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Ma J, Gao X, Li J, Gao H, Wang Z, Zhang L, Xu L, Gao H, Li H, Wang Y, Zhu B, Cai W, Wang C, Chen Y. Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array. Animals (Basel) 2021; 11:ani11123469. [PMID: 34944246 PMCID: PMC8698132 DOI: 10.3390/ani11123469] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/24/2021] [Accepted: 12/02/2021] [Indexed: 11/16/2022] Open
Abstract
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. The admixture analysis showed that Huaxi cattle has distinct genetic structures among all populations at K = 4. It can be concluded that Huaxi cattle has formed its own unique genetic features. Using integrated haplotype score (iHS) and composite likelihood ratio (CLR) methods, we identified 143 and 199 potentially selected genes in Huaxi cattle, respectively, among which nine selected genes (KCNK1, PDLIM5, CPXM2, CAPN14, MIR2285D, MYOF, PKDCC, FOXN3, and EHD3) related to ion binding, muscle growth and differentiation, and immunity were detected by both methods. Our study sheds light on the unique genetic feature and phylogenetic relationship of Huaxi cattle, provides a basis for the genetic mechanism analysis of important economic traits, and guides further intensive breeding improvement of Huaxi cattle.
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Affiliation(s)
- Jun Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Xue Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Zezhao Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Han Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Hongwei Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Yahui Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Bo Zhu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Wentao Cai
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
| | - Congyong Wang
- Beijing Lianyu Beef Cattle Breeding Technology Limited Company, Beijing 100193, China;
| | - Yan Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.M.); (X.G.); (J.L.); (H.G.); (Z.W.); (L.Z.); (L.X.); (H.G.); (H.L.); (Y.W.); (B.Z.); (W.C.)
- Correspondence:
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Zhang X, Chu Q, Guo G, Dong G, Li X, Zhang Q, Zhang S, Zhang Z, Wang Y. Genome-wide association studies identified multiple genetic loci for body size at four growth stages in Chinese Holstein cattle. PLoS One 2017; 12:e0175971. [PMID: 28426785 PMCID: PMC5398616 DOI: 10.1371/journal.pone.0175971] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 04/03/2017] [Indexed: 12/14/2022] Open
Abstract
The growth and maturity of cattle body size affect not only feed efficiency, but also productivity and longevity. Dissecting the genetic architecture of body size is critical for cattle breeding to improve both efficiency and productivity. The volume and weight of body size are indicated by several measurements. Among them, Heart Girth (HG) and Hip Height (HH) are the most important traits. They are widely used as predictors of body weight (BW). Few association studies have been conducted for HG and HH in cattle focusing on single growth stage. In this study, we extended the Genome-wide association studies to a full spectrum of four growth stages (6-, 12-, 18-, and 24-months after birth) in Chinese Holstein heifers. The whole genomic single nucleotide polymorphisms (SNPs) were obtained from the Illumina BovineSNP50 v2 BeadChip genotyped on 3,325 individuals. Estimated breeding values (EBVs) were derived for both HG and HH at the four different ages and analyzed separately for GWAS by using the Fixed and random model Circuitous Probability Unification (FarmCPU) method. In total, 27 SNPs were identified to be significantly associated with HG and HH at different growth stages. We found 66 candidate genes located nearby the associated SNPs, including nine genes that were known as highly related to development and skeletal and muscular growth. In addition, biological function analysis was performed by Ingenuity Pathway Analysis and an interaction network related to development was obtained, which contained 16 genes out of the 66 candidates. The set of putative genes provided valuable resources and can help elucidate the genomic architecture and mechanisms underlying growth traits in dairy cattle.
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Affiliation(s)
- Xu Zhang
- Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Qin Chu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, P.R. China
| | - Gang Guo
- Beijing Sunlon Livestock Development Co. Ltd, Beijing, P.R. China
| | - Ganghui Dong
- Beijing Sunlon Livestock Development Co. Ltd, Beijing, P.R. China
| | - Xizhi Li
- Beijing Sunlon Livestock Development Co. Ltd, Beijing, P.R. China
| | - Qin Zhang
- Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| | - Shengli Zhang
- Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Yachun Wang
- Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
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Deng H, Guo Y, Song H, Xiao B, Sun W, Liu Z, Yu X, Xia T, Cui L, Guo J. MicroRNA-195 and microRNA-378 mediate tumor growth suppression by epigenetical regulation in gastric cancer. Gene 2013; 518:351-9. [PMID: 23333942 DOI: 10.1016/j.gene.2012.12.103] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 10/30/2012] [Accepted: 12/24/2012] [Indexed: 12/19/2022]
Abstract
The epigenetic regulation of microRNAs is one of several mechanisms underlying carcinogenesis. We found that microRNA-195 (miR-195) and microRNA-378 (miR-378) were significantly down-regulated in gastric cancer tissues and gastric cancer cell lines. The expression of miR-195 and miR-378 in gastric cancer cells was significantly restored by 5-aza-dC, a demethylation reagent. The low expression of miR-195 and miR-378 was closely related to the presence of promoter CpG island methylation. Treatment with miR-195/miR-378 mimics strikingly suppressed the growth of gastric cancer cells whereas promoted the growth of normal gastric epithelial cells. In contrast, administration of miR-195/miR-378 inhibitors significantly prevented the growth of normal gastric epithelial cells. Expression of cyclin-dependent kinase 6 and vascular endothelial growth factor was down-regulated by exogenous miR-195 and miR-378, respectively. In conclusion, miR-195 and miR-378 are abnormally expressed and epigenetically regulated in gastric cancer cell lines and tissues via the suppression of CDK6 and VEGF signaling, suggesting that miR-195 and miR-378 have tumor suppressor properties in gastric cancer.
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Affiliation(s)
- Hongxia Deng
- Department of Biochemistry and Molecular Biology, and Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211, China
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