Xiaodian Cai
A5069435054- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Cancer-related molecular mechanisms research
- Genetics and Plant Breeding
- Animal Genetics and Reproduction
- Molecular Biology Techniques and Applications
- Single-cell and spatial transcriptomics
- Animal Nutrition and Physiology
- Livestock Management and Performance Improvement
- Livestock and Poultry Management
- Identification and Quantification in Food
- Meat and Animal Product Quality
- Wheat and Barley Genetics and Pathology
- Animal Disease Management and Epidemiology
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 Background Compared to medium-density single nucleotide polymorphism (SNP) data, high-density SNP data contain abundant genetic variants and provide more information for the evaluation of livestock, but it has been shown that they do not confer any advantage genomic prediction heritability estimation. One possible reason is uneven distribution linkage disequilibrium (LD) along genome, i.e., LD heterogeneity among regions. The aim this study was effectively use genome-wide estimation...
Small white-feather chickens (SWFC) have become popular as a hybrid strain recently. Shank color is notable economic trait in this strain. Despite numerous studies on the green shank from both physiological and genetic perspectives, research focusing specifically (HC) remains limited. In study, to investigate mechanisms molecular basis of HC, we created population by intercrossing white-feathered yellow-feathered broilers, with yellow shanks. Physiological analysis confirmed that melanin...
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...
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 Breed identification utilizing multiple information sources and methods is widely applicated in the field of animal genetics breeding. Simultaneously, with development artificial intelligence, integration high‐throughput genomic data machine learning techniques increasingly used for breed identification. In this context, we 654 individuals from 15 pig breeds, evaluating performance stacking ensemble classifiers, as well function feature selection anomaly detection different...
The size of reference population is an important factor affecting genomic prediction. Thus, combining different populations in prediction attractive way to improve ability. However, multireference roughly cannot increase the accuracy as well expected pig. This may be due linkage disequilibrium (LD) pattern differences between population. In this study, we used imputed whole-genome sequencing (WGS) data construct LD-based haplotypes for combined explore impact single-nucleotide polymorphism...
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,...
Preselected variants associated with the trait of interest from genome-wide association studies (GWASs) are available to improve genomic prediction in pigs. The objectives this study were use preselected a large GWAS meta-analysis assess impact single-nucleotide polymorphism (SNP) preselection strategies on genome growth and carcass traits We genotyped 1018 Large White pigs using medium (50k) SNP arrays then imputed SNPs sequence level by utilizing reference panel 1602 whole-genome...
The domestic pig (
Multiple environment phenotypes may be utilized to implement genomic prediction in plant breeding, while it is unclear about optimal utilization strategies according its different availability. It necessary assess the of models based on availability multiple phenotypes. Here, we compared accuracy three (genomic model best linear unbiased (GBLUP), (GFBLUP), and multi-trait (mtGBLUP)) which leveraged diverse information from using a rice dataset containing 19 agronomic traits two disparate...
Heritability enrichment analysis is an important means of exploring the genetic architecture complex traits in human genetics. typically defined as proportion SNP subset explained heritability, divided by SNPs. enables better study underlying traits, such functional variant/gene subsets, biological networks and metabolic pathways detected through integrating explosively increased omics data. This would be beneficial for genomic prediction disease risk humans values estimation economical...
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...