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Wang X, Wei C, Zhang Z, Liu D, Guo Y, Sun G, Wang Y, Li H, Tian Y, Kang X, Han R, Li Z. Association of growth traits with a structural variation downstream of the KCNJ11 gene: a large population-based study in chickens. Br Poult Sci 2020; 61:320-327. [PMID: 32008360 DOI: 10.1080/00071668.2020.1724878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
1. The potassium voltage-gated channel subfamily J member 11 gene (KCNJ11) is involved in the insulin secretion pathway. Studies have shown that mutation in this gene is associated with muscle weakness. The objective of the present study was to establish the association between KCNJ11 gene polymorphism and chicken growth performance and to analyse its expression pattern. 2. A novel 163-bp insertion/deletion (indel) polymorphism was identified in the region downstream of the KCNJ11 gene in 2330 individuals from ten populations by polymerase chain reaction (PCR). An F2 resource population was used to investigate the genetic effects of the chicken KCNJ11 gene. Association analysis showed that the indel was significantly associated with chicken growth traits and that the phenotypic value of the ins-ins (II) genotype is higher than that of the ins-del (ID) and del-del (DD) genotypes. 3. Gene expression for different genotypes showed that birds carrying the II allele had a higher expression level than the DD genotypes. Analysis of tissue and spatiotemporal expression patterns indicated that the KCNJ11 gene was highly expressed in muscle tissues, with the highest levels in muscle tissue at one week of age, and that a 10% crude protein diet reduced the expression of this gene, average daily gain and muscle fibre diameter. 4. The results suggested that this novel 163-bp indel has the potential to become a new target for marker-assisted selection.
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Affiliation(s)
- X Wang
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
| | - C Wei
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
| | - Z Zhang
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
| | - D Liu
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
| | - Y Guo
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
| | - G Sun
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
| | - Y Wang
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
| | - H Li
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
| | - Y Tian
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
| | - X Kang
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
| | - R Han
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
| | - Z Li
- Department of Animal Breeding and Genetics, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, No.15 Longzihu University Area, Zhengdong New District, College of Animal Science and Veterinary Medicine, Henan Agricultural University , Zhengzhou, China
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Liu D, Han R, Wang X, Li W, Tang S, Li W, Wang Y, Jiang R, Yan F, Wang C, Liu X, Kang X, Li Z. A novel 86-bp indel of the motilin receptor gene is significantly associated with growth and carcass traits in Gushi-Anka F 2 reciprocal cross chickens. Br Poult Sci 2019; 60:649-658. [PMID: 31469320 DOI: 10.1080/00071668.2019.1655710] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
1. A previous whole-genome association analysis has identified the motilin receptor gene (MLNR), which regulates gastrointestinal motility and gastric emptying, as a candidate gene related to chicken growth.2. MLNR mRNA was expressed in all tissues tested, and the expression level in digestive tissues was greater than in other tissues. Expression levels in the pancreas, duodenum and glandular stomach at day old and one, two and three weeks of age indicated a possible correlation with the digestive system. This suggested that the MLNR gene plays a central role in gastrointestinal tract function and affects the growth and development of chickens. Moreover, there was a significant difference in expression in the glandular stomach tissue between Ross 308 and Gushi chickens at six weeks of age.3. Re-sequencing revealed an 86-bp insertion/deletion polymorphism in the downstream region of the MLNR gene. The mutation locus was genotyped in 2,261 individuals from nine different chicken breeds. MLNR expression levels in the glandular stomach of chickens with DD genotypes were greater than those in chickens with the ID and II genotypes. The DD genotype was the most dominant genotype in commercial broiler's (Ross 308 and Arbor Acres broilers), and the D allele frequency in these breeds exceeded 91%. The deletion mutation tended towards fixation in commercial broilers.4. Association with growth and carcass traits analysed in a Gushi-Anka F2 intercrossed population, showed that the DD genotype was significantly associated with the greatest growth and carcass trait values, whereas values associated with the II genotype were the lowest in the F2 reciprocal cross chickens.5. The results suggest that the mutation is strongly associated with growth related traits and it is likely to be useful for marker-assisted selection of chickens.
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Affiliation(s)
- D Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, Henan, China
| | - R Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, Henan, China
| | - X Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, Henan, China
| | - W Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, Henan, China
| | - S Tang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - W Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, Henan, China
| | - Y Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, Henan, China
| | - R Jiang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, Henan, China
| | - F Yan
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, Henan, China
| | - C Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, Henan, China
| | - X Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, Henan, China
| | - X Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, Henan, China
| | - Z Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, Henan, China
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Wang Y, Wang S, Wang S, Li G, Jiang R, Li Z, Han R, Kang X, Sun G. Target gene identification and functional characterization of miR-1704 in chicken. Anim Biotechnol 2019; 31:229-236. [PMID: 31039664 DOI: 10.1080/10495398.2019.1585365] [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: 10/26/2022]
Abstract
MiRNAs are small non-coding RNAs that negatively regulate gene expression at the post-transcriptional level. SNPs in miRNA genes may lead to phenotypic variation by altering miRNA expression and their targets. In this study, miR-1704 expression profiles in nine tissues at 1 d, 6 weeks and 16 weeks old Gushi chickens were detected. MiR-1704 was widely expressed in the detection of tissues. The expression in 1 d and 6 weeks old was low abundance, while its expression at 16 weeks was very high. An rs14668705 (C > G) SNP was detected within the pre-miR-1704 in an F2 resource population of Gushi chicken crossed with Anka broiler. Bioinformatic analysis indicated that the C > G mutation could introduce a base-pair mismatch and cause the change of free energy. Experiments further revealed that the rs14668705 in precursor miR-1704 could significantly affect mature miR-1704 biogenesis and was significantly associated with body weight at the age of 0, 6, 8, 10, and 12 weeks, shank circumference at 4, 8, and 12 weeks, carcass weight, and semi-evisceration weight (p < 0.05). Insulin receptor 2 (IRS2) gene, one of the potential targets of miR-1704 was identified and further confirmed. These data suggested that miR-1704 targeted IRS2 and have an effect on body weight in chicken.
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Affiliation(s)
- Yongcai Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, PR China
| | - Shunhong Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, PR China
| | - Shanghe Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, PR China
| | - Guoxi Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, PR China
| | - RuiRui Jiang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, PR China
| | - Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, PR China
| | - Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, PR China
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, PR China
| | - Guirong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, PR China
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4
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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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5
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Xu W, He H, Zheng L, Xu JW, Lei CZ, Zhang GM, Dang RH, Niu H, Qi XL, Chen H, Huang YZ. Detection of 19-bp deletion within PLAG1 gene and its effect on growth traits in cattle. Gene 2018; 675:144-149. [DOI: 10.1016/j.gene.2018.06.041] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/10/2018] [Accepted: 06/14/2018] [Indexed: 12/24/2022]
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6
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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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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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8
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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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Bagnato A, Strillacci MG, Pellegrino L, Schiavini F, Frigo E, Rossoni A, Fontanesi L, Maltecca C, Prinsen RT, Dolezal MA. Identification and Validation of Copy Number Variants in Italian Brown Swiss Dairy Cattle Using Illumina Bovine SNP50 Beadchip®. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2015.3900] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Alessandro Bagnato
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, University of Bologna, Italy
| | - Maria G. Strillacci
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
| | - Laura Pellegrino
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
| | - Fausta Schiavini
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
| | - Erika Frigo
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
| | - Attilio Rossoni
- Associazione Nazionale Allevatori Razza Bruna, Bussolengo (VR), Italy
| | - Luca Fontanesi
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, University of Bologna, Italy
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA
| | - Raphaelle T.M.M. Prinsen
- Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, University of Milan, Italy
| | - Marlies A. Dolezal
- Institut für Populationsgenetik Veterinärmedizinische, University of Wien, Austria
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10
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Genome-wide association study (GWAS) for growth rate and age at sexual maturation in Atlantic salmon (Salmo salar). PLoS One 2015; 10:e0119730. [PMID: 25757012 PMCID: PMC4355585 DOI: 10.1371/journal.pone.0119730] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 01/25/2015] [Indexed: 11/26/2022] Open
Abstract
Early sexual maturation is considered a serious drawback for Atlantic salmon aquaculture as it retards growth, increases production times and affects flesh quality. Although both growth and sexual maturation are thought to be complex processes controlled by several genetic and environmental factors, selection for these traits has been continuously accomplished since the beginning of Atlantic salmon selective breeding programs. In this genome-wide association study (GWAS) we used a 6.5K single-nucleotide polymorphism (SNP) array to genotype ∼480 individuals from the Cermaq Canada broodstock program and search for SNPs associated with growth and age at sexual maturation. Using a mixed model approach we identified markers showing a significant association with growth, grilsing (early sexual maturation) and late sexual maturation. The most significant associations were found for grilsing, with markers located in Ssa10, Ssa02, Ssa13, Ssa25 and Ssa12, and for late maturation with markers located in Ssa28, Ssa01 and Ssa21. A lower level of association was detected with growth on Ssa13. Candidate genes, which were linked to these genetic markers, were identified and some of them show a direct relationship with developmental processes, especially for those in association with sexual maturation. However, the relatively low power to detect genetic markers associated with growth (days to 5 kg) in this GWAS indicates the need to use a higher density SNP array in order to overcome the low levels of linkage disequilibrium observed in Atlantic salmon before the information can be incorporated into a selective breeding program.
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11
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Huang YZ, Jing YJ, Sun YJ, Lan XY, Zhang CL, Song EL, Chen H. Exploring genotype-phenotype relationships of the LHX3 gene on growth traits in beef cattle. Gene 2015; 561:219-24. [PMID: 25688878 DOI: 10.1016/j.gene.2015.02.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 01/06/2015] [Accepted: 02/12/2015] [Indexed: 11/17/2022]
Abstract
The LIM-homeobox gene 3 (LHX3) plays an essential role in pituitary gland and nervous system development. Sequence variants (SVs) in coding and non-coding regions of LHX3 gene have an impact on LHX3 transcription and growth traits in cattle. Previously, we have identified 3 single nucleotide polymorphisms (SNPs: 1-3) in all exons and intron 2 regions of the LHX3 gene in cattle. Here, 7 novel SNPs (SNPs: 4-10) were identified by DNA sequencing and polymerase chain reaction single-stranded conformational polymorphism (PCR-SSCP) methods. In the present study, a total of 10 SNPs were assessed linkage disequilibrium (LD) in 802 cows representing four main cattle breeds from China (Nanyang, Qinchuan, Jiaxian, and Chinese Holstein). The assessment results demonstrated that 17 haplotypes and 18 diplotypes were revealed in these cattle populations. Moreover, association analysis indicated that the genotypes of SNPs 1-6 are associated with the body weight at 6, 12 and 18months of age in Nanyang cattle (P<0.01 or P<0.05), whereas no significant association was found between the 18 diplotypes and growth traits. Our results provide evidence that some SNPs in LHX3 gene may be associated with body weight at certain age, and LHX3 gene may be used as candidate gene for marker-assisted selection (MAS) in beef cattle breeding.
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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.
| | - Yong-Jie Jing
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, China
| | - Yu-Jia Sun
- 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
| | - Chun-Lei Zhang
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - En-Liang Song
- Institute of Animal Husbandry and Veterinary, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, 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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12
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Hariharan N, Sussman MA. Stressing on the nucleolus in cardiovascular disease. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1842:798-801. [PMID: 24514103 PMCID: PMC3972279 DOI: 10.1016/j.bbadis.2013.09.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 09/18/2013] [Indexed: 12/23/2022]
Abstract
The nucleolus is a multifunctional organelle with multiple roles involving cell proliferation, growth, survival, ribosome biogenesis and stress response signaling. Alteration of nucleolar morphology and architecture signifies an early response to increased cellular stress. This review briefly summarizes nucleolar response to cardiac stress signals and details the role played by nucleolar proteins in cardiovascular pathophysiology. This article is part of a Special Issue entitled: Role of the Nucleolus in Human Disease.
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Affiliation(s)
- Nirmala Hariharan
- Department of Biology, San Diego State University Heart Institute, San Diego State University, San Diego, CA 92182, USA
| | - Mark A Sussman
- Department of Biology, San Diego State University Heart Institute, San Diego State University, San Diego, CA 92182, USA.
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13
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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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14
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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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15
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Rothammer S, Seichter D, Förster M, Medugorac I. A genome-wide scan for signatures of differential artificial selection in ten cattle breeds. BMC Genomics 2013; 14:908. [PMID: 24359457 PMCID: PMC3878089 DOI: 10.1186/1471-2164-14-908] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 12/16/2013] [Indexed: 11/11/2022] Open
Abstract
Background Since the times of domestication, cattle have been continually shaped by the influence of humans. Relatively recent history, including breed formation and the still enduring enormous improvement of economically important traits, is expected to have left distinctive footprints of selection within the genome. The purpose of this study was to map genome-wide selection signatures in ten cattle breeds and thus improve the understanding of the genome response to strong artificial selection and support the identification of the underlying genetic variants of favoured phenotypes. We analysed 47,651 single nucleotide polymorphisms (SNP) using Cross Population Extended Haplotype Homozygosity (XP-EHH). Results We set the significance thresholds using the maximum XP-EHH values of two essentially artificially unselected breeds and found up to 229 selection signatures per breed. Through a confirmation process we verified selection for three distinct phenotypes typical for one breed (polledness in Galloway, double muscling in Blanc-Bleu Belge and red coat colour in Red Holstein cattle). Moreover, we detected six genes strongly associated with known QTL for beef or dairy traits (TG, ABCG2, DGAT1, GH1, GHR and the Casein Cluster) within selection signatures of at least one breed. A literature search for genes lying in outstanding signatures revealed further promising candidate genes. However, in concordance with previous genome-wide studies, we also detected a substantial number of signatures without any yet known gene content. Conclusions These results show the power of XP-EHH analyses in cattle to discover promising candidate genes and raise the hope of identifying phenotypically important variants in the near future. The finding of plausible functional candidates in some short signatures supports this hope. For instance, MAP2K6 is the only annotated gene of two signatures detected in Galloway and Gelbvieh cattle and is already known to be associated with carcass weight, back fat thickness and marbling score in Korean beef cattle. Based on the confirmation process and literature search we deduce that XP-EHH is able to uncover numerous artificial selection targets in subpopulations of domesticated animals.
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Affiliation(s)
| | | | | | - Ivica Medugorac
- Chair of Animal Genetics and Husbandry, Ludwig-Maximilians-University Munich, Veterinärstr, 13, 80539 Munich , Germany.
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16
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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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17
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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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18
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He H, Zhang HL, Li ZX, Liu Y, Liu XL. Expression, SNV identification, linkage disequilibrium, and combined genotype association analysis of the muscle-specific gene CSRP3 in Chinese cattle. Gene 2013; 535:17-23. [PMID: 24279998 DOI: 10.1016/j.gene.2013.11.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 11/04/2013] [Accepted: 11/08/2013] [Indexed: 11/28/2022]
Abstract
The cysteine and glycine-rich protein 3 (CSRP3) plays an important role in the myofiber differentiation. Here, we identified five SNVs in all exon and intron regions of the CSRP3 gene using DNA sequencing, PCR-RFLP and forced-PCR-RFLP methods in 554 cattle. Four of the five SNVs were significantly associated with growth performance and carcass traits of the cattle. In addition, we evaluated haplotype frequency and linkage disequilibrium coefficient of five sequence variants. The result of haplotype analysis demonstrated 28 haplotypes present in Qinchuan and two haplotypes in Chinese Holstein. Only haplotypes 1 and 8 were being shared by two populations, haplotype 14 had the highest haplotype frequency in Qinchuan (17.4%) and haplotype 8 had the highest haplotype frequency in Chinese Holstein (94.4%). Statistical analyses of combined genotypes indicated that some combined genotypes were significantly or highly significantly associated with growth and carcass traits in the Qinchuan cattle population. qPCR analyses also showed that bovine CSRP3 gene was exclusively expressed in longissimus dorsi muscle and heart tissues. The data support the high potential of the CSRP3 as a marker gene for the improvement of growth performance and carcass traits in selection programs.
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Affiliation(s)
- Hua He
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China
| | - Hui-Lin Zhang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China
| | - Zhi-Xiong Li
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China
| | - Yu Liu
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China
| | - Xiao-Lin Liu
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling, Shaanxi 712100, PR China.
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19
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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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20
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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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21
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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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22
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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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23
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He H, Liu XL, Zhang HL, Yang J, Niu FB, Li ZX, Liu Y, Chen L. SNV and haplotype analysis reveals new CSRP1 variants associated with growth and carcass traits. Gene 2013; 522:206-13. [PMID: 23537997 DOI: 10.1016/j.gene.2013.03.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 03/08/2013] [Indexed: 11/27/2022]
Abstract
The cysteine and glycine-rich protein 1 and 2 genes (CSRP1 and CSRP2) are an effective growth factor in promoting skeletal muscle growth in vitro and vivo. However, in cattle, the information on the CSRP1 and CSRP2 genes is very limited. The aim of this study was to examine the association of the CSRP1 and CSRP2 variants with growth and carcass traits in cattle breeds. Three single nucleotide variants (SNVs) were identified within the bovine CSRP1 gene, whereas CSRP2 gene has not detected any SNVs, using DNA pooled sequencing, PCR-RFLP, and forced PCR-RFLP methods. These SNVs include g. 801T>C (Intron 2), g. 46T>C (Exon 3) and g. 99C>G (Intron 3). Besides, we also investigated haplotype frequencies and linkage disequilibrium (LD) coefficients for three SNVs in all study populations. LD and haplotype structure of CSRP1 were different between breeds. The result of haplotype analysis demonstrated eight haplotype present in QC (Qinchuan) and one haplotype in CH (Chinese Holstein). Only haplotype 1 (TTC), shared by all two populations, comprised 10.74% and 100.00%, of all haplotypes observed in QC and CH, respectively. Haplotype 5 (CTC) had the highest haplotype frequencies in QC (30.98%) and haplotype 1 had the highest haplotype frequencies in CH (100.00%). The statistical analyses indicated that one single SNV and 19 combined haplotypes were significantly or highly significantly associated with growth and carcass traits in the QC cattle population (P<0.05 or P<0.01). Quantitative real-time PCR (qRT-PCR) analyses showed that the bovine CSRP1 and CSRP2 genes were widely expressed in many tissues. The results of this study suggest that the CSRP1 gene possibly is a strong candidate gene that affects growth and carcass traits in the Chinese beef cattle breeding.
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Affiliation(s)
- Hua He
- 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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24
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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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25
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Zhou Y, Lan X, Xu Y, Zhang B, Li M, Huang Y, Sun J, Cai H, Lei C, Chen H. Exploring polymorphisms and potential application roles of the bovine Nfix gene in breeding. Genome 2012; 55:845-51. [DOI: 10.1139/gen-2012-0114] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The aim of this study was to detect mutations of the nuclear factor I/X (Nfix) gene and examine the association of its polymorphisms with growth traits in cattle. Six sequence variants (SVs) including five single-nucleotide mutations and an indel with multiple alleles were detected, among which four polymorphisms within the Nfix gene were identified in 1159 individuals of five cattle breeds by sequencing and forced PCR–RFLP methods. The results of haplotype analysis showed 14 haplotypes within the breeds. Three haplotypes were shared by the five cattle breeds. Hap1 (ACAI) was extremely predominant in all test populations, which suggested that individuals with Hap1 (ACAI) were more adapted to the steppe environment. Association analysis in Nanyang cattle showed that two SVs of the Nfix gene were significantly associated with growth traits at different ages. In addition, the locations of the SVs showed that the 3′ terminal of the bovine Nfix gene was unstable. Combining this instability with its characteristic of multiple alternative splicing, we conjectured that some SVs might have a relationship with the formation of the splices through which growth traits are modulated. This study will provide useful information for the selection and detection of multiple forms of alternative splicing of the bovine Nfix gene.
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Affiliation(s)
- Yang Zhou
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi 712100, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi 712100, China
| | - Yao Xu
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi 712100, China
| | - Bao Zhang
- College of Medicine, Xi’an Jiaotong University, Key Laboratory of National Ministry of Health for Forensic Sciences, Xi’an, Shaanxi 710061, China
| | - Mijie Li
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi 712100, China
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi 712100, China
| | - Jiajie Sun
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi 712100, China
| | - Hanfang Cai
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi 712100, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi 712100, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Agricultural Molecular Biology, Yangling, Shaanxi 712100, China
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26
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Zhao J, Zhang C, Fang X, Zhang H, Liu X, Li J, Liu Y, Yang D, Chen H. Polymorphisms of the bovine WNT10B gene and their associations with growth traits. Res Vet Sci 2012; 93:1301-6. [PMID: 22840331 DOI: 10.1016/j.rvsc.2012.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 07/01/2012] [Accepted: 07/03/2012] [Indexed: 12/21/2022]
Abstract
Wingless-type MMTV integration site family, member 10B (WNT10B) may play an important role in inhibiting differentiation of preadipocytes in vitro and impairing adipose development in vivo. In this study, based on DNA sequencing and PCR-RFLP methods, we attempted to characterize the associations between common genetic polymorphisms in WNT10B and growth traits of 435 female cattle from three breeds (Jiaxian, Qinchuan and Luxi cattle). The results indicated that g.220A>G was in the intron 1, and g.1617C>T, g.3980G>T, g.4711G>C were in the coding region. At the g.3980G>T locus, Jiaxian cattle individuals with genotype TT had greater body length than those with genotypes GG and GT (P<0.05). At the g.220A>G locus, Qinchuan cattle individuals with genotype GG had greater growth traits than those with genotype AA and AG (P<0.05 or P<0.01). These statistical results showed that the WNT10B gene might be a potential candidate gene for marker-assisted selection (MAS).
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Affiliation(s)
- Jing Zhao
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, Jiangsu 221116, PR China
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27
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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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He H, Liu X, Gu Y, Liu Y, Yang J. Effect of genetic variation of CEBPA gene on body measurement and carcass traits of Qinchuan cattle. Mol Biol Rep 2010; 38:4965-9. [DOI: 10.1007/s11033-010-0640-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 12/03/2010] [Indexed: 11/27/2022]
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