Genetic variants of the growth differentiation factor 8 affect body conformation traits in Chinese Dabieshan cattle
2
조회
0
다운로드
0
인용
0
참고문헌
키워드
초록
Objective: The growth differentiation factor 8 (GDF8) gene plays a key role in bone formation, resorption, and skeletal muscle development in mammals. Here, we studied the genetic variants of GDF8 and their contribution to body conformation traits in Chinese Dabieshan cattle. Methods: Single nucleotide polymorphisms (SNPs) were identified in the bovine GDF8 gene by DNA sequencing. Phylogenetic analysis, motif analysis, and genetic diversity analysis were conducted using bioinformatics software. Association analysis between five SNPs, haplotype combinations, and body conformation traits was conducted in 380 individuals. Results: The GDF8 was highly conserved in seven species, and the GDF8 sequence of cattle was most similar to the sequences of sheep and goat based on the phylogenetic analysis. The motif analysis showed that there were 12 significant motifs in GDF8. Genetic diversity analysis indicated that the polymorphism information content of the five studied SNPs was within 0.25 to 0.5. Haplotype analysis revealed a total of 12 different haplotypes and those with a frequency of <0.05 were excluded. Linkage disequilibrium analysis showed a strong linkage (r2>0.330) between the following SNPs: g.5070C>A, g.5076T>C, and g.5148A>C. Association analysis indicated these five SNPs were associated with some of the body conformation traits (p<0.05), and the animals with haplotype combination H1H1 (-GGGG CCTTAA-) had greater wither height, hip height, heart girth, abdominal girth, and pin bone width than the other (p<0.05) Dabieshan cattle. Conclusion: Overall, our results indicate that the genetic variants of GDF8 affected the body conformation traits of Chinese Dabieshan cattle, and the GDF8 gene could make a strong candidate gene in Dabieshan cattle breeding programs.
Abstract
Objective: The growth differentiation factor 8 (GDF8) gene plays a key role in bone formation, resorption, and skeletal muscle development in mammals. Here, we studied the genetic variants of GDF8 and their contribution to body conformation traits in Chinese Dabieshan cattle. Methods: Single nucleotide polymorphisms (SNPs) were identified in the bovine GDF8 gene by DNA sequencing. Phylogenetic analysis, motif analysis, and genetic diversity analysis were conducted using bioinformatics software. Association analysis between five SNPs, haplotype combinations, and body conformation traits was conducted in 380 individuals. Results: The GDF8 was highly conserved in seven species, and the GDF8 sequence of cattle was most similar to the sequences of sheep and goat based on the phylogenetic analysis. The motif analysis showed that there were 12 significant motifs in GDF8. Genetic diversity analysis indicated that the polymorphism information content of the five studied SNPs was within 0.25 to 0.5. Haplotype analysis revealed a total of 12 different haplotypes and those with a frequency of <0.05 were excluded. Linkage disequilibrium analysis showed a strong linkage (r2>0.330) between the following SNPs: g.5070C>A, g.5076T>C, and g.5148A>C. Association analysis indicated these five SNPs were associated with some of the body conformation traits (p<0.05), and the animals with haplotype combination H1H1 (-GGGG CCTTAA-) had greater wither height, hip height, heart girth, abdominal girth, and pin bone width than the other (p<0.05) Dabieshan cattle. Conclusion: Overall, our results indicate that the genetic variants of GDF8 affected the body conformation traits of Chinese Dabieshan cattle, and the GDF8 gene could make a strong candidate gene in Dabieshan cattle breeding programs.
참고문헌 (31)
- China national commission of animal genetic resources, "Animal genetic research in China, bovines" (2010), Chinese Agricultural Press
- McPherron A, "Regulation of skeletal muscle mass in mice by a new TGF-beta superfamily member", Nature, 387, pp.83~90 (1997)[DOI]
- Thomas M, "Myostatin, a negative regulator of muscle growth, functions by inhibiting myoblast proliferation", J Biol Chem, 275, pp.40235~40243 (2000)[DOI]
- Grobet L, "A deletion in the bovine myostatin gene causes the double-muscled phenotype in cattle", Nat Genet, 17, pp.71~74 (1997)[DOI]
- Bi Y, "Myostatin (MSTN) gene indel variation and its associations with body traits in Shaanbei White Cashmere goat", Animals(Basel), 10, pp.168~ (2020)[DOI]
- Yang DY, "Study on molecular markers of growth and development in cattle by candidate genes", Doctor, pp.2006
- Saitou N, "The neighbor-joining method : a new method for reconstructing phylogenetic trees", Mol Biol Evol, 4, pp.406~425 (1987)[DOI]
- Bailey TL, "MEME SUITE : tools for motif discovery and searching", Nucleic Acids Res, 37, pp.W202~W208 (2009)[DOI]
- Marchler-Bauer A, "CDD", SPARCLE : functional classification of proteins via subfamily domain architectures, 2016, pp.45, D200~D203
- Wang G, "Novel polymorphisms of SIX4gene and their association with body measurement traits in Qinchuan cattle", Gene, 539, pp.107~110 (2014)[DOI]
- Yang W, "Association study and expression analysis of MTNR1A as a candidate gene for body measurement and meat quality traits in Qinchuan cattle", Gene, 570, pp.199~204 (2015)[DOI]
- Chakraborty R, "Bottleneck effects on average heterozygosity and genetic distance with the stepwise mutation model", Evolution, 31, pp.347~356 (1977)[DOI]
- Slatkin M, "Linkage disequilibrium—understanding the evolutionary past and mapping the medical future", Nat Rev Genet, 9, pp.477~485 (2008)[DOI]
- Li Z, "A partition-ligation-combinationsubdivision EM algorithm for haplotype inference with multiallelic markers: update of the SHEsis (http:", CellRes, pp.2009, 19[DOI]
- Ardlie KG, "Patterns of linkage disequilibrium in the human genome", Nat Rev Genet, 3, pp.299~309 (2002)[DOI]
- Lin-sheng Gui, "Analysis of the oxidized low density lipoprotein receptor 1 gene as a potential marker for carcass quality traits in Qinchuan cattle", Animal Bioscience, 32(1), pp.58~62 (2019), 아세아·태평양축산학회[DOI]
- Akey J, "Haplotypes vs single marker linkage disequilibrium tests : what do we gain?", Eur J Hum Genet, 9, pp.291~300 (2001)[DOI]
- Chen YS, "GDF8 inhibits bone formation and promotes bone resorption in mice", Clin Exp Pharmacol Physiol, 44, pp.500~508 (2017)[DOI]
- Na R, "SNP screening of the MSTN gene and correlation analysis between genetic polymorphisms and growth traits in Dazu black goat", Anim Biotechnol, 32, pp.558~565 (2020)[DOI]
- Liang CN, "Association of single nucleotide polymorphism at intron 2 of MSTN gene with growth traits in yak", Journal of Huazhong Agricultural University, 30, pp.285~289 (2011)[DOI]
- Tozaki T, "Sequence variants at the myostatin gene locus influence the body composition of Thoroughbred horses", J Vet Med Sci, 73, pp.1617~1624 (2011)[DOI]
- Wu S, "Genetic variants and haplotype combination in the bovine CRTC3 affected conformation traits in two Chinese native cattle breeds(Bos Taurus)", Genomics, 111, pp.1736~1744 (2019)[DOI]
- Wen YF, "Exploring genotype-phenotype relationships of the CRABP2 gene on growth traits in beef cattle", Anim Biotechnol, 31, pp.42~51 (2020)[DOI]
- Huang YZ, "Haplotype combination of SREBP-1c gene sequence variants is associated with growth traits in cattle", Genome, 54, pp.507~516 (2011)[DOI]
- Xu Y, "SNP and haplotype analysis of paired box 3(PAX3) gene provide evidence for association with growth traits in Chinese cattle", Mol Biol Rep, 41, pp.4295~4303 (2014)[DOI]
- Komar A, "Methods in molecular biology (Methods and Protocols) vol 578", pp.23~39 (2009)
- Nakano M, "Single-nucleotide polymorphisms in cytochrome P450 2E1 (CYP2E1) 3'-untranslated region affect the regulation of CYP2E1 by miR-570", Drug Metab Dispos, 43, pp.1450~1457 (2015)[DOI]
- Yie SM, "A single base-pair mutation in the 3'-untranslated region of HLA-G mRNA is associated with preeclampsia", Mol Hum Reprod, 14, pp.649~653 (2008)[DOI]
- Schwerin M, "A 3'-UTR variant of the inducible porcine hsp70. 2 gene affects mRNA stability", Biochim Biophys Acta, 1578, pp.90~94 (2002)[DOI]
- Lee I, "New class of microRNA targets containing simultaneous 5'-UTR and 3'-UTR interaction sites", Genome Res, 19, pp.1175~1183 (2009)[DOI]
- Hou J, "Two mutations in the caprine MTHFR 3'UTR regulated by microRNAs are associated with milk production traits", PLoS One, 10, pp.e0133015~ (2015)[DOI]
