16 results on '"Zhang, Tianliu"'
Search Results
2. A draft genome of Drung cattle reveals clues to its chromosomal fusion and environmental adaptation
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Chen, Yan, Zhang, Tianliu, Xian, Ming, Zhang, Rui, Yang, Weifei, Su, Baqi, Yang, Guoqiang, Sun, Limin, Xu, Wenkun, Xu, Shangzhong, Gao, Huijiang, Xu, Lingyang, Gao, Xue, and Li, Junya
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- 2022
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3. Comparative transcriptomic analysis reveals region-specific expression patterns in different beef cuts
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Zhang, Tianliu, Wang, Tianzhen, Niu, Qunhao, Zheng, Xu, Li, Haipeng, Gao, Xue, Chen, Yan, Gao, Huijiang, Zhang, Lupei, Liu, George E., Li, Junya, and Xu, Lingyang
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- 2022
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4. Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle
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Zhang, Tianliu, Wang, Tianzhen, Niu, Qunhao, Xu, Lei, Chen, Yan, Gao, Xue, Gao, Huijiang, Zhang, Lupei, Liu, George E., Li, Junya, and Xu, Lingyang
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- 2022
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5. Integration of selection signatures and multi-trait GWAS reveals polygenic genetic architecture of carcass traits in beef cattle
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Niu, Qunhao, Zhang, Tianliu, Xu, Ling, Wang, Tianzhen, Wang, Zezhao, Zhu, Bo, Zhang, Lupei, Gao, Huijiang, Song, Jiuzhou, Li, Junya, and Xu, Lingyang
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- 2021
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6. Research Progress and Applications of Bovine Genome in the Tribe Bovini.
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Du, Xingjie, Sun, Yu, Fu, Tong, Gao, Tengyun, and Zhang, Tianliu
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YAK ,NUCLEOTIDE sequencing ,ZEBUS ,CATTLE ,BOS ,GENOMES ,CATTLE genetics ,WATER buffalo - Abstract
Various bovine species have been domesticated and bred for thousands of years, and they provide adequate animal-derived products, including meat, milk, and leather, to meet human requirements. Despite the review studies on economic traits in cattle, the genetic basis of traits has only been partially explained by phenotype and pedigree breeding methods, due to the complexity of genomic regulation during animal development and growth. With the advent of next-generation sequencing technology, genomics projects, such as the 1000 Bull Genomes Project, Functional Annotation of Animal Genomes project, and Bovine Pangenome Consortium, have advanced bovine genomic research. These large-scale genomics projects gave us a comprehensive concept, technology, and public resources. In this review, we summarize the genomics research progress of the main bovine species during the past decade, including cattle (Bos taurus), yak (Bos grunniens), water buffalo (Bubalus bubalis), zebu (Bos indicus), and gayal (Bos frontalis). We mainly discuss the development of genome sequencing and functional annotation, focusing on how genomic analysis reveals genetic variation and its impact on phenotypes in several bovine species. [ABSTRACT FROM AUTHOR]
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- 2024
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7. Population Structure and Selection Signal Analysis of Nanyang Cattle Based on Whole-Genome Sequencing Data.
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Zhang, Yan, Wei, Zhitong, Zhang, Man, Wang, Shiwei, Gao, Tengyun, Huang, Hetian, Zhang, Tianliu, Cai, Hanfang, Liu, Xian, Fu, Tong, and Liang, Dong
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CATTLE genetics ,WHOLE genome sequencing ,BREEDING ,CATTLE ,GENETIC variation ,NATURAL selection ,MEAT quality - Abstract
With a rich breeding history, Nanyang cattle (NY cattle) have undergone extensive natural and artificial selection, resulting in distinctive traits such as high fertility, excellent meat quality, and disease resistance. This makes them an ideal model for studying the mechanisms of environmental adaptability. To assess the population structure and genetic diversity of NY cattle, we performed whole-genome resequencing on 30 individuals. These data were then compared with published whole-genome resequencing data from 432 cattle globally. The results indicate that the genetic structure of NY cattle is significantly different from European commercial breeds and is more similar to North–Central Chinese breeds. Furthermore, among all breeds, NY cattle exhibit the highest genetic diversity and the lowest population inbreeding levels. A genome-wide selection signal analysis of NY cattle and European commercial breeds using Fst, θπ-ratio, and θπ methods revealed significant selection signals in genes associated with reproductive performance and immunity. Our functional annotation analysis suggests that these genes may be responsible for reproduction (MAP2K2, PGR, and GSE1), immune response (NCOA2, HSF1, and PAX5), and olfaction (TAS1R3). We provide a comprehensive overview of sequence variations in the NY cattle genome, revealing insights into the population structure and genetic diversity of NY cattle. Additionally, we identify candidate genes associated with important economic traits, offering valuable references for future conservation and breeding efforts of NY cattle. [ABSTRACT FROM AUTHOR]
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- 2024
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8. Cis-eQTL Analysis and Functional Validation of Candidate Genes for Carcass Yield Traits in Beef Cattle.
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Wang, Tianzhen, Niu, Qunhao, Zhang, Tianliu, Zheng, Xu, Li, Haipeng, Gao, Xue, Chen, Yan, Gao, Huijiang, Zhang, Lupei, Liu, George E., Li, Junya, and Xu, Lingyang
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SIMMENTAL cattle ,BEEF cattle ,MYOBLASTS ,LOCUS (Genetics) ,GENETIC variation ,FUNCTIONAL analysis ,GENOME-wide association studies ,FEEDLOTS - Abstract
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 carcass yield traits in beef cattle. However, their functions are not effectively illustrated. In this study, we performed an integrative analysis of gene-based GWAS with expression quantitative trait locus (eQTL) analysis to detect candidate genes for carcass yield traits and validate their effects on bovine skeletal muscle satellite cells (BSCs). The gene-based GWAS and cis-eQTL analysis revealed 1780 GWAS and 1538 cis-expression genes. Among them, we identified 153 shared genes that may play important roles in carcass yield traits. Notably, the identified cis-eQTLs of PON3 and PRIM2 were significantly (p < 0.001) enriched in previous GWAS loci for carcass traits. Furthermore, overexpression of PON3 and PRIM2 promoted the BSCs' proliferation, increased the expression of MYOD and downregulated the expression of MYOG, which indicated that these genes may inhibit myogenic differentiation. In contrast, PON3 and PRIM2 were significantly downregulated during the differentiation of BSCs. These findings suggested that PON3 and PRIM2 may promote the proliferation of BSCs and inhibit them in the pre-differentiation stage. Our results further contribute to the understanding of the molecular mechanisms of carcass yield traits in beef cattle. [ABSTRACT FROM AUTHOR]
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- 2022
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9. Long-Term Impact of Genomic Selection on Genetic Gain Using Different SNP Density.
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Zheng, Xu, Zhang, Tianliu, Wang, Tianzhen, Niu, Qunhao, Wu, Jiayuan, Wang, Zezhao, Gao, Huijiang, Li, Junya, and Xu, Lingyang
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LIVESTOCK breeding ,BEEF cattle ,HERITABILITY ,LIVESTOCK breeds ,INBREEDING ,DENSITY ,KINSHIP - Abstract
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 analysis using different approaches involving two types of SNP density (54 K and 100 K) and three levels of heritability traits (h
2 = 0.1, 0.3, and 0.5) to explore the long-term effects of selection strategies on genetic gain and average kinship coefficients. Our results showed that GS can improve the genetic gain across generations, and the GBLUP strategy showed slightly better performance than the BayesA model. Higher trait heritability can generate higher genetic gain in all scenarios. Moreover, simulation results using GBLUP and BayesA strategies showed higher average kinship coefficients compared with other strategies. Our study suggested that it is important to design GS strategies by considering the SNP density and trait heritability to achieve long-term and sustainable genetic gain and to effectively control inbreeding levels. [ABSTRACT FROM AUTHOR]- Published
- 2022
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10. Comparative Transcriptome Analysis of Gayal (Bos frontalis), Yak (Bos grunniens), and Cattle (Bos taurus) Reveal the High-Altitude Adaptation.
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Ma, Jun, Zhang, Tianliu, Wang, Wenxiang, Chen, Yan, Cai, Wentao, Zhu, Bo, Xu, Lingyang, Gao, Huijiang, Zhang, Lupei, Li, Junya, and Gao, Xue
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CATTLE ,YAK ,SMOOTH muscle contraction ,GENE expression profiling ,CARDIAC contraction ,LUNGS ,REGULATOR genes - Abstract
Gayal and yak are well adapted to the local high-altitude environments, yet the transcriptional regulation difference of the plateau environment among them remains obscure. Herein, cross-tissue and cross-species comparative transcriptome analysis were performed for the six hypoxia-sensitive tissues from gayal, yak, and cattle. Gene expression profiles for all single-copy orthologous genes showed tissue-specific expression patterns. By differential expression analysis, we identified 3020 and 1995 differentially expressed genes (DEGs) in at least one tissue of gayal vs. cattle and yak vs. cattle, respectively. Notably, we found that the adaptability of the gayal to the alpine canyon environment is highly similar to the yak living in the Qinghai-Tibet Plateau, such as promoting red blood cell development, angiogenesis, reducing blood coagulation, immune system activation, and energy metabolism shifts from fatty acid β-oxidation to glycolysis. By further analyzing the common and unique DEGs in the six tissues, we also found that numerous expression regulatory genes related to these functions are unique in the gayal and yak, which may play important roles in adapting to the corresponding high-altitude environment. Combined with WGCNA analysis, we found UQCRC1 , COX5A are the shared differentially expression hub genes related to the energy supply of myocardial contraction in the heart-related modules of gayal and yak, and CAPS is a shared differentially hub gene among the hub genes of the lung-related module, which is related to pulmonary artery smooth muscle contraction. Additionally, EDN3 is the unique differentially expression hub gene related to the tracheal epithelium and pulmonary vasoconstriction in the lung of gayal. CHRM2 is a unique differentially expression hub gene that was identified in the heart of yak, which has an important role in the autonomous regulation of the heart. These results provide a basis for further understanding the complex transcriptome expression pattern and the regulatory mechanism of high-altitude domestication of gayal and yak. [ABSTRACT FROM AUTHOR]
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- 2022
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11. Identification of Candidate Variants Associated With Bone Weight Using Whole Genome Sequence in Beef Cattle.
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Niu, Qunhao, Zhang, Tianliu, Xu, Ling, Wang, Tianzhen, Wang, Zezhao, Zhu, Bo, Gao, Xue, Chen, Yan, Zhang, Lupei, Gao, Huijiang, Li, Junya, and Xu, Lingyang
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WHOLE genome sequencing ,BEEF cattle ,GENOME-wide association studies ,SIMMENTAL cattle ,SINGLE nucleotide polymorphisms - Abstract
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. Remarkably, we identified four potential variants in a candidate region on BTA6 using Bayesian fine-mapping. Several important candidate genes were captured, including LAP3 , MED28 , NCAPG , LCORL , SLIT2 , and IBSP , which have been previously reported to be associated with carcass traits, body measurements, and growth traits. Notably, we found that the transcription factors related to MED28 and LCORL showed high conservation across multiple species. Our findings provide some valuable information for understanding the genetic basis of body stature in beef cattle. [ABSTRACT FROM AUTHOR]
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- 2021
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12. Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle.
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Zhao, Guoyao, Liu, Yuqiang, Niu, Qunhao, Zheng, Xu, Zhang, Tianliu, Wang, Zezhao, Xu, Lei, Zhu, Bo, Gao, Xue, Zhang, Lupei, Gao, Huijiang, Li, Junya, and Xu, Lingyang
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SIMMENTAL cattle ,HOMOZYGOSITY ,BEEF cattle ,FISHER exact test ,DOMESTIC animals ,MEAT quality ,BODY size - Abstract
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 2.47Gb across the genome in the studied population. The average number of ROH per individual was 99.03 and the average length was 117.29 Mb. Notably, we detected 42 regions with a frequency of more than 0.2. We obtained 17 candidate genes related to body size, meat quality, and reproductive traits. Furthermore, using Fisher's exact test, we found 101 regions were associated with production traits by comparing high groups with low groups in terms of production traits. Of those, we identified several significant regions for production traits (P < 0.05) by association analysis, within which candidate genes including ECT2, GABRA4, and GABRB1 have been previously reported for those traits in beef cattle. Conclusions: Our study explored ROH patterns and their potential associations with production traits in beef cattle. These results may help to better understand the association between production traits and genome homozygosity and offer valuable insights into managing inbreeding by designing reasonable breeding programs in farm animals. [ABSTRACT FROM AUTHOR]
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- 2021
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13. Selection and effectiveness of informative SNPs for paternity in Chinese Simmental cattle based on a high-density SNP array.
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Zhang, Tianliu, Guo, Liping, Xu, Lingyang, Chen, Yan, Zhang, Lupei, Gao, Huijiang, Li, Junya, Gao, Xue, and Shi, Mingyan
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PATERNITY , *SINGLE nucleotide polymorphisms , *SIMMENTAL cattle , *HETEROZYGOSITY , *CATTLE - Abstract
Incorrect paternity assignment in cattle can significantly influence the accuracy of genetic evaluation. Recent advances in high-throughput technology have facilitated the identification of single nucleotide polymorphism (SNP) markers and their applications for filiation and individual identification. We genotyped 1074 bulls from a reference population of Chinese Simmental cattle for genomic selection using a BovineSNP770K BeadChip. Among them, a total of 136 bulls were randomly selected to design a suitable low-density SNP panel for paternity testing in Simmental cattle. Our results showed that 50 SNPs were determined to be the most informative markers in parental testing, with an accuracy of 99.89% for CPE (cumulative probability of exclusion) in the unknown female parent case. The 50 highly informative SNP markers were distributed across 25 chromosomes, and the mean intermarker distance per chromosome was 26.72 Mb. The average minor allele frequency (MAF), expected heterozygosity (HE), and polymorphic information content (PIC) values were 0.3748, 0.4998, and 0.4818, respectively. Finally, the 50 identified SNPs were used to estimate paternity for the remaining 938 of 1074 bulls from 23 farms. Our results revealed that 76.75% of the 938 bulls were assigned parentage to the pedigree sires with 95% confidence, and the rate of pedigree record mistakes ranged from 9.52%–39.29% in different herds. Our study is the first attempt to provide valuable insights into the extraction of informative markers through the application of high-density SNP chips for paternity testing in Chinese Simmental cattle. [ABSTRACT FROM AUTHOR]
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- 2018
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14. Comparative Transcriptomic Analysis Reveals Diverse Expression Pattern Underlying Fatty Acid Composition among Different Beef Cuts.
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Zhang, Tianliu, Niu, Qunhao, Wang, Tianzhen, Zheng, Xu, Li, Haipeng, Gao, Xue, Chen, Yan, Gao, Huijiang, Zhang, Lupei, Liu, George E., Li, Junya, and Xu, Lingyang
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FATTY acids ,NUTRITION ,BEEF cattle ,COMPARATIVE studies ,AMINO acids ,GENE regulatory networks ,LIPID metabolism - Abstract
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 understanding of the expression changes underlying fatty acid composition in representative beef cuts is needed in cattle. This study aimed to characterize the dynamics of fatty acid composition using comparative transcriptomic analysis in five different type of beef cuts. We identified 7545 differentially expressed genes (DEGs) among 10 pair-wise comparisons. Co-expression gene network analysis identified two modules, which were significantly correlated with 2 and 20 fatty acid composition, respectively. We also identified 38 candidate genes, and functional enrichment showed that these genes were involved in fatty acid biosynthetic process and degradation, PPAR, and AMPK signaling pathway. Moreover, we observed a cluster of DEGs (e.g., SCD, LPL, FABP3, and PPARD) which were involved in the regulation of lipid metabolism and adipocyte differentiation. Our results provide some valuable insights into understanding the transcriptome regulation of candidate genes on fatty acid composition of beef cuts, and our findings may facilitate the designs of genetic selection program for beneficial fatty acid composition in beef cattle. [ABSTRACT FROM AUTHOR]
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- 2022
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15. Genome-Wide Assessment of Runs of Homozygosity in Chinese Wagyu Beef Cattle.
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Zhao, Guoyao, Zhang, Tianliu, Liu, Yuqiang, Wang, Zezhao, Xu, Lei, Zhu, Bo, Gao, Xue, Zhang, Lupei, Gao, Huijiang, Liu, George E., Li, Junya, and Xu, Lingyang
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BEEF cattle , *SIMMENTAL cattle , *HOMOZYGOSITY , *STATURE , *NUCLEOTIDE sequence , *MATE selection , *BODY weight - Abstract
Simple Summary: 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 understanding the genetic architecture of complex traits. We assessed genome-wide homozygosity patterns and inbreeding levels in Chinese Wagyu beef cattle. We identified several high frequency regions overlapped with QTLs which are associated with body weight, calving ease, and stillbirth. Based on these regions, we carried out a region-based association for eight economically important traits. Of these, nine regions were significantly associated with six traits including body height, chest circumference, fat coverage, backfat thickness, ribeye area, and carcass length. Our study identified that many candidate regions and genes overlapped with ROH for several important traits, which could be unitized to assist the design of a selection mating strategy in 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. We identified a total of 29,271 ROH segments from 462 animals. Within each animal, an average number of ROH was 63.36 while an average length was 62.19 Mb. To evaluate the enrichment of ROH across genomes, we initially identified 280 ROH regions by merging ROH events across all individuals. Of these, nine regions containing 154 candidate genes, were significantly associated with six traits (body height, chest circumference, fat coverage, backfat thickness, ribeye area, and carcass length; p < 0.01). Moreover, we found 26 consensus ROH regions with frequencies exceeding 10%, and several regions overlapped with QTLs, which are associated with body weight, calving ease, and stillbirth. Among them, we observed 41 candidate genes, including BCKDHB, MAB21L1, SLC2A13, FGFR3, FGFRL1, CPLX1, CTNNA1, CORT, CTNNBIP1, and NMNAT1, which have been previously reported to be related to body conformation, meat quality, susceptibility, and reproductive traits. In summary, we assessed genome-wide autozygosity patterns and inbreeding levels in Chinese Wagyu beef cattle. Our study identified many candidate regions and genes overlapped with ROH for several important traits, which could be unitized to assist the design of a selection mating strategy in beef cattle. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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16. Genomic sequencing analysis reveals copy number variations and their associations with economically important traits in beef cattle.
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Yang, Liu, Niu, Qunhao, Zhang, Tianliu, Zhao, Guoyao, Zhu, Bo, Chen, Yan, Zhang, Lupei, Gao, Xue, Gao, Huijiang, Liu, George E., Li, Junya, and Xu, Lingyang
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BEEF cattle , *GENOMICS , *DNA copy number variations , *SIMMENTAL cattle , *SEQUENCE analysis , *GENETIC regulation - Abstract
Copy number variation (CNV) represents a major source of genetic variation, which may have potentially large effects, including alternating gene regulation and dosage, as well as contributing to gene expression and risk for normal phenotypic variability. We carried out a comprehensive analysis of CNV based on whole genome sequencing in Chinese Simmental beef cattle. Totally, we found 9313 deletion and 234 duplication events, covering 147.5 Mb autosomal regions. Within them, 257 deletion events of high frequency overlapped with 193 known RefGenes. Among these genes, we observed several genes were related to economically important traits, like residual feed intake, immune responding, pregnancy rate and muscle differentiation. Using a locus-based analysis, we identified 11 deletions and 1 duplication, which were significantly associated with three traits including carcass weight, tenderloin and longissimus muscle area. Our sequencing-based study provided important insights into investigating the association of CNVs with important traits in beef cattle. • We carried out a comprehensive analysis of CNV based on whole genome sequencing in Chinese Simmental beef cattle. • We discovered 11 and 1 significant loci within deletion and duplication regions associated with three production traits. • Our sequencing-based study provided valuable insights into the association of CNVs with important traits in beef cattle. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
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