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The Farm animal Genotype-Tissue Expression (FarmGTEx, https://www.farmgtex.org/) project has been established to develop a comprehensive public resource of genetic regulatory variants in domestic animal species, which is essential for linking genetic polymorphisms to variation in phenotypes, helping fundamental biology discovery and exploitation in animal breeding and human biomedicine. Here we present results from the pilot phase of PigGTEx (http://piggtex.farmgtex.org/), where we processed 9,530 RNA-sequencing and 1,602 whole-genome sequencing samples from pigs. We build a pig genotype imputation panel, characterize the transcriptional landscape across over 100 tissues, and associate millions of genetic variants with five types of transcriptomic phenotypes in 34 tissues. We study interactions between genotype and breed/cell type, evaluate tissue specificity of regulatory effects, and elucidate the molecular mechanisms of their action using multi-omics data. Leveraging this resource, we decipher regulatory mechanisms underlying about 80% of the genetic associations for 207 pig complex phenotypes, and demonstrate the similarity of pigs to humans in gene expression and the genetic regulation behind complex phenotypes, corroborating the importance of pigs as a human biomedical model.

Simple Summary Mastitis caused by zoonotic Staphylococcus aureus (S. aureus) is hard to cure. The cross-talk between host, pathogen, and environment influences bovine resistance to S. aureus infection. Our previous study observed that the inflammation of bovine mammary gland could be reduced by folic acid, i.e., a kind of beneficial micronutrient. However, the heterogeneity of inflammatory responses in bovine mammary epithelial cells challenged with different virulent S. aureus strains and the protective effects of folic acid on improving host defense against S. aureus infection are still unclear. RNA-seq was performed to investigate the effects of different S. aureus lineages and folic acid on the global transcriptome of bovine mammary epithelial cells (Mac-T cell line). Functional enrichment analysis indicated different S. aureus strains share few differentially expressed and spliced genes and activate host differentially inflammatory responses, and folic acid plays the protective role in host defense against the S. aureus challenge partially through activating cytoplasmic DNA sensing and tight junction pathway. This study provides novel insights into the improvement of S. aureus mastitis defense. Abstract Mastitis caused by Staphylococcus aureus (S. aureus) infection is one of the most difficult diseases to treat in dairy cattle. Exploring the biological progression of S. aureus mastitis via the interaction between host, pathogen, and environment is the key to an effective and sustainable improvement of animal health. Here, two strains of S. aureus and a strain of MRSA (Methicillin-resistant Staphylococcus aureus) isolated from cows with different inflammation phenotypes were used to challenge Mac-T cells and to investigate their effects on the global transcriptome of the cells, then to explore the potential regulatory mechanisms of folic acid on S. aureus mastitis prevention. Differential gene expression or splicing analysis showed that different strains of S. aureus led to distinct transcriptional responses from the host immune system. Folic acid could protect host defense against the challenge of S. aureus and MRSA partially through activating cytoplasmic DNA sensing and tight junction pathway. ZBP1 at the upstream of cytoplasmic DNA sensing pathway was verified and related to anti-pathogen through RNA interference. Further enrichment analysis using these transcriptome data with cattle large-scale genome-wide association study (GWAS) data confirmed that ZBP1 gene is highly associated with bovine somatic cell score (SCS) trait. Our data shed light on the potential effect of FA through regulating key gene and then protect host cells’ defense against S. aureus and MRSA.

The functional annotation of livestock genomes is crucial for understanding the molecular mechanisms that underpin complex traits of economic importance, adaptive evolution and comparative genomics. Here, we provide the most comprehensive catalogue to date of regulatory elements in the pig (Sus scrofa) by integrating 223 epigenomic and transcriptomic data sets, representing 14 biologically important tissues. We systematically describe the dynamic epigenetic landscape across tissues by functionally annotating 15 different chromatin states and defining their tissue-specific regulatory activities. We demonstrate that genomic variants associated with complex traits and adaptive evolution in pig are significantly enriched in active promoters and enhancers. Furthermore, we reveal distinct tissue-specific regulatory selection between Asian and European pig domestication processes. Compared with human and mouse epigenomes, we show that porcine regulatory elements are more conserved in DNA sequence, under both rapid and slow evolution, than those under neutral evolution across pig, mouse, and human. Finally, we provide novel biological insights on tissue-specific regulatory conservation and demonstrate that, depending on the traits, mouse or pig might be more appropriate biomedical models for different complex traits and diseases in humans through integrating comparative epigenomes with 47 human genome-wide association studies.

Characterization of genetic regulatory variants acting on the transcriptome of livestock is essential for interpreting the molecular mechanisms underlying traits of economic value and for increasing the rate of genetic gain through artificial selection. Here, we build a cattle Genotype-Tissue Expression atlas (cattle GTEx, http://cgtex.roslin.ed.ac.uk/) as part of the pilot phase of Farm animal GTEx (FarmGTEx) project for the research community based on publicly available 11,642 RNA-Seq datasets. We describe the landscape of the transcriptome across over 100 tissues and report hundreds of thousands of genetic associations with gene expression and alternative splicing for 24 major tissues. We evaluate the tissue-sharing patterns of these genetic regulatory effects, and functionally annotate them using multi-omics data. Finally, we link gene expression in different tissues to 43 economically important traits using both transcriptome-wide association study (TWAS) and colocalization analyses to decipher the molecular regulatory mechanisms underpinning such agronomic traits in cattle.

Characterization of genetic regulatory variants acting on livestock gene expression is essential for interpreting the molecular mechanisms underlying traits of economic value and for increasing the rate of genetic gain through artificial selection. Here we build a Cattle Genotype-Tissue Expression atlas (CattleGTEx) as part of the pilot phase of the Farm animal GTEx (FarmGTEx) project for the research community based on 7,180 publicly available RNA-sequencing (RNA-seq) samples. We describe the transcriptomic landscape of more than 100 tissues/cell types and report hundreds of thousands of genetic associations with gene expression and alternative splicing for 23 distinct tissues. We evaluate the tissue-sharing patterns of these genetic regulatory effects, and functionally annotate them using multiomics data. Finally, we link gene expression in different tissues to 43 economically important traits using both transcriptome-wide association and colocalization analyses to decipher the molecular regulatory mechanisms underpinning such agronomic traits in cattle.

Taking BRT line in Dalian as study object, this paper evaluates the changes of traffic flow and its environmental load corresponding to several schemes of BRT lanes with micro traffic simulator. First, the capacity of BRT lane and the being removed bus routes and bus vehicles are calculated. Second, spatial model of the corresponding area is established in the Simulating Platform, and several BRT lane schemes are built in the model, then the attributes of the corresponding traffic flows are analyzed. Third, environmental load model is used to calculate the corresponding traffic environmental loads.

Considering the fact that BRT (bus rapid transit) lines are generally constructed in built-up areas, this paper develops a method for BRT planning. The method can be used to design and optimize BRT lines in urban areas in terms of qualitative analysis and analytical calculation. Firstly, to calculate the density of bus lines on each road, Polygon Data is used to denote urban roads in GIS, and Polyline Data is used to denote bus lines. The number of overlapping bus lines could be computed with space calculation functions in GIS, and roads with a large number of bus lines can be found. Secondly, an optimization model based on the maximization of direct traveler density is developed to lay the lines one by one and form a network step by step. Finally, considering the actual situation, a BRT network of Dalian is built based on the result of qualitative analysis and analytical calculation.

FeTa films with thickness of 110 nm are fabricated on glass substrates by magnetron sputtering, and then a series of strips is designed on the FeTa films by conventional optical lithography and the ion beam etching method. Patterned FeTa strips show a tunable in-plane uniaxial magnetic anisotropy property in contrast with the magnetic isotropic property of as-deposited FeTa thin films. The magnetization reversal mechanism of the patterned FeTa strips is investigated via the in-plane angular dependences of magnetization and coercivity. The angular dependence of coercivity (ADC) is explained well in terms of the two-phase model, giving good quantitative agreement with the experimentally measured M-shaped ADC curve. The domain structure and spatial resolution magneto-optical Kerr effect measurement indicate that the smaller the strip width, the stronger will be the anisotropy field. Regarding the dynamic magnetic properties, a transformation from Debye dispersion spectrum for strips with weak anisotropy to natural resonance spectrum for strips with strong anisotropy is finally obtained. The tunable in-plane anisotropy fields of the FeTa strips result in tunable high-frequency soft magnetic properties by altering the strip width, indicating that patterned FeTa strips have great potential in high-frequency soft magnetic application fields.

Amorphous Fe nanoparticles and a nanonecklace were synthesized at room temperature by an aqueous reduction procedure, which provided a simple and potential method for volume production of ferromagnetic materials. The morphology was examined by scanning electron microscopy and transmission electron microscopy. The amorphism of Fe nanoparticles and the nanonecklace was confirmed by x-ray diffraction and electron diffraction patterns in transmission electron microscopy. The complex permittivity and permeability behaviour of amorphous iron nanoparticles/paraffin wax (NPPW) and nanonecklace/paraffin wax (NCPW) composites was investigated in 0.1–18 GHz by a coaxial method. The strongest reflection loss values of NPPW and NCPW calculated from permittivity and permeability reached −53.2 dB and −47.8 dB at 6.4 GHz and 4.6 GHz with matching thicknesses of 2.4 mm and 2.3 mm, respectively. Moreover, the frequency ranges of microwave absorption exceeding 90% were around 4.9–8.8 GHz and 3.7–6.1 GHz for NPPW and NCPW, respectively. Comparing the microwave absorption property with crystallized Fe nanostructures, we may conclude that the relatively high resistivity and low permittivity of amorphous Fe nanostructures are favourable for impedance matching, and consequently result in the attracting microwave absorption property of amorphous Fe nanostructures. Thus, amorphous iron nanoparticles and the nanonecklace prepared by a high-yield method have great potential to be a highly efficient microwave absorber.

FeNi thin films with the in-plane uniaxial anisotropy were fabricated by direct current magnetron sputtering. An FeNi/piezoelectric actuator hybrid structure was used to investigate the voltage-controlled magnetization switching. A theoretical calculation was performed to provide a simplified vision of the magnetoelastic contribution to the magnetic anisotropy. Magneto-optical Kerr effect measurements were performed and the rotation of the magnetization easy axis in the FeNi film upon application of a voltage with or without the application of a magnetic field was demonstrated. A film-thickness dependent in-plane magnetization easy axis rotation angle was observed and explained by the variation of the magnetostriction.