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Sun SX, Zhang YN, Lu DL, Wang WL, Limbu SM, Chen LQ, Zhang ML, Du ZY. Concentration-dependent effects of 17β-estradiol and bisphenol A on lipid deposition, inflammation and antioxidant response in male zebrafish (Danio rerio). CHEMOSPHERE 2019; 237:124422. [PMID: 31352104 DOI: 10.1016/j.chemosphere.2019.124422] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 07/18/2019] [Accepted: 07/20/2019] [Indexed: 06/10/2023]
Abstract
Environmental estrogenic compounds are important pollutants, which are widely distributed in natural water bodies. They produce various adverse effects on fish, but their concentration-dependent toxicities in fish metabolism and health are not fully understood. This study investigated the effects of 17β-estradiol (E2) and bisphenol A (BPA) at low and high concentrations on lipid deposition, inflammation and antioxidant response in male zebrafish. We measured fish growth parameters, gonad development, lipid contents and the activities of inflammatory and antioxidant enzymes, as well as their mRNA expressions. All E2 and BPA concentrations used increased body weight, damaged gonad structure and induced feminization in male zebrafish. The exposure of zebrafish to E2 and BPA promoted lipid accumulation by increasing total fat, liver triglycerides and free fatty acid contents, and also upregulated lipogenic genes expression, although they decreased total cholesterol content. Notably, zebrafish exposed to low concentrations of E2 (200 ng/L) and BPA (100 μg/L) had higher lipid synthesis and deposition compared to high concentrations (2000 ng/L and 2000 μg/L, respectively). However, the high concentrations of E2 and BPA increased inflammation and antioxidant response. Furthermore, BPA caused greater damage to fish gonad development and more severe lipid peroxidation compared to E2. Overall, the results suggest that the toxic effects of E2 and BPA on zebrafish are concentration-dependent such that, the relative low concentrations used induced lipid deposition, whereas the high ones caused adverse effects on inflammation and antioxidant response.
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Affiliation(s)
- Sheng-Xiang Sun
- Laboratory of Aquaculture Nutrition and Environmental Health (LANEH), School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yun-Ni Zhang
- Laboratory of Aquaculture Nutrition and Environmental Health (LANEH), School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Dong-Liang Lu
- Laboratory of Aquaculture Nutrition and Environmental Health (LANEH), School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Wei-Li Wang
- Laboratory of Aquaculture Nutrition and Environmental Health (LANEH), School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Samwel Mchele Limbu
- Laboratory of Aquaculture Nutrition and Environmental Health (LANEH), School of Life Sciences, East China Normal University, Shanghai, 200241, China; Department of Aquatic Sciences and Fisheries Technology, University of Dar as Salaam, Dar es Salaam, Tanzania
| | - Li-Qiao Chen
- Laboratory of Aquaculture Nutrition and Environmental Health (LANEH), School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Mei-Ling Zhang
- Laboratory of Aquaculture Nutrition and Environmental Health (LANEH), School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Zhen-Yu Du
- Laboratory of Aquaculture Nutrition and Environmental Health (LANEH), School of Life Sciences, East China Normal University, Shanghai, 200241, China.
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2
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Yang SZ, He H, Zhang ZJ, Niu H, Chen FY, Wen YF, Xu JW, Dang RH, Lan XY, Lei CZ, Chen H, Huang BZ, Huang YZ. Determination of genetic effects of SERPINA3 on important growth traits in beef cattle. Anim Biotechnol 2019; 31:164-173. [PMID: 30929567 DOI: 10.1080/10495398.2018.1560306] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Serine protease inhibitor protein 3 (serpin peptidase inhibitor, clade A, member 3, SERPINA3) is a member of the serpin superfamily, probably related to the yield and quality of muscle. This study focuses on the relationship between SERPINA3 gene polymorphism and growth traits in beef cattle. The study first uses sequencing pooled DNA samples (Pool-Seq), PCR-RFLP and Tetra-primer ARMS-PCR techniques to determine the genetic polymorphisms of SERPINA3 in 765 beef cattle. Then, the polymorphic loci were correlated with the growth characters of cattle. Five SNPs (SNP1:A-648G, SNP2:T6496A, SNP3:G2495A, SNP4:T2595A, SNP5:A2615G) were found, located in the promoter, introns 5 and SNP 3, 4, 5 were in exons 2, respectively. The observed He was from 0.44 to 0.5, Ne were approaching 2 (1.78 to 2.00). The maximum and minimum PIC (polymorphism information content) values were 0.37 and 0.34, respectively. The association analysis results showed that the SNPs had a significant height in the chest girth and body length. (p < 0.05 or p < 0.01). This will provide important information for the rapid breeding of Chinese yellow cattle and the establishment of a molecular genetic marker database.
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Affiliation(s)
- Shi-Zhen Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Hua He
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China.,College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Zi-Jing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, People's Republic of China
| | - Hui Niu
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, People's Republic of China
| | - Fu-Ying Chen
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, People's Republic of China
| | - Yi-Fan Wen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Jia-Wei Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Rui-Hua Dang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Xian-Yong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Chu-Zhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Bi-Zhi Huang
- Yunnan Academy of Grassland Animal Science, Xiaoshao, Kunming, People's Republic of China
| | - Yong-Zhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
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3
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Wen YF, Zheng L, Niu H, Zhang GL, Zhang GM, Ma YL, Tian YR, Liu YR, Yang P, Yang DY, Lei CZ, Dang RH, Qi XL, Chen H, Huang BZ, Huang YZ. Exploring genotype-phenotype relationships of the CRABP2 gene on growth traits in beef cattle. Anim Biotechnol 2018; 31:42-51. [PMID: 30570383 DOI: 10.1080/10495398.2018.1531015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Cellular retinoic acid binding protein 2 (CRABP2) is essential to myoblast differentiation. However, there was no report about the function of CRABP2 gene in cattle. This study explored the association of CRABP2 gene polymorphisms with growth traits in cattle breeds by several methods, such as DNA sequencing, PCR, PCR-RFLP and forced PCR-RFLP. Two sequence variants were determined. There were 621 individuals in six cattle breeds from China for the experiment, and three breeds were used to test validation of polymorphisms and extent of linkage disequilibrium (LD). The results showed that both SNPs (SNP1, g.2458 G > T, SNP2, g.3878 G > A) were in intron1. Two SNPs were in low linkage disequilibrium. Association analysis suggested that SNP1 had the significant difference on growth traits with body height, height at hip cross and body slanting length (P < .05), while SNP2 showed a significant difference in growth traits with body height, height at hip cross and body slanting length(P < .05). The results of this investigation displayed that the CRABP2 gene is an available candidate gene and may be used for breed selection and conservation.
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Affiliation(s)
- Yi-Fan Wen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Li Zheng
- Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, People's Republic of China
| | - Hui Niu
- Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, People's Republic of China
| | - Guo-Liang Zhang
- Branch of Animal Science, Jilin Academy of Agricultural Sciences, Gongzhuling, Jilin, People's Republic of China
| | - Gui-Min Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Yi-Lei Ma
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Yi-Ran Tian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Yan-Rong Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Peng Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Di-Yi Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Chu-Zhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Rui-Hua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Xing-Lei Qi
- Bureau of Animal Husbandry of Biyang County, Biyang, Henan, People's Republic of China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
| | - Bi-Zhi Huang
- Yunnan Academy of grassland animal science, Kunming, People's Republic of China
| | - Yong-Zhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, People's Republic of China
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Huang YZ, Qian LN, Wang J, Zhang CL, Fang XT, Lei CZ, Lan XY, Ma Y, Bai YY, Lin FP, Chen H. Genetic Variants in ADD1 Gene and their Associations with Growth Traits in Cattle. Anim Biotechnol 2018. [PMID: 29527980 DOI: 10.1080/10495398.2017.1398754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The α-adducin (ADD1) is a subunit of adducin which is a cytoskeleton heterodimeric protein. Adducin participates in oocytes chromosome meiosis of mice, prompting adducin has an effect on embryonic development. Adducin gene mutation has significantly functional change. So the present study was to identify and characterize polymorphisms within the coding region of the bovine ADD1 gene among different cattle breeds. Here, 11 novel single nucleotide polymorphisms (SNPs 1-11) were identified by DNA sequencing and polymerase chain reaction-single stranded conformational polymorphism, there were one synonymous mutation in exon 1 (SNP1); four missense mutations in exons 4, 7, and 8 (SNPs 3-6); and six mutations in introns 4, 12, 13, and 14 (SNPs 2, 7-10). The statistical analyses indicated that the some SNPs are associated with the growth traits (body length, body height, chest circumference, and hucklebone width) in Chinese Jiaxian cattle population. Our results provide evidence that polymorphisms in the ADD1 gene are associated with growth traits, and may be used for marker-assisted selection in beef cattle breeding program.
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Affiliation(s)
- Yong-Zhen Huang
- a Institute of Cellular and Molecular Biology, School of Life Sciences , Jiangsu Normal University , Xuzhou , Jiangsu , China.,b Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - Li-Na Qian
- b Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - Jian Wang
- a Institute of Cellular and Molecular Biology, School of Life Sciences , Jiangsu Normal University , Xuzhou , Jiangsu , China
| | - Chun-Lei Zhang
- b Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - Xing-Tang Fang
- b Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - Chu-Zhao Lei
- a Institute of Cellular and Molecular Biology, School of Life Sciences , Jiangsu Normal University , Xuzhou , Jiangsu , China
| | - Xian-Yong Lan
- a Institute of Cellular and Molecular Biology, School of Life Sciences , Jiangsu Normal University , Xuzhou , Jiangsu , China
| | - Yun Ma
- c College of Life Sciences , Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang Normal University , Xinyang , Henan , China
| | - Yue-Yu Bai
- d Animal Health Supervision in Henan Province , Zhengzhou , Henan , China
| | - Feng-Peng Lin
- e Bureau of Animal Husbandry of Biyang County , Biyang , Henan , China
| | - Hong Chen
- a Institute of Cellular and Molecular Biology, School of Life Sciences , Jiangsu Normal University , Xuzhou , Jiangsu , China.,b Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
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5
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Tao X, Liang Y, Yang X, Pang J, Zhong Z, Chen X, Yang Y, Zeng K, Kang R, Lei Y, Ying S, Gong J, Gu Y, Lv X. Transcriptomic profiling in muscle and adipose tissue identifies genes related to growth and lipid deposition. PLoS One 2017; 12:e0184120. [PMID: 28877211 PMCID: PMC5587268 DOI: 10.1371/journal.pone.0184120] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 08/18/2017] [Indexed: 11/23/2022] Open
Abstract
Growth performance and meat quality are important traits for the pig industry and consumers. Adipose tissue is the main site at which fat storage and fatty acid synthesis occur. Therefore, we combined high-throughput transcriptomic sequencing in adipose and muscle tissues with the quantification of corresponding phenotypic features using seven Chinese indigenous pig breeds and one Western commercial breed (Yorkshire). We obtained data on 101 phenotypic traits, from which principal component analysis distinguished two groups: one associated with the Chinese breeds and one with Yorkshire. The numbers of differentially expressed genes between all Chinese breeds and Yorkshire were shown to be 673 and 1056 in adipose and muscle tissues, respectively. Functional enrichment analysis revealed that these genes are associated with biological functions and canonical pathways related to oxidoreductase activity, immune response, and metabolic process. Weighted gene coexpression network analysis found more coexpression modules significantly correlated with the measured phenotypic traits in adipose than in muscle, indicating that adipose regulates meat and carcass quality. Using the combination of differential expression, QTL information, gene significance, and module hub genes, we identified a large number of candidate genes potentially related to economically important traits in pig, which should help us improve meat production and quality.
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Affiliation(s)
- Xuan Tao
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Yan Liang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Xuemei Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Jianhui Pang
- Chengdu Biotechservice Institute, Chengdu, Sichuan, China
| | - Zhijun Zhong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Xiaohui Chen
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Yuekui Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Kai Zeng
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Runming Kang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Yunfeng Lei
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Sancheng Ying
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Jianjun Gong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Yiren Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
- * E-mail: (YRG); (XBL)
| | - Xuebin Lv
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
- * E-mail: (YRG); (XBL)
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Yan LJ, Fang XT, Liu Y, Zhang CL, Chen H. Polymorphisms and their Haplotype Combinations in the Lysozyme Gene Associated with the Production Traits of a Chinese Native Chicken Breed. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2017. [DOI: 10.1590/1806-9061-2016-0359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- LJ Yan
- Jiangsu Normal University, China; Nantong College of Science and Technology, China
| | - XT Fang
- Jiangsu Normal University, China
| | - Y Liu
- Jiangsu Normal University, China
| | - CL Zhang
- Jiangsu Normal University, China
| | - H Chen
- Jiangsu Normal University, China
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7
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Huang YZ, Wang Q, Zhang CL, Fang XT, Song EL, Chen H. Genetic Variants in SDC3 Gene are Significantly Associated with Growth Traits in Two Chinese Beef Cattle Breeds. Anim Biotechnol 2016; 27:190-8. [PMID: 27119984 DOI: 10.1080/10495398.2016.1164178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Identification of the genes and polymorphisms underlying quantitative traits, and understanding these genes and polymorphisms affect economic growth traits, are important for successful marker-assisted selection and more efficient management strategies in commercial cattle (Bos taurus) population. Syndecan-3 (SDC3), a member of the syndecan family of type I transmembrane heparan sulfate proteoglycans is a novel regulator of feeding behavior and body weight. The aim of this study is to examine the association of the SDC3 polymorphism with growth traits in Chinese Jiaxian and Qinchuan cattle breeds (). Four single nucleotide polymorphisms (SNPs: 1-4) were detected in 555 cows from three Chinese native cattle breeds by means of sequencing pooled DNA samples and polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) methods. We found one SNP (g.28362A > G) in intron and three SNPs (g.30742T > G, g.30821C > T and 33418 A > G) in exons. The statistical analyses indicated that these SNPs of SDC3 gene were associated with bovine body height, body length, chest circumference, and circumference of cannon bone (P < 0.05). The mutant-type variant was superior for growth traits; the heterozygote was associated with higher growth traits compared to wild-type homozygote. Our result confirms the polymorphisms in the SDC3 gene are associated with growth traits that may be used for marker-assisted selection in beef cattle breeding programs.
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Affiliation(s)
- Yong-Zhen Huang
- a Institute of Cellular and Molecular Biology , Jiangsu Normal University , Xuzhou Jiangsu , China.,b College of Animal Science and Technology , Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture , Yangling Shaanxi , China
| | - Qin Wang
- a Institute of Cellular and Molecular Biology , Jiangsu Normal University , Xuzhou Jiangsu , China
| | - Chun-Lei Zhang
- a Institute of Cellular and Molecular Biology , Jiangsu Normal University , Xuzhou Jiangsu , China
| | - Xing-Tang Fang
- a Institute of Cellular and Molecular Biology , Jiangsu Normal University , Xuzhou Jiangsu , China
| | - En-Liang Song
- c Institute of Animal Husbandry and Veterinary , Shandong Academy of Agricultural Sciences , Jinan , Shandong , China
| | - Hong Chen
- a Institute of Cellular and Molecular Biology , Jiangsu Normal University , Xuzhou Jiangsu , China
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Huang YZ, Li JJ, Zhang CL, Fang XT, Lan XY, Qi XL, Chen H. Effect of Genetic Variations within the I-mfa Gene on the Growth Traits of Chinese Cattle. Anim Biotechnol 2016; 27:278-86. [DOI: 10.1080/10495398.2016.1183500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Yong-Zhen Huang
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu, China
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Jing-Jing Li
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Chun-Lei Zhang
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Xing-Tang Fang
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Xian-Yong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi, China
| | - Xing-Lei Qi
- Bureau of Animal Husbandry of Biyang County, Biyang, Henan, China
| | - Hong Chen
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu, China
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9
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Linkage disequilibrium and haplotype distribution of the bovine LHX4 gene in relation to growth. Gene 2014; 538:354-60. [DOI: 10.1016/j.gene.2013.12.037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 12/04/2013] [Accepted: 12/12/2013] [Indexed: 11/20/2022]
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10
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Huang YZ, Zhan ZY, Li XY, Wu SR, Sun YJ, Xue J, Lan XY, Lei CZ, Zhang CL, Jia YT, Chen H. SNP and haplotype analysis reveal IGF2 variants associated with growth traits in Chinese Qinchuan cattle. Mol Biol Rep 2013; 41:591-8. [PMID: 24374893 DOI: 10.1007/s11033-013-2896-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 12/09/2013] [Indexed: 12/17/2022]
Abstract
Insulin-like growth factor 2 (IGF2) is a potent cell growth and differentiation factor and is implicated in mammals' growth and development. The objective of this study was to evaluate the effects of the mutations in the bovine IGF2 with growth traits in Chinese Qinchuan cattle. Four single nucleotide polymorphisms (SNPs) were detected of the bovine IGF2 by DNA pool sequencing and forced polymerase chain reaction-restriction fragment length polymorphism (forced PCR-RFLP) methods. We also investigated haplotype structure and linkage disequilibrium (LD) coefficients for four SNPs in 817 individuals representing two main cattle breeds from China. The result of haplotype analysis showed eight different haplotypes and 27 combined genotypes within the study population. The statistical analyses indicated that the four SNPs, combined genotypes and haplotypes are associated with the withers height, body length, chest breadth, chest depth and body weight in Qinchuan cattle population (P < 0.05 or <0.01). The mutant-type variants and mutant haplotype (Hap 8: ATGG; likely to be the beneficial QTN allele) was superior for growth traits; the heterozygote diplotype was associated with higher growth traits compared to wild-type homozygote. Our results provide evidence that polymorphisms in the IGF2 gene are associated with growth traits, and may be used for marker-assisted selection in beef cattle breeding program.
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Affiliation(s)
- Yong-Zhen Huang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, No. 22 Xinong Road, Yangling, 712100, Shaanxi, China
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Huang YZ, Sun YJ, Zhan ZY, Li MX, Wang J, Xue J, Lan XY, Lei CZ, Zhang CL, Chen H. Expression, SNP Identification, Linkage Disequilibrium, and Haplotype Association Analysis of the Growth Suppressor GeneZBED6in Qinchuan Beef Cattle. Anim Biotechnol 2013; 25:35-54. [DOI: 10.1080/10495398.2013.814572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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12
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Huang YZ, Wang XL, He H, Lan XY, Lei CZ, Zhang CL, Chen H. Identification and genetic effect of haplotype in the bovine BMP7 gene. Gene 2013; 532:281-7. [DOI: 10.1016/j.gene.2013.03.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 01/25/2013] [Accepted: 03/01/2013] [Indexed: 02/06/2023]
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13
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Bivariate genome-wide association analysis of the growth and intake components of feed efficiency. PLoS One 2013; 8:e78530. [PMID: 24205251 PMCID: PMC3812149 DOI: 10.1371/journal.pone.0078530] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 09/20/2013] [Indexed: 11/19/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) associated with average daily gain (ADG) and dry matter intake (DMI), two major components of feed efficiency in cattle, were identified in a genome-wide association study (GWAS). Uni- and multi-SNP models were used to describe feed efficiency in a training data set and the results were confirmed in a validation data set. Results from the univariate and bivariate analyses of ADG and DMI, adjusted by the feedlot beef steer maintenance requirements, were compared. The bivariate uni-SNP analysis identified (P-value <0.0001) 11 SNPs, meanwhile the univariate analyses of ADG and DMI identified 8 and 9 SNPs, respectively. Among the six SNPs confirmed in the validation data set, five SNPs were mapped to KDELC2, PHOX2A, and TMEM40. Findings from the uni-SNP models were used to develop highly accurate predictive multi-SNP models in the training data set. Despite the substantially smaller size of the validation data set, the training multi-SNP models had slightly lower predictive ability when applied to the validation data set. Six Gene Ontology molecular functions related to ion transport activity were enriched (P-value <0.001) among the genes associated with the detected SNPs. The findings from this study demonstrate the complementary value of the uni- and multi-SNP models, and univariate and bivariate GWAS analyses. The identified SNPs can be used for genome-enabled improvement of feed efficiency in feedlot beef cattle, and can aid in the design of empirical studies to further confirm the associations.
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The effect of haplotype variation in the bovine PAX6 gene. Mol Biol Rep 2013; 40:6775-84. [PMID: 24072657 DOI: 10.1007/s11033-013-2794-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 09/14/2013] [Indexed: 10/26/2022]
Abstract
The transcription factor paired box 6 gene (PAX6) plays a key role during the early development of various organs. In this study, three single nucleotide polymorphisms (SNPs) have been identified in the introns 2, 8 and 11 of the bovine PAX6 gene. 8 haplotypes and 13 diplotypes were revealed and the linkage disequilibrium (LD) was assessed in 817 cows representing four main cattle breeds from China (Nanyang, NY; Qinchuan, QC; Jiaxian, JX; Chinese Holstein, CH). The LD analysis revealed that the additional three SNPs were not in strong LD, the wild haplotype (Hap 1: CTT) and mutant haplotype (Hap 8: TCC) have a frequency of 9.36, 35.61, 18.32, 57.15 % and 15.60, 14.19, 0.83, 0 % in the four cattle populations. The statistical analyses indicated that the SNP2 and 3 are associated with the body weight at birth, 6 and 12 months in NY and JX cattle population (P < 0.01 or P < 0.05); and significant association was detected between 19 (NY) or 13 (JX) diplotype (combined genotypes) and body weight at different ages (birth, 6 and 12 months). Our results provide evidence that some polymorphisms in PAX6 are associated with growth traits at some ages, and may be used as candidates for marker-assisted selection in beef cattle breeding program.
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15
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Huang YZ, He H, Zhan ZY, Sun YJ, Li MX, Lan XY, Lei CZ, Zhang CL, Chen H. Relationship of polymorphisms within ZBED6 gene and growth traits in beef cattle. Gene 2013; 526:107-11. [DOI: 10.1016/j.gene.2013.04.049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 04/13/2013] [Accepted: 04/15/2013] [Indexed: 10/26/2022]
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16
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Huang YZ, Wang J, Zhan ZY, Cao XK, Sun YJ, Lan XY, Lei CZ, Zhang CL, Chen H. Assessment of association between variants and haplotypes of the IGF2 gene in beef cattle. Gene 2013; 528:139-45. [PMID: 23900197 DOI: 10.1016/j.gene.2013.07.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Revised: 06/20/2013] [Accepted: 07/08/2013] [Indexed: 02/07/2023]
Abstract
Insulin-like growth factor 2 (IGF2) is a fetal growth and differentiation factor that plays an important role in muscle growth and in myoblast proliferation and differentiation. The aim of this study was to examine the association of the IGF2 polymorphism with growth traits in beef cattle breed. Four single nucleotide polymorphisms (SNPs: 1-4) were identified in the bovine IGF2 by sequencing pooled DNA samples (Pool-Seq) and forced polymerase chain reaction-restriction fragment length polymorphism (Forced PCR-RFLP) methods. The result of haplotype analysis of four SNPs showed that eight haplotypes and eighteen combined genotypes were revealed, and the linkage disequilibrium and evolutionary relationship were assessed in 1522 individuals representing four purebred cattle breeds from China. The statistical analyses indicated that the 4 SNPs and 18 combined genotypes or haplotypes are associated with the body weight at 18 and 24 months in Jiaxian cattle population (P<0.05 or P<0.01). Our results provide evidence that polymorphisms in the IGF2 gene are associated with growth traits, and may be used for marker-assisted selection in beef cattle breeding program.
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Affiliation(s)
- Yong-Zhen Huang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China.
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17
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GAO YUAN, LIU DONG, MA WEI, LI AIMIN, LAN XIANYONG, ZHANG CHUNLEI, LEI CHUZHAO, CHEN HONG. Two novel SNPs in the coding region of bovine VDR gene and their associations with growth traits. J Genet 2013. [DOI: 10.1007/s12041-013-0244-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Huang YZ, Zhan ZY, Sun YJ, Wang J, Li MX, Lan XY, Lei CZ, Zhang CL, Chen H. Comparative analysis of the IGF2 and ZBED6 gene variants and haplotypes reveals significant effect of growth traits in cattle. Genome 2013; 56:327-34. [DOI: 10.1139/gen-2013-0062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Muscle growth is a complex phenomenon regulated by many factors, whereby net growth results from the combined action of synthesis and turnover. Insulin-like growth factor 2 (IGF2) is a fetal growth and differentiation factor that plays an important role in muscle growth and in myoblast proliferation and differentiation; Zinc finger, BED-type containing 6 (ZBED6) is a novel transcription factor that was identified and shown to act as a repressor of IGF2 transcription in skeletal muscle. In this study, a total of seven single nucleotide polymorphisms (SNPs) were identified, four SNPs in intron 8 of IGF2 and one promoter SNP and two missense mutations in the coding region of ZBED6, two of which were in complete linkage disequilibrium (LD) in the bovine IGF2. The 58 haplotypes were inferred in 1522 individuals representing four purebred cattle breeds from China. The seven SNPs, 79 and 66 combined diplotypes were revealed for association with body mass in Nanyang and Jiaxian cattle populations at five different ages (P < 0.05 or 0.01). The mutant-type variants and haplotype 58 (likely in LD with the beneficial quantitative trait nucleotide allele) was superior for body mass; the heterozygote diplotype of the most common haplotypes 58 was associated with higher body mass compared to either heterozygote or homozygote. The statistical analyses indicated that the mutant-type variants and haplotypes are significantly associated with body mass in study cattle populations at different ages. These data demonstrate that variants and haplotypes are associated with growth traits, and these results may provide important biological insights into the phenotypic differentiation that is associated with adaptation and specialization of cattle breeds.
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Affiliation(s)
- Yong-Zhen Huang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi 712100, China
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19
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Haplotype distribution in the GLI3 gene and their associations with growth traits in cattle. Gene 2013; 513:141-6. [DOI: 10.1016/j.gene.2012.10.052] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 09/08/2012] [Accepted: 10/11/2012] [Indexed: 11/19/2022]
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20
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Huang YZ, He H, Sun JJ, Wang J, Li ZJ, Lan XY, Lei CZ, Zhang CL, Zhang EP, Wang JQ, Chen H. Haplotype combination of SREBP-1c gene sequence variants is associated with growth traits in cattle. Genome 2011; 54:507-16. [DOI: 10.1139/g11-016] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The aim of this study was to examine the association of the SREBP-1c polymorphism with growth traits in cattle breeds. Five sequence variants (SVs) were identified within the bovine sterol regulatory element-binding protein-1c gene (SREBP-1c), using DNA sequencing, PCR, PCR–RFLP, and forced PCR–RFLP methods. These polymorphisms include three missense mutations (SV1, SV4, and SV5) in exons 7, 9, and 12, a silent mutation (SV3) in exon 9, and a large deletion (SV2) in intron 7. Overall, we report the validation of polymorphisms within the bovine SREBP-1c gene, and the haplotype variability and extent of linkage disequilibrium (LD) in 1061 individuals representing the five main cattle breeds from China. We also investigated haplotype frequencies and LD coefficients for five SVs in all study populations. LD and haplotype structure of SREBP-1c were different between breeds. The result of haplotype analysis of five SVs showed that 27 different haplotypes were identified by all breeds. Two haplotypes (Hap1 and Hap2) shared by all five populations accounted for 42.75%, 35.68%, 36.44%, 25.43%, and 96.26% of all haplotypes observed in the cattle breeds Nanyang, Qinchuan, Jiaxian, Jinnan, and Chinese Holstein, respectively. The statistical analyses indicated that one single SV and 38 combined haplotypes were significantly associated with growth traits in the Nanyang cattle population (P < 0.05 or P < 0.01). The results of this study suggest that the SREBP-1c gene possibly is a strong candidate gene that affects growth traits in the Chinese beef cattle breeding program.
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Affiliation(s)
- Yong-Zhen Huang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi 712100, China
| | - Hua He
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi 712100, China
| | - Jia-Jie Sun
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi 712100, China
| | - Jing Wang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi 712100, China
| | - Zhuan-Jian Li
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi 712100, China
| | - Xian-Yong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi 712100, China
| | - Chu-Zhao Lei
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi 712100, China
| | - Chun-Lei Zhang
- Institute of Cellular and Molecular Biology, Xuzhou Normal University, Xuzhou Jiangsu, 221116, China
| | - En-Ping Zhang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi 712100, China
| | - Ju-Qiang Wang
- Research Center of Cattle Engineering Technology in Henan, Zhengzhou Henan, 450003, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling Shaanxi 712100, China
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