1
|
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.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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: 2] [Impact Index Per Article: 0.3] [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.
Collapse
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
| |
Collapse
|
4
|
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
| |
Collapse
|
5
|
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]
|
6
|
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.
Collapse
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
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
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]
|
8
|
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]
|
9
|
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.
Collapse
|
10
|
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]
|
11
|
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.
Collapse
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.
| | | | | | | | | | | | | | | | | |
Collapse
|
12
|
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.
Collapse
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
| | | | | | | | | | | | | | | | | |
Collapse
|
13
|
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]
|