Qunhao Niu
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View article: Comprehensive Multi-omics Analysis of Regulatory Variants for Body Weight in Cattle
Comprehensive Multi-omics Analysis of Regulatory Variants for Body Weight in Cattle Open
Body weight is a polygenic trait with intricate inheritance patterns. Functional genomics enriched with multi-layer annotations offers essential resources for exploring the genetic architecture of complex traits. In this study, we conducte…
View article: Multiple strategies association revealed functional candidate FASN gene for fatty acid composition in cattle
Multiple strategies association revealed functional candidate FASN gene for fatty acid composition in cattle Open
View article: Integrating multi-layered biological priors to improve genomic prediction accuracy in beef cattle
Integrating multi-layered biological priors to improve genomic prediction accuracy in beef cattle Open
Our findings suggest that integrating biological prior information from multiple layers can enhance our understanding of the genetic architecture underlying complex traits and further improve genomic prediction in beef cattle.
View article: Comparative Analysis of Genomic Prediction for Production Traits Using Genomic Annotation and a Genome-Wide Association Study at Sequencing Levels in Beef Cattle
Comparative Analysis of Genomic Prediction for Production Traits Using Genomic Annotation and a Genome-Wide Association Study at Sequencing Levels in Beef Cattle Open
Leveraging whole-genome sequencing (WGS) that includes the full spectrum of genetic variation provides a better understanding of the biological mechanisms involved in the economically important traits of farm animals. However, the effectiv…
View article: Genetic Association Analysis of Copy Number Variations for Meat Quality in Beef Cattle
Genetic Association Analysis of Copy Number Variations for Meat Quality in Beef Cattle Open
Meat quality is an economically important trait for global food production. Copy number variations (CNVs) have been previously implicated in elucidating the genetic basis of complex traits. In this article, we detected a total of 112,198 C…
View article: Evaluation of Linear Programming and Optimal Contribution Selection Approaches for Long-Term Selection on Beef Cattle Breeding
Evaluation of Linear Programming and Optimal Contribution Selection Approaches for Long-Term Selection on Beef Cattle Breeding Open
The optimized selection method can maximize the genetic gain in offspring under the premise of controlling the inbreeding level of the population. At present, genetic gain has been largely improved by using genomic selection in multiple fa…
View article: Identifying Candidate Genes for Litter Size and Three Morphological Traits in Youzhou Dark Goats Based on Genome-Wide SNP Markers
Identifying Candidate Genes for Litter Size and Three Morphological Traits in Youzhou Dark Goats Based on Genome-Wide SNP Markers Open
This study aimed to reveal the potential genetic basis for litter size, coat colour, black middorsal stripe and skin colour by combining genome-wide association analysis (GWAS) and selection signature analysis and ROH detection within the …
View article: Cis-eQTL Analysis and Functional Validation of Candidate Genes for Carcass Yield Traits in Beef Cattle
Cis-eQTL Analysis and Functional Validation of Candidate Genes for Carcass Yield Traits in Beef Cattle Open
Carcass yield traits are of considerable economic importance for farm animals, which act as a major contributor to the world’s food supply. Genome-wide association studies (GWASs) have identified many genetic variants associated with carca…
View article: Long-Term Impact of Genomic Selection on Genetic Gain Using Different SNP Density
Long-Term Impact of Genomic Selection on Genetic Gain Using Different SNP Density Open
Genomic selection (GS) has been widely used in livestock breeding. However, the long-term impact of GS on genetic gain, as well as inbreeding levels, has not been fully explored in beef cattle. In this study, we carried out simulation anal…
View article: Comparative transcriptomic analysis reveals region-specific expression patterns in different beef cuts
Comparative transcriptomic analysis reveals region-specific expression patterns in different beef cuts Open
View article: Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle
Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle Open
Background A comprehensive analysis of gene expression profiling across tissues can provide necessary information for an in-depth understanding of their biological functions. We performed a large-scale gene expression analysis and generate…
View article: Comparative Transcriptomic Analysis Reveals Diverse Expression Pattern Underlying Fatty Acid Composition among Different Beef Cuts
Comparative Transcriptomic Analysis Reveals Diverse Expression Pattern Underlying Fatty Acid Composition among Different Beef Cuts Open
Beef is an important dietary source of quality animal proteins and amino acids in human nutrition. The fatty acid composition is one of the indispensable indicators affecting nutritional value of beef. However, a comprehensive understandin…
View article: Additional file 4 of Comparative transcriptomic analysis reveals region-specific expression patterns in different beef cuts
Additional file 4 of Comparative transcriptomic analysis reveals region-specific expression patterns in different beef cuts Open
Additional file 4: Table S4. RSGs transcription factor analysis.
View article: Additional file 3 of Comparative transcriptomic analysis reveals region-specific expression patterns in different beef cuts
Additional file 3 of Comparative transcriptomic analysis reveals region-specific expression patterns in different beef cuts Open
Additional file 3: Table S3. Functional annotation and enrichment analysis of RSGs.
View article: Additional file 9 of Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle
Additional file 9 of Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle Open
Additional file 9: Table S9. The identified functional modules using dynamic cutting method. Table S10. Tissue-specific modules detection and hub genes screening. Table S11. Tissue-specific module gene function annotation (Top10). Table S1…
View article: Additional file 5 of Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle
Additional file 5 of Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle Open
Additional file 5: Table S7. Tissue specific genes (TSGs) and tissue-specific transcripts (TSTs) identified based on stringent criteria.
View article: Additional file 7 of Comparative transcriptomic analysis reveals region-specific expression patterns in different beef cuts
Additional file 7 of Comparative transcriptomic analysis reveals region-specific expression patterns in different beef cuts Open
Additional file 7: Table S6. The summarize of candidate genes related to meat quality traits in longissimus lumborum, chuck, neck, rump and tenderloin beef cuts.
View article: Additional file 13 of Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle
Additional file 13 of Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle Open
Additional file 13: Table S19. RT-qPCR primer sequences of TSGs in the current study.
View article: Additional file 3 of Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle
Additional file 3 of Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle Open
Additional file 3: Table S6. The expression levels of 32 HKGs across 51 tissues.
View article: Additional file 6 of Comparative transcriptomic analysis reveals region-specific expression patterns in different beef cuts
Additional file 6 of Comparative transcriptomic analysis reveals region-specific expression patterns in different beef cuts Open
Additional file 6: Table S5. The identified region-specific modules.
View article: Additional file 8 of Comparative transcriptomic analysis reveals region-specific expression patterns in different beef cuts
Additional file 8 of Comparative transcriptomic analysis reveals region-specific expression patterns in different beef cuts Open
Additional file 8: Table S7. RT-qPCR primer sequences for candidate genes related to meat quality traits.
View article: Additional file 7 of Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle
Additional file 7 of Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle Open
Additional file 7: Table S8. Tissue specific gene (TSG) function annotation (Top5) and pathway enrichment (Top5).
View article: Additional file 2 of Comparative transcriptomic analysis reveals region-specific expression patterns in different beef cuts
Additional file 2 of Comparative transcriptomic analysis reveals region-specific expression patterns in different beef cuts Open
Additional file 2: Table S2. Identification of region-specific genes (RSGs).
View article: Additional file 1 of Comparative transcriptomic analysis reveals region-specific expression patterns in different beef cuts
Additional file 1 of Comparative transcriptomic analysis reveals region-specific expression patterns in different beef cuts Open
Additional file 1: Table S1. Reads mapping summary of chuck, neck, rump, tenderloin and longissimus lumborum.
View article: Additional file 1 of Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle
Additional file 1 of Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle Open
Additional file 1: Table S1. Sample information and classification of tissue samples from beef cattle in this study. Table S2. The summary of raw reads, clean reads and the total mapped read rate. Table S3. Assemble the transcript statisti…
View article: Additional file 15 of Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle
Additional file 15 of Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle Open
Additional file 15: Table S20. Summary of shared TSG identified in this study and previous studies.
View article: Additional file 11 of Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle
Additional file 11 of Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle Open
Additional file 11: Table S14. Tissue-specific module transcription factor analysis. Table S15. Cross-species conservation of HKGs, TSGs, HUBGs and full genes set. Table S16. The expression level of cattle full genes set, HKGs, TSGs and HU…
View article: Identification of Candidate Variants Associated With Bone Weight Using Whole Genome Sequence in Beef Cattle
Identification of Candidate Variants Associated With Bone Weight Using Whole Genome Sequence in Beef Cattle Open
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 3…
View article: Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle
Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle Open
View article: Validation of the Prediction Accuracy for 13 Traits in Chinese Simmental Beef Cattle Using a Preselected Low-Density SNP Panel
Validation of the Prediction Accuracy for 13 Traits in Chinese Simmental Beef Cattle Using a Preselected Low-Density SNP Panel Open
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 lo…