204
Views
0
CrossRef citations to date
0
Altmetric
Articles

Bioinformatics and genetic variants analysis of FGF10 gene promoter with their association at carcass quality and body measurement traits in Qinchuan beef cattle

, , , , , , , , & show all

References

  • Chen N, Huang J, Zulfiqar A, et al. Population structure and ancestry of Qinchuan cattle. Anim Genet. 2018;49(3):246–248.
  • Guo H, Raza SHA, Schreurs NM, et al. Genetic variants in the promoter region of the KLF3 gene associated with fat deposition in Qinchuan cattle. Gene. 2018b;672:50–55.
  • Khan R, Raza SHA, Junjvlieke Z, et al. RNA-seq reveal role of bovine TORC2 in the regulation of adipogenesis. Arch Biochem Biophys. 2020b;680:108236.
  • Mei C, Wang H, Liao Q, Khan R, Haidar S, Raza A, Zhao C, Wang H, et al. Genome-wide analysis reveals the effects of artificial selection on production and meat quality traits in Qinchuan cattle. Genomics. 2019;111(6):1201–1208.
  • Raza SHA, Gui L, Khan R, et al. Association between FASN gene polymorphisms ultrasound carcass traits and intramuscular fat in Qinchuan cattle. Gene. 2018;645:55–59.
  • Raza SHA, Khan R, Schreurs NM, et al. Expression of the bovine KLF6 gene polymorphisms and their association with carcass and body measures in Qinchuan cattle (Bos Taurus). Genomics. 2020;112(1):423–431.
  • Martins TS, Sanglard LMP, Silva W, Chizzotti ML, et al. Molecular factors underlying the deposition of intramuscular fat and collagen in skeletal muscle of nellore and angus cattle. PLoS One. 2015;10(10):e0139943.
  • Wei D, Raza SHA, Zhang J, et al. Polymorphism in promoter of SIX4 gene shows association with its transcription and body measurement traits in Qinchuan cattle. Gene. 2018;656:9–16.
  • Cai H, M Li, Sun X, Plath M, et al. Global transcriptome analysis during adipogenic differentiation and involvement of transthyretin gene in adipogenesis in cattle. Front Genet. 2018;9:13.
  • Frank D, Joo ST, Warner R. Consumer Acceptability of Intramuscular Fat. Korean Journal for Food Science of Animal Resources 2016;36(6):699.
  • Guo H, Khan R, Abbas Raza SH, et al. RNA-Seq reveals function of Bta-miR-149-5p in the regulation of bovine adipocyte differentiation. Animals (Basel). 2021;11(5):1207.
  • Hongfang G, Khan R, Raza SHA, et al. Transcriptional regulation of adipogenic marker genes for the improvement of intramuscular fat in Qinchuan beef cattle. Anim Biotechnol. 2020;2020:1–20.
  • Khan R, Raza SHA, Junjvlieke Z, et al. Bta-miR-149-5p inhibits proliferation and differentiation of bovine adipocytes through targeting CRTCs at both transcriptional and posttranscriptional levels. J Cell Physiol. 2020c;235(7–8):5796–5810.
  • Khan R, Raza SHA, Schreurs N, et al. Bioinformatics analysis and transcriptional regulation of TORC1 gene through transcription factors NRF1 and Smad3 in bovine preadipocytes. Genomics. 2020d;112(2):1575–1587.
  • Elnour IE, Wang X, Zhansaya T, et al. Circular RNA circMYL1 inhibit proliferation and promote differentiation of myoblasts by sponging miR-2400. Cells. 2021;10(1):176.
  • Elsaeid Elnour I, Dong D, Wang X, et al. Bta-miR-885 promotes proliferation and inhibits differentiation of myoblasts by targeting MyoD1. J Cell Physiol. 2020;235(10):6625–6636.
  • Zhao C, Raza SHA, Khan R, et al. Genetic variants in MYF5 affected growth traits and beef quality traits in Chinese Qinchuan cattle. Genomics. 2020;112(4):2804–2812.
  • Sakaue H, Konishi M, Ogawa W, et al. Requirement of fibroblast growth factor 10 in development of white adipose tissue. Genes Dev. 2002;16(8):908–912.
  • Ohta H, Konishi M, Itoh N. FGF10 and FGF21 as regulators in adipocyte development and metabolism. Endocr Metab Immune Disord Drug Targets. 2011;11(4):302–309.
  • Meuwissen TH, Hayes BJ, Goddard ME. Prediction of total genetic value using genome-wide dense marker maps. Genetics. 2001;157(4):1819–1829.
  • Schaeffer LR. Strategy for applying genome-wide selection in dairy cattle. J Anim Breed Genet. 2006;123(4):218–223.
  • de Roos AP, Schrooten C, Mullaart E, Calus MP, Veerkamp RF. Breeding value estimation for fat percentage using dense markers on Bos taurus autosome 14. J Dairy Sci. 2007;90(10):4821–4829.
  • Guillaume F, Fritz S, Boichard D, Druet T. Estimation by simulation of the efficiency of the French marker-assisted selection program in dairy cattle. Genet Sel Evol. 2008;40(1):91–102.
  • Fragomeni BO, Lourenco DAL, Legarra A, VanRaden PM, Misztal I. Alternative SNP weighting for single-step genomic best linear unbiased predictor evaluation of stature in US Holsteins in the presence of selected sequence variants. J Dairy Sci. 2019;102(11):10012–10019.
  • Zhao Z-D, Zan L-S, Li A-N, et al. Characterization of the promoter region of the bovine long-chain acyl-CoA synthetase 1 gene: roles of E2F1, Sp1, KLF15, and E2F4. Sci Rep. 2016;6:19661.,
  • Liu S, Yin H, Li C, et al. Genetic effects of PDGFRB and MARCH1 identified in GWAS revealing strong associations with semen production traits in Chinese Holstein bulls. BMC Genet. 2017;18(1):63.
  • Wei D-W, Gui L-S, Raza SHA, et al. NRF1 and ZSCAN10 bind to the promoter region of the SIX1 gene and their effects body measurements in Qinchuan cattle. Sci Rep. 2017;7(1):7.
  • Wu S, Wang Y, Ning Y, et al. Genetic variants in STAT3 promoter regions and their application in molecular breeding for body size traits in Qinchuan cattle. Int J Mol Sci. 2018;:19.
  • Gui L, Hong J, Raza SH, Zan L. Genetic variants in SIRT3 transcriptional regulatory region affect promoter activity and fat deposition in three cattle breeds. Mol Cell Probes. 2017;32:40–45.
  • Khan R, Raza SHA, Guo H, et al. Genetic variants in the TORC2 gene promoter and their association with body measurement and carcass quality traits in Qinchuan cattle. PLoS One. 2020a;15(2):e0227254.
  • Gilbert RP, Bailey DR, Shannon N. Linear body measurements of cattle before and after 20 years of selection for postweaning gain when fed two different diets. J Anim Sci. 1993;71:8.
  • Sambrook J, Russell DW. Molecular Clonning: A Laboratory Manual. In: Molecular Clonning: A Laboratory Manual. New York: Cold Spring Harbor Laboratory Press, 2001.
  • K C. MatInspector: Analysing Promoters for Transcription Factor Binding Sites in "Analytical tools for DNA, genes and genomes: nuts & bolts", DNA Press, 2005.
  • Raza SHA, Khan R, Gui L, et al. Bioinformatics analysis and genetic polymorphisms in genomic region of the bovine SH2B2 gene and their associations with molecular breeding for body size traits in qinchuan beef cattle. Biosci Reports. 2020a;40(3):BSR20192113.
  • Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4(4):406–425.
  • Zuckerkandl E, Pauling L. Evolutionary Divergence and Convergence in Proteins, Evolving Genes and Proteins. Elsevier, pp. 97–166, 1965.
  • Junjvlieke Z, Khan R, Mei C, et al. Effect of ELOVL6 on the lipid metabolism of bovine adipocytes. Genomics. 2020;112(3):2282–2290.
  • Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33(7):1870–1874.
  • Vineeth MR, Surya T, Sivalingam J, et al. Genome-wide discovery of SNPs in candidate genes related to production and fertility traits in Sahiwal cattle. Trop Anim Health Prod. 2020;52(4):1707–1715.
  • Zhou L, Raza SHA, Ma B, et al. Mutations in FGFR1 were associated with growth traits in sheep (Ovis aries). Anim Biotechnol. 2021;1–7.
  • Sham P, Bader JS, Craig I, O'Donovan M, Owen M. DNA pooling: a tool for large-scale association studies. Nat Rev Genet. 2002;3:9.
  • Chung HY, McClure MC. Effects of SNPs from the differentially expressed swine odorant binding protein gene on average daily gain. J Appl Anim Res. 2011;39(1):61–64.
  • Guo H, Khan R, Raza SHA, et al. KLF15 promotes transcription of KLF3 gene in bovine adipocytes. Gene. 2018a;659:77–83.
  • Gauthier M, Marteyn A, Denis JA, et al. A defective Krab-domain zinc-finger transcription factor contributes to altered myogenesis in myotonic dystrophy type 1. Hum Mol Genet. 2013;22(25):5188–5198.
  • Tao C, Ren H, Xu P, et al. Adipocyte miR-200b/a/429 ablation in mice leads to high-fat-diet-induced obesity. Oncotarget. 2016;7(42):67796–67807.
  • Sunami Y, Yokoyama T, Yoshino S, et al. BCL11A promotes myeloid leukemogenesis by repressing PU.1 target genes. Blood Adv. 2021;

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.