Genome-Wide Scans for Selection Signatures in Ningxia Angus Cattle Reveal Genetic Variants Associated with Economic and Adaptive Traits.

The genetic improvement of beef cattle breeds is crucial for the advancement of the beef cattle industry. Whole-genome resequencing technology has been widely applied in genetic breeding as well as research on selection signatures in beef cattle. In this study, 20× whole-genome resequencing was performed on 282 Angus cattle from the Ningxia region, and a high-quality dataset encompassing extensive genomic variations across the entire genome was constructed.

Integrating multi-layered biological priors to improve genomic prediction accuracy in beef cattle.

Background: Integrating multi-layered information can enhance the accuracy of genomic prediction for complex traits. However, the improvement and application of effective strategies for genomic prediction (GP) using multi-omics data remains challenging.

Methods: We generated 11 feature sets for sequencing variants from genomics, transcriptomics, metabolomics, and epigenetics data in beef cattle, then we assessed the contribution of functional variants using genomic restricted maximum likelihood (GREML).

Evaluation of genomic mating approach based on genetic algorithms for long-term selection in Huaxi cattle.

Background: Genomic mating (GM) can effectively control the growth rate of inbreeding in population and achieve long-term sustainable genetic progress. However, the design of GM method and assessment of its effects during long-term selection have not been fully explored in beef cattle breeding.

Results: In this study, we constructed a simulated population based on the real genotypes of Huaxi cattle, where five generations of simulated breeding were carried out using the genomic optimal contribution selection (GOCS), genetic algorithms strategy and three traditional mating strategies.

The eQTL colocalization and transcriptome-wide association study identify potentially causal genes responsible for economic traits in Simmental beef cattle.

Background: A detailed understanding of genetic variants that affect beef merit helps maximize the efficiency of breeding for improved production merit in beef cattle. To prioritize the putative variants and genes, we ran a comprehensive genome-wide association studies (GWAS) analysis for 21 agronomic traits using imputed whole-genome variants in Simmental beef cattle. Then, we applied expression quantitative trait loci (eQTL) mapping between the genotype variants and transcriptome of three tissues (longissimus dorsi muscle, backfat, and liver) in 120 cattle.

Genomic prediction of carcass traits using different haplotype block partitioning methods in beef cattle.

Genomic prediction (GP) based on haplotype alleles can capture quantitative trait loci (QTL) effects and increase predictive ability because the haplotypes are expected to be in linkage disequilibrium (LD) with QTL. In this study, we constructed haploblocks using LD-based and the fixed number of single nucleotide polymorphisms (fixed-SNP) methods with Illumina BovineHD chip in beef cattle. To evaluate the performance of different haplotype block partitioning methods, we constructed haploblocks based on LD thresholds (from  > 0.

Transcriptional states and chromatin accessibility during bovine myoblasts proliferation and myogenic differentiation.

Objectives: 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 the time course of fetal skeletal muscle development in vitro, and explore the dynamic changes of chromatin accessibility and gene expression during bovine myoblasts proliferation and differentiation.

Methods: PDGFR- cells were isolated from bovine fetal skeletal muscle, then cultured and induced myogenic differentiation in vitro in a time-course study (P, D0, D2,and D4).

Transcriptome Analysis of Bovine Rumen Tissue in Three Developmental Stages.

Rumen development is a crucial physiological challenge for ruminants. However, the molecular mechanism regulating rumen development has not been clearly elucidated. In this study, we investigated genes involved in rumen development in 13 rumen tissues from three developmental stages (birth, youth, and adult) using RNA sequencing.

Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array.

Huaxi cattle, a specialized beef cattle breed in China, has the characteristics of fast growth, high slaughter rate, and net meat rate, good reproductive performance, strong stress resistance, and wide adaptability. In this study, we evaluated the genetic diversity, population structure, and genetic relationships of Huaxi cattle and its ancestor populations at the genome-wide level, as well as detecting the selection signatures of Huaxi cattle. Principal component analysis (PCA) and phylogenetic analysis revealed that Huaxi cattle were obviously separated from other cattle populations.

Identification of Candidate Variants Associated With Bone Weight Using Whole Genome Sequence in Beef Cattle.

Bone weight is critical to affect body conformation and stature in cattle. In this study, we conducted a genome-wide association study for bone weight in Chinese Simmental beef cattle based on the imputed sequence variants. We identified 364 variants associated with bone weight, while 350 of them were not included in the Illumina BovineHD SNP array, and several candidate genes and GO terms were captured to be associated with bone weight.

Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle.

Background: Genomic regions with a high frequency of runs of homozygosity (ROH) are related to important traits in farm animals. We carried out a comprehensive analysis of ROH and evaluated their association with production traits using the BovineHD (770 K) SNP array in Chinese Simmental beef cattle.

Results: We detected a total of 116,953 homozygous segments with 2.

Genomic Prediction Using LD-Based Haplotypes Inferred From High-Density Chip and Imputed Sequence Variants in Chinese Simmental Beef Cattle.

A haplotype is defined as a combination of alleles at adjacent loci belonging to the same chromosome that can be transmitted as a unit. In this study, we used both the Illumina BovineHD chip (HD chip) and imputed whole-genome sequence (WGS) data to explore haploblocks and assess haplotype effects, and the haploblocks were defined based on the different LD thresholds. The accuracies of genomic prediction (GP) for dressing percentage (DP), meat percentage (MP), and rib eye roll weight (RERW) based on haplotype were investigated and compared for both data sets in Chinese Simmental beef cattle.

Integration of selection signatures and multi-trait GWAS reveals polygenic genetic architecture of carcass traits in beef cattle.

Carcass merits are widely considered as economically important traits affecting beef production in the beef cattle industry. However, the genetic basis of carcass traits remains to be well understood. Here, we applied multiple methods, including the Composite of Likelihood Ratio (CLR) and Genome-wide Association Study (GWAS), to explore the selection signatures and candidate variants affecting carcass traits.

Validation of the Prediction Accuracy for 13 Traits in Chinese Simmental Beef Cattle Using a Preselected Low-Density SNP Panel.

Chinese Simmental beef cattle play a key role in the Chinese beef industry due to their great adaptability and marketability. To achieve efficient genetic gain at a low breeding cost, it is crucial to develop a customized cost-effective low-density SNP panel for this cattle population. Thirteen growth, carcass, and meat quality traits and a BovineHD Beadchip genotyping of 1346 individuals were used to select trait-associated variants and variants contributing to great genetic variance.

Genome-Wide Assessment of Runs of Homozygosity in Chinese Wagyu Beef Cattle.

Runs of homozygosity (ROH) are continuous homozygous regions that generally exist in the DNA sequence of diploid organisms. Identifications of ROH leading to reduction in performance can provide valuable insight into the genetic architecture of complex traits. Here, we evaluated genome-wide patterns of homozygosity and their association with important traits in Chinese Wagyu beef cattle.

Incorporating Genome Annotation Into Genomic Prediction for Carcass Traits in Chinese Simmental Beef Cattle.

Various methods have been proposed for genomic prediction (GP) in livestock. These methods have mainly focused on statistical considerations and did not include genome annotation information. In this study, to improve the predictive performance of carcass traits in Chinese Simmental beef cattle, we incorporated the genome annotation information into GP.

Genomic Prediction and Association Analysis with Models Including Dominance Effects for Important Traits in Chinese Simmental Beef Cattle.

Non-additive effects play important roles in determining genetic changes with regard to complex traits; however, such effects are usually ignored in genetic evaluation and quantitative trait locus (QTL) mapping analysis. In this study, a two-component genome-based restricted maximum likelihood (GREML) was applied to obtain the additive genetic variance and dominance variance for carcass weight (CW), dressing percentage (DP), meat percentage (MP), average daily gain (ADG), and chuck roll (CR) in 1233 Simmental beef cattle. We estimated predictive abilities using additive models (genomic best linear unbiased prediction (GBLUP) and BayesA) and dominance models (GBLUP-D and BayesAD).

Theoretical Evaluation of Multi-Breed Genomic Prediction in Chinese Indigenous Cattle.

Genomic selection (GS) has been widely considered as a valuable strategy for enhancing the rate of genetic gain in farm animals. However, the construction of a large reference population is a big challenge for small populations like indigenous cattle. In order to evaluate the potential application of GS for Chinese indigenous cattle, we assessed the influence of combining multiple populations on the reliability of genomic predictions for 10 indigenous breeds of Chinese cattle using simulated data.

Identification of muscle-specific candidate genes in Simmental beef cattle using imputed next generation sequencing.

Genome-wide association studies (GWAS) have commonly been used to identify candidate genes that control economically important traits in livestock. Our objective was to detect potential candidate genes associated mainly with muscle development traits related to dimension of hindquarter in cattle. A next generation sequencing (NGS) dataset to imputed to 12 million single nucleotide polymorphisms (SNPs) (from 1252 Simmental beef cattle) were used to search for genes affecting hindquarter traits using a linear, mixed model approach.

Genome-wide scan reveals genetic divergence and diverse adaptive selection in Chinese local cattle.

Background: Understanding the population structure and genetic bases of well-adapted cattle breeds to local environments is one of the most essential tasks to develop appropriate genetic improvement programs.

Results: We performed a comprehensive study to investigate the population structure, divergence and selection signatures at genome-wide level in diverse Chinese local cattle using Bovine HD SNPs array, including two breeds from North China, one breed from Northwest China, three breeds from Southwest China and two breeds from South China. Population genetic analyses revealed the genetic structures of these populations were mostly related to the geographic locations.

Genome-Wide Scan Identifies Selection Signatures in Chinese Wagyu Cattle Using a High-Density SNP Array.

Selective breeding can lead to genetic diversity and diverse phenotypes in farm animals. Analysis of the genomic regions under selection can provide important insights into the genetic basis of complex traits. In this study, a high-density SNP array was used for analysis of genome selection signatures in Chinese Wagyu cattle.