A5100711597- Genetic and phenotypic traits in livestock
- Cancer-related molecular mechanisms research
- Genetic Mapping and Diversity in Plants and Animals
- Animal Genetics and Reproduction
- Mycobacterium research and diagnosis
- Diatoms and Algae Research
- Chromosomal and Genetic Variations
- Marine and coastal ecosystems
- Plant Pathogens and Fungal Diseases
- Molecular Biology Techniques and Applications
- Genomics and Chromatin Dynamics
- Water Quality Monitoring and Analysis
- Genomics and Phylogenetic Studies
- Animal health and immunology
- Epigenetics and DNA Methylation
- Mycorrhizal Fungi and Plant Interactions
- Microplastics and Plastic Pollution
- T-cell and Retrovirus Studies
- Genetic diversity and population structure
- Milk Quality and Mastitis in Dairy Cows
- Animal Nutrition and Physiology
- Cancer-related gene regulation
- Marine Biology and Environmental Chemistry
- RNA Research and Splicing
- Gene expression and cancer classification
South China Agricultural University
2023-2025
Agricultural Research Service
2020-2025
China Agricultural University
2008-2025
Beltsville Agricultural Research Center
2020-2025
University of Maryland, College Park
2020-2025
United States Department of Agriculture
2022-2025
University of Maryland, Baltimore
2025
China Pharmaceutical University
2024
Jiangnan University
2022-2023
Xiamen University
2003-2023
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...
Previous studies have shown that our understanding of species diversity within
Indigenous Chinese cattle combine taurine and indicine origins occupy a broad range of different environments. By 50 K SNP genotyping we found discontinuous distribution ancestries with extremes less than 10% in the north more 90% far south southwest China. Model-based clustering f4-statistics indicate introgression both banteng gayal into southern while sporadic yak influence or near Tibetan area validate earlier findings mitochondrial DNA analysis. Geographic patterns Y-chromosomal...
Many quantitative trait loci (QTLs) are in non-coding regions. Therefore, QTLs assumed to affect gene regulation. Gene expression and RNA splicing primary steps of transcription, so DNA variants changing (eVariants) or (sVariants) expected significantly phenotypes. We quantify the contribution eVariants sVariants detected from 16 tissues (n = 4,725) 37 traits ∼120,000 cattle (average magnitude genetic correlation between 0.13). Analyzed Bayesian mixture models, averaged across traits, cis...
Abstract To fully unlock the potential of pigs as both agricultural species for animal-based protein food and biomedical models human biology disease, a comprehensive understanding molecular cellular mechanisms underlying various complex phenotypes in how findings can be translated to other species, especially humans, are urgently needed. Here, within Farm animal Genotype-Tissue Expression (FarmGTEx) project, we build PigBiobank (http://pigbiobank.farmgtex.org) systematically investigate...
Copy number variations (CNVs) are important and widely distributed in the genome. CNV detection opens a new avenue for exploring genes associated with complex traits humans, animals plants. Herein, we present genome-wide assessment of CNVs that potentially milk composition dairy cattle. In this study, were detected based on whole genome re-sequencing data eight Holstein bulls from four half- and/or full-sib families, extremely high low estimated breeding values (EBVs) protein percentage fat...
The genus Diaporthe (syn. Phomopsis) comprises important pathogens, endophytes or saprobes with diverse host associations and worldwide distribution. Phomopsis theae is the first hitherto only recorded species on Camellia in China. aim of this study was to investigate associated symptomatic asymptomatic tissues spp. from several provinces Eighty-three strains were isolated present study. Based multi-locus (ITS, HIS, TEF1, TUB) phylogenetic analyses phenotypic characters, four novel (D....
Abstract Background Plant growth-promoting rhizobacteria (PGPR) release volatile organic compounds (VOCs), which promote plant growth. Results A potential PGPR strain GX14001 was isolated from marine samples, and the VOCs produced by significantly promoted tobacco ( Nicotiana benthamiana ) growth in a plate experiment. Based on 16S rRNA sequence alignment physiological biochemical characterization, identified as Microbacterium aurantiacum . Comparative transcriptome analysis conducted...
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...
Abstract Background Efforts to improve animal health, and understand genetic bases for production, may benefit from a comprehensive analysis of genomes epigenomes. Although DNA methylation has been well studied in humans other model species, its distribution patterns regulatory impacts cattle are still largely unknown. Here, we present the largest collection epigenomic data date. Results Using Holstein cattle, generated 29 whole genome bisulfite sequencing (WGBS) datasets 16 tissues, 47...
Abstract Objective As one of the most important ruminant breeds, Holstein cattle supply a significant portion milk and dairy for human consumption, playing crucial role in agribusiness. The goal our study was to examine molecular adaptation gastrointestinal tissues that facilitate synthesis cattle. Data description We performed RNA-seq analysis on epithelial cells from rumen, duodenum, colon at eight different time points: Days 3, 14, 28, 45, 120, 220, 305 milk, as well dry period. Samples...
Paratuberculosis (Johne's disease, JD) is a chronic and enteric disease in range of ruminants, often caused by Mycobacterium avium subspecies paratuberculosis (MAP) infection, leading to substantial economic losses worldwide. Yet, the molecular underpinning remains elusive. Here we performed RNA sequencing (RNA-seq) small (sRNA-seq) jejunum tissues from Holstein cows with three distinct statuses paratuberculosis, i.e., healthy, subclinical, clinical screen potential genes, lncRNAs, miRNAs...
High-quality semen is an essential factor for the success of artificial insemination, and revealing genetic structure pig traits helps improve quality. This study aimed to identify candidate genes associated with in three breeds (Duroc, Landrace, Yorkshire) through weighted GWAS multi-tissue transcriptome analysis. In this study, Duroc, Yorkshire, we performed four (sperm motility, sperm progressive abnormality rate, total count) using 936 pigs analysis 34 tissues RNA-seq data 5457 from...
<title>Abstract</title> Molecular quantitative trait loci (molQTL) mapping is one of the most popular approaches to systematically characterize functional impacts genomic variants, leading advanced understanding regulatory mechanisms underpinning complex traits and diseases. However, when applied high-throughput molecular phenotypes, existing molQTL tools often implement simple linear models, overlooking inter-individual relatedness, false positives insufficient statistical power. Here, we...
Abstract Understanding the molecular and cellular mechanisms underlying complex traits in pigs is crucial for enhancing genetic gain via artificial selection utilizing as models human disease biology. Here, we conducted a comprehensive genome-wide association studies (GWAS) followed by cross-breed meta-analysis 232 within-breed 12 traits, using 28.3 million imputed sequence variants 70 328 animals across 14 pig breeds. We identified 6 878 quantitative trait loci (QTL) 139 traits. Leveraging...
Due to the carrier’s role of microplastics, attached microalgae may be transported further, posing a threat marine ecosystems, especially those red tide species. By combining investigated results Dongshan Bay and Quanzhou with simulation transport trajectories using Lagrangian particle tracking model, this study systematically characteristics epimicroplastic Based on investigations respectively in summer 2022, species were learned. Results showed that totally 13 found two bays, 6 Dinophyta,...