Haonan Zeng
A5062947279- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Cancer-related molecular mechanisms research
- Molecular Biology Techniques and Applications
- Animal Genetics and Reproduction
- Single-cell and spatial transcriptomics
- Animal Disease Management and Epidemiology
- Wheat and Barley Genetics and Pathology
- Genetics and Plant Breeding
South China Agricultural University
2022-2025
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 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...
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 comprehensive genome-wide association studies (GWAS) followed by a 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 6878 quantitative trait loci (QTL) 139 traits. Leveraging...
RNA sequencing (RNA-seq) is a powerful tool for transcriptome profiling, enabling integrative studies of expression quantitative trait loci (eQTL). As it identifies fewer genetic variants than DNA (DNA-seq), reference panel-based genotype imputation often required to enhance its utility. This study evaluated the accuracy using SNPs called from RNA-seq data (RNA-SNPs). SNP features 6,567 samples across 28 pig tissues were used mask whole genome (WGS) data, with Pig Genomic Reference Panel...
Abstract In livestock, genome‐wide association studies (GWAS) are usually conducted in a single population (single‐GWAS) with limited sample size and detection power. To enhance the power of GWAS, meta‐analysis GWAS (meta‐GWAS) mega‐analysis (mega‐GWAS) have been proposed to integrate data from multiple populations at level summary statistics or individual data, respectively. However, there is lack comparison for these different strategies, which makes it difficult guide best practice...
Abstract 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 species, which is essential for linking polymorphisms variation phenotypes, helping fundamental biology discovery and exploitation breeding human biomedicine. Here we present results from the pilot phase PigGTEx (http://piggtex.farmgtex.org/), where processed 9,530 RNA-sequencing 1,602...
Growth and carcass traits are of economic importance in the pig production, which affect pork quality profitability finishing production. This study used whole-genome transcriptome sequencing technologies to identify potential candidate genes affecting growth Duroc pigs. The medium (50-60 k) single nucleotide polymorphism (SNP) arrays 4 154 pigs from three populations were imputed sequence data, yielding 10 463 227 markers on 18 autosomes. dominance heritabilities estimated for ranged 0.000...
Abstract The systematic characterization of cellular heterogeneity among tissues and cell-type-specific regulation underlying complex phenotypes remains elusive in pigs. Within the Pig Genotype-Tissue Expression (PigGTEx) project, we present a single-cell transcriptome atlas adult pigs encompassing 229,268 high-quality nuclei from 19 tissues, annotated to 67 major cell types. Besides within across further characterize prominent tissue-specific features functions muscle, epithelial, immune...
Abstract Understanding the molecular and cellular mechanisms that underlie complex traits in pigs is crucial for enhancing their genetic improvement program unleashing substantial potentials human biomedicine research. Here, we conducted a meta-GWAS analysis 232 with 28.3 million imputed whole-genome sequence variants 70,328 individuals from 14 pig breeds. We identified total of 6,878 genomic regions associated 139 traits. By integrating Pig Genotype-Tissue Expression (PigGTEx) resource,...
The domestic pig (
The domestic pig (Sus scrofa) and subfamilies have a long-term extensive gene flow, especially in Southeast Asia. Demographically, as gateway of southern China, Yunnan province with unique geographical location complex climate system, but genomic, genetic introgression indigenous pigs is insufficient. Here, we analyzed population structure, differentiation, adaptive introgression, signature selection function pigs, European commercial other Asia using genomics reference panel (PGRP v1) from...
Abstract The systematic characterization of cellular heterogeneity among tissues and cell-type-specific regulation underlying complex phenotypes remains elusive in pigs. Within the Pig Genotype-Tissue Expression (PigGTEx) project, we present a single-cell transcriptome atlas adult pigs encompassing 229,268 high-quality nuclei from 19 tissues, annotated to 67 major cell types. Besides within across further characterize prominent tissue-specific features functions muscle, epithelial, immune...