A5070661880- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Cancer-related molecular mechanisms research
- Livestock Farming and Management
- Animal Genetics and Reproduction
- Meat and Animal Product Quality
- Ruminant Nutrition and Digestive Physiology
- Genetics and Plant Breeding
- Genetic Associations and Epidemiology
- Genomic variations and chromosomal abnormalities
- Effects of Environmental Stressors on Livestock
- RNA Research and Splicing
- Congenital heart defects research
- Animal Nutrition and Physiology
- Genetic diversity and population structure
- Chromosomal and Genetic Variations
- Stress Responses and Cortisol
- Muscle Physiology and Disorders
- Peroxisome Proliferator-Activated Receptors
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Osteoarthritis Treatment and Mechanisms
- Thermoregulation and physiological responses
- RNA modifications and cancer
- Climate Change and Health Impacts
- Muscle metabolism and nutrition
Chinese Academy of Agricultural Sciences
2017-2025
Ministry of Agriculture and Rural Affairs
2020-2024
Institute of Animal Sciences
2017-2024
Institute of Animal Science
2020
China Agricultural University
2015-2019
Innovation Team (China)
2017-2019
Abstract Large‐scale genotyping at a low cost is crucial for molecular breeding of livestock. In this study, the Cattle110K capture chip was developed, based on by target sequencing system. The panel included 112,180 single necleotide polymorphisms (SNPs), from potential functional regions screened genome‐wide associated BayesB, expression quantitative trait loci‐mapping, ATAC‐seq, and reported markers. All SNPs were distributed evenly cattle genome, with more than 99% markers having minor...
Fatty acid composition of muscle is an important trait contributing to meat quality. Recently, genome-wide association study (GWAS) has been extensively used explore the molecular mechanism underlying traits in cattle. In this study, we performed GWAS using high density SNP array analyze between SNPs and fatty acids evaluated accuracy genomic prediction for Chinese Simmental cattle.Using BayesB method, identified 35 7 regions cattle that displayed significant associations with individual...
A detailed understanding of genetic variants that affect beef merit helps maximize the efficiency breeding for improved production in cattle. To prioritize putative and genes, we ran a comprehensive genome-wide association studies (GWAS) analysis 21 agronomic traits using imputed whole-genome Simmental Then, applied expression quantitative trait loci (eQTL) mapping between genotype transcriptome three tissues (longissimus dorsi muscle, backfat, liver) 120 cattle.We identified 1,580 signals...
Abstract
 Background: Numerous studies have demonstrated that the amalgamation of populations belonging to same breed or closely related breeds leads enhanced accuracies in genomic predictions (GP). Extensive experimentation with diverse Bayesian and Genome-enabled best linear unbiased prediction (GBLUP) models has been conducted explore multi-breed selection (GS) livestock, ultimately establishing they as successful approaches for predicting estimated breeding value (GEBV). This study...
Fatty acids are important traits that affect meat quality and nutritive values in beef cattle. Detection of genetic variants for fatty acid composition can help to elucidate the mechanism underpinning these promote improvement profiles. In this study, we performed a genome-wide association study (GWAS) on using high-density single nucleotide polymorphism (SNP) arrays Chinese Wagyu cattle.In total, detected 15 8 significant SNPs individual groups cattle, respectively. Also, identified nine...
Although major advances have been made in bovine epigenome study, the epigenetic basis for fetal skeletal muscle development still remains poorly understood. The aim is to recapitulated time course of vitro, and explore dynamic changes chromatin accessibility gene expression during myoblasts proliferation differentiation.PDGFR- cells were isolated from muscle, then cultured induced myogenic differentiation vitro a time-course study (P, D0, D2,and D4). assay transposase-accessible sequencing...
Fatty acid composition (FA) is an important indicator of meat quality in beef cattle. We investigated potential functional candidate genes for FA cattle by integrating genomic and transcriptomic dataset through multiple strategies. In this study, we observed 65 SNPs overlapping with five (CCDC57, FASN, HDAC11, ALG14, ZMAT4) using two steps association based on the imputed sequencing variants. Using traits GWAS, further identified three significant located upstream FASN one SNP...
Understanding the population structure and genetic bases of well-adapted cattle breeds to local environments is one most essential tasks develop appropriate improvement programs. We performed a comprehensive study investigate structure, divergence selection signatures at genome-wide level in diverse Chinese using Bovine HD SNPs array, including two from North China, breed Northwest three Southwest China South China. Population analyses revealed structures these populations were mostly...
Runs of homozygosity (ROH) are continuous homozygous regions that generally exist in the DNA sequence diploid organisms. Identifications ROH leading to reduction performance can provide valuable insight into genetic architecture complex traits. Here, we evaluated genome-wide patterns and their association with important traits Chinese Wagyu beef cattle. We identified a total 29,271 segments from 462 animals. Within each animal, an average number was 63.36 while length 62.19 Mb. To evaluate...
Improvement for carcass traits related to beef quality is the key concern in production. Recent reports found that epigenetics mediates interaction of individuals with environment and nutrition. The present study was designed analyze genetic effect single nucleotide polymorphisms (SNPs) seven epigenetic-related genes (DNMT1, DNMT3a, DNMT3b, DNMT3L, Ago1, Ago2, HDAC5) two meat candidate (CAPN1 PRKAG3) on fourteen a Snow Dragon population, also identify SNPs total cattle populations. Sixteen...
Principal component analysis (PCA) is a potential approach that can be applied in multiple-trait genome-wide association studies (GWAS) to explore pleiotropy, as well increase the power of quantitative trait loci (QTL) detection. In this study, relationship test single nucleotide polymorphisms (SNPs) was determined between single-trait GWAS and PCA-based GWAS. We found estimated pleiotropic nucleotides (QTNs) β * ^ were most cases larger than model estimations ( 1 2 ). Analysis using...
Understanding the linkage disequilibrium (LD) across genome, haplotype structure, and persistence of phase between breeds can enable us to appropriately design implement genome-wide association (GWAS) genomic selection (GS) in beef cattle. We estimated extent LD, block 10 Chinese cattle population using high density BovinHD BeadChip. The overall LD measured by r² adjacent SNPs were 0.60, 0.67, 0.58, 0.73, 0.71 for South (SCHC), North (NCC), Southwest (SWC), Simmental (SIM), Wagyu (WAG)....
Various methods have been proposed for genomic prediction (GP) in livestock. These mainly focused on statistical considerations and did not include genome annotation information. In this study, to improve the predictive performance of carcass traits Chinese Simmental beef cattle, we incorporated information into GP. Single nucleotide polymorphisms (SNPs) were annotated five classes: intergenic, gene, exon, protein coding sequences, 3'/5' untranslated region. Haploblocks constructed all...
Selective breeding can lead to genetic diversity and diverse phenotypes in farm animals. Analysis of the genomic regions under selection provide important insights into basis complex traits. In this study, a high-density SNP array was used for analysis genome signatures Chinese Wagyu cattle. total, we obtained 478,903 SNPs 24,820 no-overlap |iHS| (integrated haplotype score) estimations. Under threshold top 1%, 239 were finally identified as candidate selected 162 genes found based on UMD3.1...
Bone weight is critical to affect body conformation and stature in cattle. In this study, we conducted a genome-wide association study for bone Chinese Simmental beef cattle based on the imputed sequence variants. We identified 364 variants associated with weight, while 350 of them were not included Illumina BovineHD SNP array, several candidate genes GO terms captured be weight. Remarkably, four potential region BTA6 using Bayesian fine-mapping. Several important captured, including LAP3,...
Abstract Background Genomic regions with a high frequency of runs homozygosity (ROH) are related to important traits in farm animals. We carried out comprehensive analysis ROH and evaluated their association production using the BovineHD (770 K) SNP array Chinese Simmental beef cattle. Results detected total 116,953 homozygous segments 2.47Gb across genome studied population. The average number per individual was 99.03 length 117.29 Mb. Notably, we 42 more than 0.2. obtained 17 candidate...
A haplotype is defined as a combination of alleles at adjacent loci belonging to the same chromosome that can be transmitted unit. In this study, we used both Illumina BovineHD chip (HD chip) and imputed whole-genome sequence (WGS) data explore haploblocks assess effects, were based on different LD thresholds. The accuracies genomic prediction (GP) for dressing percentage (DP), meat (MP), rib eye roll weight (RERW) investigated compared sets in Chinese Simmental beef cattle. GP using entire...
Huaxi cattle, a specialized beef cattle breed in China, has the characteristics of fast growth, high slaughter rate, and net meat good reproductive performance, strong stress resistance, wide adaptability. In this study, we evaluated genetic diversity, population structure, relationships its ancestor populations at genome-wide level, as well detecting selection signatures cattle. Principal component analysis (PCA) phylogenetic revealed that were obviously separated from other populations....
Copy number variation (CNV) serves as a significant source of genetic diversity in mammals and exerts substantial effects on various complex traits. Pingliang red cattle, an outstanding indigenous resource China, possess remarkable breeding value attributed to their tender meat superior marbling quality. However, the mechanisms influencing carcass quality traits cattle are not well understood. We generated comprehensive genome-wide CNV map for using GGP Bovine 100K SNP chip. A total 755 copy...
This study aimed to investigate the carcass traits and meat quality of typical Chinese indigenous cattle breeds, compare difference in beef composition between breeds. We measured 5 61 indicators each striploin outside flat cuts. The results showed that northern breeds had superior production performance terms slaughter weight, weight lean compared southern improved for specialized significantly higher weights than local (P<0.01). With respect edibility, Pingliang red demonstrated tenderness...
Non-additive effects play important roles in determining genetic changes with regard to complex traits; however, such are usually ignored evaluation and quantitative trait locus (QTL) mapping analysis. In this study, a two-component genome-based restricted maximum likelihood (GREML) was applied obtain the additive variance dominance for carcass weight (CW), dressing percentage (DP), meat (MP), average daily gain (ADG), chuck roll (CR) 1233 Simmental beef cattle. We estimated predictive...
Genome-wide association studies (GWAS) have commonly been used to identify candidate genes that control economically important traits in livestock. Our objective was detect potential associated mainly with muscle development related dimension of hindquarter cattle. A next generation sequencing (NGS) dataset imputed 12 million single nucleotide polymorphisms (SNPs) (from 1252 Simmental beef cattle) were search for affecting using a linear, mixed model approach. We also haplotype and linkage...
Rumen development is a crucial physiological challenge for ruminants. However, the molecular mechanism regulating rumen has not been clearly elucidated. In this study, we investigated genes involved in 13 tissues from three developmental stages (birth, youth, and adult) using RNA sequencing. We identified that 6,048 were differentially expressed among stages. Using weighted correlation network analysis, found 12 modules significantly associated with Functional annotation protein-protein...