George E. Liu
A5065672294- Genetic and phenotypic traits in livestock
- Cancer-related molecular mechanisms research
- Genetic Mapping and Diversity in Plants and Animals
- Chromosomal and Genetic Variations
- Genomic variations and chromosomal abnormalities
- Animal Genetics and Reproduction
- Molecular Biology Techniques and Applications
- Genomics and Phylogenetic Studies
- Epigenetics and DNA Methylation
- Genomics and Chromatin Dynamics
- Genetic diversity and population structure
- RNA modifications and cancer
- Milk Quality and Mastitis in Dairy Cows
- RNA Research and Splicing
- Meat and Animal Product Quality
- Gene expression and cancer classification
- RNA and protein synthesis mechanisms
- Plant Reproductive Biology
- CRISPR and Genetic Engineering
- Reproductive Physiology in Livestock
- Cancer-related gene regulation
- MicroRNA in disease regulation
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Herpesvirus Infections and Treatments
- Single-cell and spatial transcriptomics
United States Department of Agriculture
2013-2025
Agricultural Research Service
2016-2025
Beltsville Agricultural Research Center
2015-2025
Johns Hopkins Medicine
2025
Johns Hopkins University
2025
Peking University
2009-2022
Agricultural Research Service - Northeast Area
2022
University of Maryland, College Park
2015-2021
University of California, San Diego
2020
University of Miami
2018
To understand the biology and evolution of ruminants, cattle genome was sequenced to about sevenfold coverage. The contains a minimum 22,000 genes, with core set 14,345 orthologs shared among seven mammalian species which 1217 are absent or undetected in noneutherian (marsupial monotreme) genomes. Cattle-specific evolutionary breakpoint regions chromosomes have higher density segmental duplications, enrichment repetitive elements, species-specific variations genes associated lactation immune...
A survey of genetic diversity cattle suggests two domestication events in Asia and selection by husbandry.
Major advances in selection progress for cattle have been made following the introduction of genomic tools over past 10-12 years. These depend upon Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety deficiencies inaccuracies. We present new cattle, ARS-UCD1.2, based on same animal as original to facilitate transfer interpretation results obtained from earlier version, but applying combination modern de novo assembly increase...
Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using read depth approach based on next-generation sequencing, we examined genome-wide copy differences among five taurine (three Angus, one Holstein, and Hereford) indicine (Nelore) cattle. Within mapped chromosomal sequence, identified 1265 CNV comprising ∼55.6-Mbp sequence—476 which (∼38%) have not previously been reported. We validated this...
Genomic structural variation is an important and abundant source of genetic phenotypic variation. Here, we describe the first systematic genome-wide analysis copy number variations (CNVs) in modern domesticated cattle using array comparative genomic hybridization (array CGH), quantitative PCR (qPCR), fluorescent situ (FISH). The CGH panel included 90 animals from 11 Bos taurus , three indicus composite breeds for beef, dairy, or dual purpose. We identified over 200 candidate CNV regions...
Meiotic recombination is an essential biological process that generates genetic diversity and ensures proper segregation of chromosomes during meiosis. From a large USDA dairy cattle pedigree with over half million genotyped animals, we extracted 186,927 three-generation families, identified 8.5 maternal paternal events, constructed sex-specific maps for 59,309 autosomal SNPs. The map spans 25.5 Morgans in males 23.2 females, total studied region 2,516 Mb (986 kb/cM 1,085 females). male 10%...
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...
Abstract Background Copy number variation (CNV) represents another important source of genetic complementary to single nucleotide polymorphism (SNP). High-density SNP array data have been routinely used detect human CNVs, many which significant functional effects on gene expression and diseases. In the dairy industry, a large quantity genotyping results are becoming available can be for CNV discovery understand accelerate improvement complex traits. Results We performed systematic analysis...
The intensive selection programs for milk made possible by mass artificial insemination increased the similarity among genomes of North American (NA) Holsteins tremendously since 1960s. This migration elite alleles has caused certain regions genome to have runs homozygosity (ROH) occasionally spanning millions continuous base pairs at a specific locus. In this study, signatures in NA born between 1953 and 2008 were identified comparing changes ROH three distinct groups under different...
Motivation: A high density of single nucleotide polymorphism (SNP) coverage on the genome is desirable and often an essential requirement for population genetics studies. Region-specific or chromosome-specific linkage studies also benefit from availability as many quality SNPs possible. The millions both Perlegen public domain development efficient microarray-based assay genotyping has brought up some interesting analytical challenges. Effective methods selection optimal subsets spanning...
We investigated diverse genomic selections using high-density single nucleotide polymorphism data of five distinct cattle breeds. Based on allele frequency differences, we detected hundreds candidate regions under positive selection across Holstein, Angus, Charolais, Brahman, and N'Dama. In addition to well-known genes such as KIT, MC1R, ASIP, GHR, LCORL, NCAPG, WIF1, ABCA12, found evidence for a variety novel less-known in cattle, LAP3, SAR1B, LRIG3, FGF5, NUDCD3. Selective sweeps near LAP3...
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...
Natural selection has molded evolution across all taxa. At an arguable date of around 330,000 years ago there were already at least two different types cattle that became ancestors nearly modern cattle, the Bos taurus more adapted to temperate climates and tropically indicus. After domestication, human exponentially intensified these differences. To better understand genetic differences between subspecies detect genomic regions potentially under divergent selection, animals from...
Recently, RNA sequencing (RNA-seq) has rapidly emerged as a major transcriptome profiling system. Elucidation of the bovine mammary gland by RNA-seq is essential for identifying candidate genes that contribute to milk composition traits in dairy cattle.We used massive, parallel, high-throughput, generate from glands four lactating Holstein cows with extremely high and low phenotypic values protein fat percentage. In total, we obtained 48,967,376-75,572,578 uniquely mapped reads covered...
Milk production is an economically important sector of global agriculture. Much attention has been paid to the identification quantitative trait loci (QTL) associated with milk, fat, and protein yield genetic molecular mechanisms underlying them. Copy number variation (CNV) emerging class variants which may be complex traits. In this study, we performed a genome-wide association between CNVs milk traits in 26,362 Holstein bulls cows. A total 99 candidate were identified using Illumina...
Abstract Background Health traits are of significant economic importance to the dairy industry due their effects on milk production and associated treatment costs. Genome-wide association studies (GWAS) provide a means identify genomic variants thus reveal insights into genetic architecture complex diseases. The objective this study is investigate basis seven health in cattle potential candidate genes with using GWAS, fine mapping, analyses multi-tissue transcriptome data. Results We studied...
The bovine genetic resources in China are diverse, but their value and potential yet to be discovered. To determine the diversity population structure of Chinese cattle, we analyzed whole genomes 46 cattle from six phenotypically geographically representative breeds, together with 18 Red Angus genomes, 11 Japanese black taurine indicine available previous studies. Our results showed that originated hybridization between Bos taurus indicus. Moreover, found level variation depends upon degree...
A cattle pangenome representation was created based on the genome sequences of 898 representing 57 breeds. The identified 83 Mb sequence not found in reference genome, 3.1% novel compared with 2.71-Gb reference. catalog structural variants developed from this population 3.3 million deletions, 0.12 inversions, and 0.18 duplications. Estimates breed ancestry hybridization between breeds using insertion/deletions as markers were similar to those produced by single nucleotide polymorphism–based...
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...
Duplicated sequences are an important source of gene innovation and structural variation within mammalian genomes. We performed the first systematic genome-wide analysis segmental duplications in modern domesticated cattle (Bos taurus). Using two distinct computational analyses, we estimated that 3.1% (94.4 Mb) bovine genome consists recently duplicated (≥ 1 kb length, ≥ 90% sequence identity). Similar to other draft assemblies, almost half (47% 94.4 these have not been assigned chromosomes....