A5100626097- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Cancer-related molecular mechanisms research
- Animal Genetics and Reproduction
- Genomics and Phylogenetic Studies
- Animal Behavior and Welfare Studies
- Reproductive Physiology in Livestock
- Molecular Biology Techniques and Applications
- Ruminant Nutrition and Digestive Physiology
- Effects of Environmental Stressors on Livestock
- Astro and Planetary Science
- Geomagnetism and Paleomagnetism Studies
- Methane Hydrates and Related Phenomena
- Solar and Space Plasma Dynamics
- Microbial infections and disease research
- Spacecraft and Cryogenic Technologies
- Gut microbiota and health
- Epigenetics and DNA Methylation
- Plant Pathogenic Bacteria Studies
- Planetary Science and Exploration
- Legume Nitrogen Fixing Symbiosis
- Plant Virus Research Studies
- Advanced biosensing and bioanalysis techniques
- Single-cell and spatial transcriptomics
- Hepatitis C virus research
Tianjin Medical University General Hospital
2024-2025
Scotland's Rural College
2020-2025
Roslin Institute
2020-2025
Shanxi Medical University
2017-2025
Shanxi Academy of Medical Sciences
2025
Chinese Academy of Agricultural Sciences
2022-2025
South China Agricultural University
2022-2025
Tobacco Research Institute
2022-2025
Anhui Medical University
2024
Shanghai Jiao Tong University
2024
Abstract The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking polymorphisms variation phenotypes, helping fundamental biological discovery and exploitation animal breeding human biomedicine. Here we show results from the pilot phase PigGTEx by processing 5,457 RNA-sequencing 1,602 whole-genome sequencing samples passing quality control pigs. We build pig...
Abstract Transcriptome-wide association study (TWAS) is a powerful approach for investigating the molecular mechanisms linking genetic loci to complex phenotypes. However, complexity of TWAS analytical pipeline including construction gene expression reference panels, prediction, and analysis using data from genome-wide studies (GWAS) poses challenges in many species. In this study, we provide Farm Animal Genotype-Tissue Expression (FarmGTEx) TWAS-server, an interactive user-friendly...
By uniformly analyzing 723 RNA-seq data from 91 tissues and cell types, we built a comprehensive gene atlas studied tissue specificity of genes in cattle. We demonstrated that tissue-specific significantly reflected the tissue-relevant biology, showing distinct promoter methylation evolution patterns (e.g., brain-specific evolve slowest, whereas testis-specific fastest). Through integrative analyses those with large-scale genome-wide association studies, detected relevant tissues/cell types...
The precise assessment of vascular heterogeneity in brain tumors is vital for diagnosing, grading, predicting progression, and guiding treatment decisions. However, currently, there a significant shortage high-resolution imaging approaches. Herein, we propose contrast-enhanced susceptibility-weighted (CE-SWI) utilizing the minimalist dextran-modified Fe
The functional annotation of genomes, including chromatin accessibility and modifications, is important for understanding effectively utilizing the increased amount genome sequences reported. However, while such has been well explored in a diverse set tissues cell types human model organisms, relatively little data are available livestock hindering our complex trait variation, domestication, adaptive evolution. Here, we present first complete global landscape regulatory elements cattle...
Abstract Background Cross-species comparison of transcriptomes is important for elucidating evolutionary molecular mechanisms underpinning phenotypic variation between and within species, yet to date it has been essentially limited model organisms with relatively small sample sizes. Results Here, we systematically analyze compare 10,830 4866 publicly available RNA-seq samples in humans cattle, respectively, representing 20 common tissues. Focusing on 17,315 orthologous genes, demonstrate...
Abstract Chicken is a valuable model for understanding fundamental biology, vertebrate evolution and diseases, as well major source of nutrient-dense lean-protein-enriched food globally. Although it the first non-mammalian amniote genome to be sequenced, chicken still lacks systematic characterization functional impacts genetic variants. Here, through integrating 7,015 RNA-Seq 2,869 whole-genome sequence data, Genotype- Tissue Expression (ChickenGTEx) project presents pilot reference...
Abstract Background Structural variations (SVs) have significant impacts on complex phenotypes by rearranging large amounts of DNA sequence. Results We present a comprehensive SV catalog based the whole-genome sequence 1060 pigs ( Sus scrofa ) representing 101 breeds, covering 9.6% pig genome. This includes 42,487 deletions, 37,913 mobile element insertions, 3308 duplications, 1664 inversions, and 45,184 break ends. Estimates breed ancestry hybridization using genotyped SVs align well with...
Staphylococcus aureus (S. aureus) is problematic for lactating mammals and public health. Understanding of mechanisms by which the hosts respond to severe invasion S. remains elusive. In this study, genome-wide expression mRNAs miRNAs in bovine mammary gland cells were interrogated at 24h after intra-mammary infection (IMI) with high or low concentrations aureus. Compared negative control quarters, a total 194 highly-confident responsive genes identified quarters concentration (109cfu/mL)...
Abstract The length of gestation can affect offspring health and performance. Both maternal fetal effects contribute to length; however, paternal contributions remain elusive. Using genome-wide association study (GWAS) in 27,214 Holstein bulls with millions records, here we identify nine genomic loci associated cattle length. We demonstrate that these GWAS signals are enriched pathways relevant embryonic development, differentially methylated regions between sperm samples long short reveal...
While studies of the regulation gene expression have generally concerned qualitative changes in selection or level a gene, much that occurs within cell involves continuous subtle optimization levels proteins used macromolecular complexes. An example is biosynthesis ribosome, which equimolar amounts nearly 80 ribosomal must be supplied by cytoplasm to nucleolus. We found transcript one protein genes Saccharomyces cerevisiae, RPL32, participates such fine tuning. Sequences from exon I RPL32...
Abstract Background Genetic improvement of wool and growth traits is a major goal in the sheep industry, but their underlying genetic architecture remains elusive. To improve our understanding these mechanisms, we conducted weighted single-step genome-wide association study (WssGWAS) then integrated results with large-scale transcriptome data for five one trait Merino sheep: mean fibre diameter (MFD), coefficient variation (CVFD), crimp number (CN), staple length (MSL), greasy fleece weight...
Abstract MicroRNAs (miRNA) are key modulators of gene expression and so act as putative fine-tuners complex phenotypes. Here, we hypothesized that causal variants traits enriched in miRNAs miRNA-target networks. First, conducted a genome-wide association study (GWAS) for seven functional milk production using imputed sequence (13~15 million) >10,000 animals from three dairy cattle breeds, i . e ., Holstein (HOL), Nordic red (RDC) Jersey (JER). Second, analyzed enrichments signals their...