, Greece (which represents a typical paradigm of an agricultural region), regarding the future prospects and the actions taken to ensure the sustainability of their farms. The research is based on a survey carried out from May to October, 2024, on ruminant farmers. Selective breeding and crossbreeding with higher-productivity breeds are some of the genetic improvements that are generally applied to increase productivity and were, therefore, investigated in this study. Through gradual crossbreeding, farmers attempt to improve the composition of their initial herds by incorporating high-productivity traits—although without officially participating in any recognized improvement program. This increases the risk of extinction for indigenous breeds, which are abandoned for use by the farmers. Our results also showed that most livestock farms derive from inheritances, with many livestock farmers practicing grazing mainly in mountainous areas and still rearing indigenous breeds. From the farmers’ point of view, more information and education regarding market conditions are needed. Furthermore, the sustainability of farms largely depends on subsidies, which are crucial due to difficulties in economic viability, particularly in mountainous areas. Encouraging the support of market differentiation and public awareness for the nutritional value of products derived from local breeds may serve as a promising agrobiodiversity conservation strategy. Full article

Accurate genomic prediction of complex phenotypes is crucial for accelerating genetic progress in swine breeding. However, conventional methods like Genomic Best Linear Unbiased Prediction (GBLUP) face limitations in capturing complex non-additive effects that contribute significantly to phenotypic variation, restricting the potential accuracy of phenotype prediction. To address this challenge, we introduce a novel framework based on a self-supervised, pre-trained encoder-only Transformer model. Its core novelty lies in tokenizing SNP sequences into non-overlapping 6-mers (sequences of 6 SNPs), enabling the model to directly learn local haplotype patterns instead of treating SNPs as independent markers. The model first undergoes self-supervised pre-training on the unlabeled version of the same SNP dataset used for subsequent fine-tuning, learning intrinsic genomic representations through a masked 6-mer prediction task. Subsequently, the pre-trained model is fine-tuned on labeled data to predict phenotypic values for specific economic traits. Experimental validation demonstrates that our proposed model consistently outperforms baseline methods, including GBLUP and a Transformer of the same architecture trained from scratch (without pre-training), in prediction accuracy across key economic traits. This outperformance suggests the model’s capacity to capture non-linear genetic signals missed by linear models. This research contributes not only a new, more accurate methodology for genomic phenotype prediction but also validates the potential of self-supervised learning to decipher complex genomic patterns for direct application in breeding programs. Ultimately, this approach offers a powerful new tool to enhance the rate of genetic gain in swine production by enabling more precise selection based on predicted phenotypes. Full article

Drought stress poses a significant threat to tree growth, making the development of drought-resistant species essential for ecological restoration. WRKY transcription factors are critical regulators of plant drought responses; however, the role of WRKY22 in the woody species Populus ussuriensis K. remains unclear. In this study, the PuWRKY22 gene was cloned from P. ussuriensis via homologous cloning and was found to be highly expressed in leaves and responsive to abscisic acid (ABA) signaling. Subcellular localization confirmed that PuWRKY22 is a nuclear protein. Using fluorescein enzyme complementation assays, PuWRKY22 was shown to bind specifically to W-box cis-elements, indicating its function as a transcriptional regulator. Under ABA and osmotic (sorbitol) stress, the seed germination rate, root growth, and biomass of tobacco and Populus davidiana × Populus bolleana strains overexpressing PuWRKY22 were significantly increased. Additionally, these overexpressed strains exhibited a reduction in reactive oxygen species (ROS) accumulation and a decrease in membrane lipid peroxidation. Transcriptomic analyses revealed that PuWRKY22 activates expression of the ABA receptor gene Ptr.PYL4 (Potri.006G104100.v4.1), which regulates stomatal closure to minimize water loss. Consistent with this, stomatal observations and photosynthetic measurements demonstrated that PuWRKY22 enhances drought tolerance by protecting photosystem II and preserving chlorophyll content. Collectively, this study elucidates the molecular mechanism by which PuWRKY22 enhances drought resistance in woody plants through ABA signaling, providing a foundation for breeding drought-tolerant forest species. Full article

The internal transcribed spacer (ITS) is one of the most extensively utilized in the taxonomy of the genus Morus due to its generally concerted evolution. Although non-concerted evolution of nuclear ribosomal DNA (nrDNA) has been reported in some species, genome-wide nrDNA characteristics in the genus Morus remain poorly understood. In this study, 158 single-nucleotide polymorphisms (SNPs) and 15 insertions and deletions (InDels) were identified within the nrDNA regions of 542 mulberry accessions representing sixteen Morus species. These wide occurrences of heterogeneous SNPs and InDels revealed the intra-individual polymorphism within the nrDNA region of Morus, indicating the incomplete concerted evolution of nrDNA. Notably, 66 out of 158 SNPs and 13 out of 15 InDels were localized within the ITS regions (ITS1-5.8S-ITS2), indicating a high degree of polymorphism in the ITS, which was further validated through classical cloning and Sanger sequencing methodologies. The 13/16 bp InDel located in the ITS1 region was utilized to develop a rapid and reliable cleaved amplified polymorphic sequence (CAPS) marker-based method for distinguishing M. alba and M. notabilis from other Morus species, eliminating the need for a clone-based sequencing step or comparative phenotypic analysis. Phylogenetic analysis based on nrDNA SNPs from 542 mulberry accessions revealed six distinct clades, corresponding to the six Morus species. These findings offer novel new insights into the taxonomy, conservation, and breeding improvement of Morus species. Full article

Rice blast is one of the main diseases of rice, causing severe economic losses to agricultural production; thus, the search for blast resistance is a top priority for rice breeding. When challenged by the blast causal fungus Magnaporthe oryzae the expression level of OsMAPKKK69 gene in rice cultivar Nipponbar was found to increase significantly. Such an induction was also found in a different genetic material, cultivar Shufanggaonuo, indicating that OsMAPKKK69 plays an important role in blast disease response. However, the function of OsMAPKKK69 remains unclear. In this study, wild type ZH11 was selected as the background material to investigate the expression and functions of OsMAPKKK69 in rice disease resistance by constructing knockout mutants. The results showed that OsMAPKKK69 is mainly expressed in four-week-old shoots and localized in cell membrane, cytoplasm, and nucleus. The two allelic knockout mutants, osmapkkk69-1 and osmapkkk69-2, were more resistant to M. oryzae and bacterial blight Xanthomonas oryzae pv. Oryzae (Xoo). Further agronomic trait analysis revealed that the osmapkkk69-1 and osmapkkk69-2 mutants had reduced plant height, smaller grain size, a significant increase in tillering number, but also a significant increase in yield per plant. Our results show that OsMAPKKK69 is involved in the immune response of rice by negatively regulating the resistance to rice blast and blight diseases, and in regulating important agronomic traits. This study lays a foundation for revealing the molecular mechanism of OsMAPKKK69 in the immune response to rice diseases and provides novel genetic resources for rice breeding. Full article

Local adaptation allows animal populations to persist in diverse and changing environments, yet its genomic underpinnings remain poorly characterized in livestock. Chinese indigenous pigs, renowned for their rich phenotypic and ecological diversity, offer a powerful model for investigating environmental adaptation. Here, we integrated whole-genome resequencing data, environmental variables, genotype–environment association (GEA) analyses, and functional annotation to explore the adaptive genomic landscape of 46 native pig breeds across China. Based on 578 individuals and 17.7 million SNPs, we performed genome-wide GEA using latent factor mixed models (LFMMs), identifying 8644 SNPs significantly associated with environmental factors, including 310 linked to precipitation in the wettest quarter (BIO16). Redundancy analysis (RDA) and gradient forest modeling identified BIO16 as a major environmental driver of genomic variation. Functional annotation of BIO16-associated SNPs revealed significant enrichment in regulatory elements and genes highly expressed in the lung, spleen, hypothalamus, and intestine, implicating immune and metabolic pathways in local adaptation. Among the candidate loci, MS4A7 exhibited strong association signals, population differentiation, and tissue-specific regulation, suggesting a role in precipitation-mediated adaptation. This work enhances our understanding of livestock adaptation and informs climate-resilient conservation and breeding strategies. Full article

Background: Aedes albopictus, the tiger mosquito, is an invasive exotic species native to Southeast Asia, currently established in Europe, including Spain and the region of Navarre. This vector poses an emerging public health threat due to its ability to transmit dengue, Zika, and chikungunya viruses, which cause diseases in humans. This study presents novel findings by documenting the progression of the invasion of Aedes albopictus in the Navarre region in northern Spain, tracing its status from initial absence to its definitive establishment in certain areas. Methods: Surveillance in Navarre within the LIFE-IP NAdapta-CC project was conducted through a network of strategically placed ovitraps and adult traps to collect eggs and adult mosquitoes. Awareness campaigns and outreach events were organized to inform local authorities and the public about monitoring results and preventive measures. Results: Monitoring confirms Aedes albopictus’ expansion across Navarre despite training, information dissemination, and control efforts, including entomological containment in targeted areas. Conclusions: Eliminating breeding sites remains the most effective strategy to limit its spread. Complete eradication is unlikely given its invasive nature, and the species is expected to expand and colonize at least part of the region in the coming years. Full article

Use of sedation for disbudding is common practice in a number European countries, with United Kingdom (UK) practices adopting its use. This study assessed the effects of disbudding with and without xylazine sedation on growth rates and calf health on a UK calf rearing unit. Data was collected from 485 dairy crossed with beef breed calves between April and August 2024 from a single calf rearing unit in England. Calves were purchased from multiple farms across the UK and arrived on site at approximately 21 days of age. Calves were disbudded—and, in the case of male calves, surgically castrated—at approximately three weeks after arrival on farm. Pens of calves were assigned to undergo disbudding with (SED, n = 238) or without (CTL = 234) xylazine sedation at a dose of 0.2 mg/kg administered intramuscularly. Calves from both groups were provided with local anaesthetic (procaine hydrochloride) as a cornual nerve block and a non-steroidal anti-inflammatory drug (meloxicam). While other studies have demonstrated some behavioural and physiological indicators of pain to be reduced with sedation, this study found that calves in the SED group had a reduced daily liveweight gain (DLWG) of 0.14 kg/day in the short term (mean 20 days) following disbudding (p < 0.001), but there was no difference in growth rates in the medium-term (mean 43 days) post-disbudding (p = 0.30). Some of this difference could be explained by the slightly higher DLWG pre-disbudding in the CTR group, and it is likely that the physiological impacts of sedation accounted for the rest of this difference. This initial reduction in DLWG following disbudding with sedation should be considered by vets, especially on farms where growth rates may already be compromised. In the sedated calves, 19.3% exhibited either some movement or entry into sternal recumbency. Specifically, a light plane of sedation with calves entering sternal recumbency was associated with a reduction in DLWG of 0.89 kg/day compared to 0.98 kg/day for those that remained in lateral recumbency throughout (p = 0.008). The light plane of sedation may have created additional calf stress, impacted feeding behaviours, and impinged welfare, with further work needed to establish the reasons for insufficient sedation. There was no difference in the number of post-disbudding treatment outcomes between calves disbudded with and without sedation (p = 0.97). Full article

A necessary step towards the development of genetic diversity is the protection of the valuable genetic resources of farm animals that are at risk of extinction. We analyzed 375 individuals of nine local sheep breeds bred in Central Europe (Carpathia area) from Czech Republic, Slovakia, Poland, Ukraine, and Romania using a panel of 13 microsatellite markers to investigate genetic differences and evaluate the genetic structure among and within breeds, thereby improving future breeding and conservation strategies. The mean number of alleles was 8.84, the mean number of effective alleles was 4.76, and the polymorphism information content (PIC) was 0.79. Diversity was measured using principal coordinate analysis (PCoA) as well as genetic structure, which revealed two main clusters. The first cluster was the Czech Wallachian sheep (CVA) and the Świniarka (SWI). The second cluster consisted the Improved Wallachian sheep (IVA), the Šumava sheep (SUM), the Slovak Wallachian sheep (SVA), the Polish Mountain sheep (POG), the Uhruska sheep (UHR), the Ukrainian sheep (UKR) and the Tsurcana sheep (TUR). The values of genetic distance and the fixation coefficient indicate sufficient differences between the analyzed breeds (Gst = 0.052 and Fst = 0.063). Negative values of the inbreeding coefficient also confirmed the predominance of outbreeding (Fis = −0.015). The results obtained may be helpful in breeding programs and conservation plans for local sheep breeds, as their genetic resources must be preserved to maintain an adequate level of biodiversity in animal husbandry. Full article