Advertisement

Journal of Genetics

, Volume 95, Issue 4, pp 939–946 | Cite as

Association and expression analyses of the Ucp2 and Ucp3 gene polymorphisms with body measurement and meat quality traits in Qinchuan cattle

  • YANING WANG
  • WUCAI YANG
  • LINSHENG GUI
  • HONGBAO WANG
  • LINSEN ZANEmail author
RESEARCH ARTICLE

Abstract

The uncoupling proteins (UCPs) belong to the mitochondrial inner membrane anion carrier superfamily and play an important role in energy homeostasis. Genetic studies have demonstrated that Ucp2 and Ucp3 gene variants are involved in obesity and metabolic syndrome. The aim of this study was to identify associations between polymorphisms of Ucp2 and Ucp3 genes and economically-important traits in Qinchuan cattle. In the present study, one single-nucleotide polymorphism (SNP) in the 5 UTR region (SNP1: g.C-754G) of the Ucp2 gene was identified by direct sequencing of 441 Qinchuan cattle. Two SNPs in exon 3 (SNP2: g.G4877A; SNP3: g.C4902T) of the Ucp3 gene were identified by sequencing and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) among 441 Qinchuan cattle. Association analysis showed that SNP1 and SNP2 were associated with the meat quality traits (MQTs) including back fat thickness, loin muscle area and intramuscular fat content. SNP3 was found to be associated with part of the body measurement traits (BMTs) which referred to withers height and chest depth. In addition, QTL pyramiding analysis showed that individuals with diplotype P3P3 (GGGGCC) exhibited the best performance in terms of back fat thickness, loin muscle area, intramuscular fat content, rump length, hip width, chest depth and chest circumference. With regard to the G4877A mutation, real time PCR analysis revealed that individuals with AA genotype of the Ucp3 gene expressed higher mRNA levels than those with GG genotype. These results suggest that the diplotype P3P3 (GGGGCC) could be used as a molecular marker of the combined genotypes for future selection of body measurement traits and meat quality traits in Qinchuan cattle.

Keywords

uncoupling protein gene single-nucleotide polymorphism body measurement traits meat quality traits Qinchuan cattle 

Notes

Acknowledgements

We thank members of the Linsen Zan lab for helpful discussions. We especially thank Dr Yang for help and consultations on the experimental design, data analyses and paper revisions. The research was supported by the National 863 Program of China (nos. 2013AA102505; 2011AA100307-02), Natural Science Foundation of Shaanxi Province (2015JQ3064), National Natural Science Foundation of China (CN) (nos. 31272411; 31402044), National Beef and Yak Industrial Technology System (CARS-38) and National Science-Technology Support Plan Projects (2012BAD28B04-03).

References

  1. Andersen G., Dalgaard L. T., Justesen J. M., Anthonsen S., Nielsen T., Thorner L. W. et al. 2013 The frequent UCP2 −866G >A polymorphism protects against insulin resistance and is associated with obesity: a study of obesity and related metabolic traits among 17,636 Danes. Int. J. Obes. (Lond.) 37, 175–181.CrossRefGoogle Scholar
  2. An X. P., Hou J. X., Zhao H. B., Li G., Bai L., Peng J. Y. et al. 2013 Polymorphism identification in goat GNRH1 and GDF9 genes and their association analysis with litter size. Anim. Genet. 44, 234–238.CrossRefPubMedGoogle Scholar
  3. Akey J., Jin L. and Xiong M. M. 2001 Haplotypes vs single marker linkage disequilibrium tests: what do we gain? Eur. J. Hum. Genet. 9, 291–300.CrossRefPubMedGoogle Scholar
  4. Ardlie K. G., Kruglyak L. and Seielstad M. 2002 Patterns of linkage disequilibrium in the human genome. Nat. Rev. Genet. 3, 299–309.CrossRefPubMedGoogle Scholar
  5. Ashikari M. and Matsuoka M. 2006 Identification, isolation and pyramiding of quantitative trait loci for rice breeding. Trends Plant Sci. 11, 344–350.CrossRefPubMedGoogle Scholar
  6. Azzu V. and Brand M. D. 2010 The on–off switches of the mitochondrial uncoupling proteins. Trends Biochem. Sci. 35, 298–307.CrossRefPubMedGoogle Scholar
  7. Brand M. D. and Esteves T. C. 2005 Physiological functions of the mitochondrial uncoupling proteins UCP2 and UCP3. Cell Metab. 2, 85–93.CrossRefPubMedGoogle Scholar
  8. Cieslak J., Nowacka-Woszuk J., Bartz M., Fijak-Nowak H., Grzes M., Szydlowski M. et al. 2009 Association studies on the porcine RETN, UCP1, UCP3 and ADRB3 genes polymorphism with fatness traits. Meat Sci. 83, 551–554.CrossRefPubMedGoogle Scholar
  9. de Almeida Brondani L, de Souza B. M., Assmann T. S., Boucas A. P., Bauer A. C., Canani L. H. et al. 2014 Association of the UCP polymorphisms with susceptibility to obesity: case–control study and meta-analysis. Mol. Biol. Rep. 41, 5053–5067.CrossRefPubMedGoogle Scholar
  10. Donadelli M., Dando I., Fiorini C. and Palmieri M. 2014 UCP2, a mitochondrial protein regulated at multiple levels. Cell Mol. Life Sci. 71, 1171–1190.CrossRefPubMedGoogle Scholar
  11. Gilbert R. P., Bailey D. R. and Shannon N. H. 1993 Linear body measurements of cattle before and after 20 years of selection for postweaning gain when fed two different diets. J. Anim. Sci. 71, 1712–1720.PubMedGoogle Scholar
  12. Gibson G. and Honeycutt E. 2002 The evolution of developmental regulatory pathways. Curr. Opin. Genet. Dev. 12, 695–700.CrossRefPubMedGoogle Scholar
  13. Han X., Jiang T., Yang H., Zhang Q., Wang W., Fan B. et al. 2012 Investigation of four porcine candidate genes (H-FABP, MYOD1, UCP3 and MASTR) for meat quality traits in large white pigs. Mol. Biol. Rep. 39, 6599–6605.CrossRefPubMedGoogle Scholar
  14. Hideyuki M. 2011 Identification and utilization of genes associated with beef qualities. Anim. Sci. J. 82, 1–7.CrossRefGoogle Scholar
  15. Hirwa C. A., Wallace P., Shen X., Nie Q., Yang G. and Zhang X. 2011 Genes related to economically important traits in beef cattle. Asian J. Anim. Sci. 5, 34–45.CrossRefGoogle Scholar
  16. Kimchi S. C., Oh J. M., Kim I. W., Sauna Z. E., Calcagno A. M., Ambudkar S. V. et al. 2007 A “silent” polymorphism in the MDR1 gene changes substrate specificity. Science 315, 525–528.CrossRefGoogle Scholar
  17. Li H., Brahi O. H., Zhao X., Xu N. and Zhao X. 2012 Association of pig UCP3 gene mutations and back fat thickness in the sixth and seventh rib. Mol. Biol. Rep. 39, 1823–1829.CrossRefPubMedGoogle Scholar
  18. Liu B. H. 1998 Statistical genomics: linkage, mapping and QTL analysis, pp. 404–409. CRC Press LLC, Boca Raton, FL, USA.Google Scholar
  19. Mayo A. E., Setty Y., Shavit S., Zaslaver A. and Alon U. 2006 Plasticity of the cis-regulatory input function of a gene. PLoS Biol. 4, e45.CrossRefPubMedPubMedCentralGoogle Scholar
  20. Morris R. W. and Kaplan N. L. 2002 On the advantage of haplotype analysis in the presence of multiple disease susceptibility alleles. Genet. Epidemiol. 23, 221–233.CrossRefPubMedGoogle Scholar
  21. Motoyuki A. and Makoto M. 2006 Identification, isolation and pyramiding of quantitative trait loci for rice breeding. Trends Plant Sci. 11, 344–350.CrossRefGoogle Scholar
  22. Muhammad I. K., Cheorun J. and Muhammad R. T. 2015 Meat flavor precursors and factors influencing flavor precursors—a systematic review. Meat Sci. 110, 278–284.CrossRefGoogle Scholar
  23. Musa C. V., Mancini A., Alfieri A., Labruna G., Valerio G., Franzese A. et al. 2012 Four novel UCP3 gene variants associated with childhood obesity: effect on fatty acid oxidation and on prevention of triglyceride storage. Int. J. Obes. (Lond.) 36, 207–217.CrossRefGoogle Scholar
  24. Pan C., Wu C., Jia W., Xu Y., Lei C., Hu S. et al. 2013 A critical functional missense mutation H173R in the bovine PROP1 gene significantly affects 338 growth traits in cattle. Gene 531, 398–402.CrossRefPubMedGoogle Scholar
  25. Pedersen L. D., Sorensen A. C. and Berg P. 2009 Marker-assisted selection can reduce true as well as pedigree-estimated inbreeding. J. Dairy Sci. 92, 2214–2223.CrossRefPubMedGoogle Scholar
  26. Raymond M. and Rousset F. 1995 GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J. Hered. 86, 248–249.Google Scholar
  27. Ricquier D. and Bouillaud F. 2000 The uncoupling protein homologues: UCP1, UCP2, UCP3, StUCP and AtUCP. Biochem. J. 345, 161–179.CrossRefPubMedPubMedCentralGoogle Scholar
  28. Ruengphayak S., Chaichumpoo E., Phromphan S., Kamolsukyunyong W., Sukhaket W., Phuvanartnarubal E. et al. 2015 Pseudo-backcrossing design for rapidly pyramiding multiple traits into a preferential rice variety. Rice 8, 7.CrossRefPubMedPubMedCentralGoogle Scholar
  29. Say Y. H., Ban Z. L., Arumugam Y., Kaur T., Tan M. L., Chia P. P. et al. 2014 Uncoupling protein 2 gene (UCP2) 45-bp I/D polymorphism is associated with adiposity among Malaysian women. J. Biosci. 39, 867–875.CrossRefPubMedGoogle Scholar
  30. Sherman E. L., Nkrumah J. D., Murdoch B. M., Li C., Wang Z., Fu A. et al. 2008 Polymorphisms and haplotypes in the bovine neuropeptide Y, growth hormone receptor, ghrelin, insulin-like growth factor 2, and uncoupling proteins 2 and 3 genes and their associations with measures of growth, performance, feed efficiency, and carcass merit in beef cattle. J. Anim. Sci. 86, 1–16.CrossRefPubMedGoogle Scholar
  31. Srivastava N., Prakash J., Lakhan R., Agarwal C. G., Pant D. C. and Mittal B. 2010 A common polymorphism in the promoter of UCP2 is associated with obesity and hyperinsulenemia in northern Indians. Mol. Cell Biochem. 337, 293–298.CrossRefPubMedGoogle Scholar
  32. Stefan K., Chen Y. -Z. and Bradford B. L. 2005 The mitochondrial uncoupling-protein homologues. Nat. Rev. Mol. Cell. Biol. 6, 248–261.CrossRefGoogle Scholar
  33. Tizioto P. C., Coutinho L. L., Decker J. E., Schnabel R. D., Rosa K. O., Oliveira P. S. et al. 2015 Global liver gene expression differences in Nelore steers with divergent residual feed intake phenotypes. BMC Genomics 16, 242.CrossRefPubMedPubMedCentralGoogle Scholar
  34. Wang G., Zhang S., Wei S., Zhang Y., Li Y., Fu C. et al. 2014 Novel polymorphisms of SIX4 gene and their association with body measurement traits in Qinchuan cattle. Gene 539, 107–110.CrossRefPubMedGoogle Scholar
  35. Wang J., Hua L. S., Pan H., Zhang L. Z., Li M. X., Huang Y. Z. et al. 2015a Haplotypes in the promoter region of the CIDEC gene associated with growth traits in Nanyang cattle. Sci. Rep. 5, 12075.CrossRefPubMedPubMedCentralGoogle Scholar
  36. Wang W., Liu S., Li F., Pan X., Li C., Zhang X. et al. 2015b Polymorphisms of the Ovine BMPR-IB, BMP-15 and FSHR and their associations with litter size in two chinese indigenous sheep breeds. Int. J. Mol. Sci. 16, 11385–11397.CrossRefPubMedPubMedCentralGoogle Scholar
  37. Xue J., Sun Y. J., Guo W. J., Yang Z. Q., Tian H. B., Zhang C. L. et al. 2013 Haplotypes and effects on growth traits of bovine Wnt7a gene in Chinese Qinchuan cattle. Gene 524, 241–245.CrossRefPubMedGoogle Scholar

Copyright information

© Indian Academy of Sciences 2016

Authors and Affiliations

  • YANING WANG
    • 1
  • WUCAI YANG
    • 1
    • 2
  • LINSHENG GUI
    • 1
  • HONGBAO WANG
    • 1
    • 2
  • LINSEN ZAN
    • 1
    • 2
    Email author
  1. 1.College of Animal Science and TechnologyNorthwest A&F UniversityShaanxiPeople’s Republic of China
  2. 2.National Beef Cattle Improvement Center of ChinaShaanxiPeople’s Republic of China

Personalised recommendations