A5101440916- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Cancer-related molecular mechanisms research
- Animal Disease Management and Epidemiology
- Animal Genetics and Reproduction
- Genetics and Plant Breeding
- Effects of Environmental Stressors on Livestock
- Meat and Animal Product Quality
- Chromosomal and Genetic Variations
- Peroxisome Proliferator-Activated Receptors
- Agriculture Sustainability and Environmental Impact
- Gut microbiota and health
- Genetic diversity and population structure
- Animal Behavior and Welfare Studies
- Medicinal Plants and Bioactive Compounds
- Food Supply Chain Traceability
- Livestock Farming and Management
- Identification and Quantification in Food
- Genomics and Phylogenetic Studies
- Genomics and Chromatin Dynamics
- Genomic variations and chromosomal abnormalities
- Pharmacological Effects of Natural Compounds
Zhejiang University
2023-2025
South China University of Technology
2023
University of Tennessee Health Science Center
2023
Institute of Animal Sciences
2017-2021
Chinese Academy of Agricultural Sciences
2017-2021
Fujian Agriculture and Forestry University
2018
Machine learning (ML) is perhaps the most useful tool for interpretation of large genomic datasets. However, performance a single machine method in selection (GS) currently unsatisfactory. To improve predictions, we constructed stacking ensemble framework (SELF), integrating three methods, to predict estimated breeding values (GEBVs). The present study evaluated prediction ability SELF by analyzing real datasets, with different genetic architecture; comparing accuracy SELF, base learners,...
Abstract Background Body size traits as one of the main breeding selection criteria was widely used to monitor cattle growth and evaluate response. In this study, body defined height (BH), length (BL), hip (HH), heart (HS), abdominal (AS), cannon bone (CS). We performed genome-wide association studies (GWAS) these over course three stages (6, 12 18 months after birth) using statistical models, single-trait GWAS, multi-trait GWAS LONG-GWAS. The Illumina Bovine HD 770 K BeadChip identify...
Cattle internal organs as accessible raw materials have a long history of being widely used in beef processing, feed and pharmaceutical industry. These traits not only are economic interest to breeders, but they intrinsically linked many valuable traits, such growth, health, productivity. Using the Illumina Bovine HD 770K SNP array, we performed genome-wide association study for heart weight, liver spleen lung kidney weight 1,217 Simmental cattle. In our research, 38 significant single...
Chinese Simmental beef cattle are the most economically important breed in China. Estimated breeding values for growth, carcass, and meat quality traits commonly used as selection criteria animal breeding. The objective of this study was to evaluate accuracy alternative statistical methods estimation genomic values. Analyses best linear unbiased prediction (GBLUP), BayesB, elastic net (EN) were performed with an Illumina BovineHD BeadChip on 1,217 animals by applying 5-fold cross-validation....
Abstract Genomic selection (GS) using the whole‐genome molecular makers to predict genomic estimated breeding values (GEBVs) is revolutionizing livestock and plant breeding. Seeking out novel strategies with higher prediction accuracy for GS has been ultimate goal of breeders. With rapid development artificial intelligence, machine learning algorithms were applied estimate GEBVs increasingly. Although some methods have better performance in phenotype prediction, there still considerable room...
Abstract Pigs are crucial sources of meat and protein, valuable animal models, potential donors for xenotransplantation. However, the existing reference genome pigs is incomplete, with thousands segments missing centromeres telomeres, which limits our understanding important traits in these genomic regions. To address this issue, we present a near complete assembly Jinhua pig (JH-T2T), constructed using PacBio HiFi ONT long reads. This includes all 18 autosomes X Y sex chromosomes, only six...
Improving reproductive performance in Yorkshire pigs, a key maternal line three-way crossbreeding systems, remains challenging due to low heritability and historical selection pressures favoring production traits. Identifying pleiotropic genetic variants that influence both reproduction traits is crucial for understanding their interplay enhancing molecular breeding strategies. Genome-wide association studies (GWAS) using 2,764 individuals identified 264,660 significant loci associated with...
Abstract Background Pigs are crucial sources of meat and protein, valuable animal models, potential donors for xenotransplantation. However, the existing reference genome pigs is incomplete, with thousands segments centromeres telomeres missing, which limits our understanding important traits in these genomic regions. Findings We present a near-complete assembly Jinhua pig (JH-T2T) provide set diploid genomes, constructed using PacBio HiFi, ONT long reads, Hi-C reads. This includes all 18...
Copy number variations (CNVs) are defined as deletions, insertions, and duplications between two individuals of a species. To investigate the diversity population-genetic properties CNVs their diverse selection patterns, we performed genome-wide CNV analysis using high density SNP array in Chinese native cattle. In this study, detected total 13,225 events 3,356 regions (CNVRs), overlapping with 1,522 annotated genes. Among them, approximately 71.43 Mb novel CNVRs were cattle population for...
Carcass meat yield is an important carcass trait that contributes to the production efficiency and economic benefits in beef cattle. It therefore critical identify quantitative loci associated with traits enable selection. Our previous studies have identified several causal variants within pleomorphic adenoma gene 1 (PLAG1) coiled-coil-helix-coiled-coil-helix domain-containing 7 (CHCHD7) genes on BTA14 for Chinese Simmental. In current study, we carried out a genome-wide association study...
Natural and artificial selection for more than 9000 years have led to a variety of domestic pig breeds. Accurate identification breeds is important breed conservation, sustainable breeding, pork traceability, local resource registration.We evaluated the performance four selectors six classifiers using wide range (N = 91). The internal cross-validation external independent testing showed that partial least squares regression (PLSR) was most effective selector squares-discriminant analysis...
Abstract Background The reliance on a solitary linear reference genome has imposed significant constraint our comprehensive understanding of genetic variation in animals. This is particularly pronounced for non-reference sequences (NRSs), which have not been extensively studied. Results In this study, we constructed pig pangenome graph using 21 assemblies and identified 23,831 NRSs with total length 105 Mb. Our findings revealed that were more prevalent breeds exhibiting greater divergence...
Summary Bone weight, defined as the total weight of bones in all forequarter and hindquarter joints, can reflect somebody conformation traits skeletal diseases. To gain a better understanding genetic determinants bone we used composite strategy including multimarker rare‐marker association to perform genomewide studies ( GWAS ) for that character Simmental cattle. Our consisted three models: (i) A traditional linear mixed model LMM was applied Q + K ‐ ); (ii) single nucleotide polymorphisms...
<title>Abstract</title> Pigs are crucial sources of meat and protein, valuable animal models, potential donors for xenotransplantation. However, the existing reference genome pigs is incomplete, with thousands segments missing centromeres telomeres, which limits our understanding genetic mechanisms underlying important traits in these genomic regions. To address this issue, we present a near complete chromosome telomere-to-telomere gap-free assembly Jinhua pig (JH-T2T), constructed using...
Abstract Understanding the genetic basis of porcine mental health (PMH)-related traits in intensive pig farming systems may promote improvement animal welfare enhancement. However, investigations on this topic have been limited to a retrospective focus, and phenotypes difficult elucidate due an unknown basis. Intensively farmed pigs, such as those Duroc, Landrace, Yorkshire breeds, undergone prolonged selection pressure systems. This has potentially subjected genes related these pigs...