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Two novel SNPs in the coding region of the bovine PRDM16 gene and its associations with growth traits

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Abstract

As a zinc-finger protein, PR domain containing 16 (PRDM16) controls brown fat determination by stimulating brown fat-selective genes expression while suppressing the expression of genes selective for white fat cells, whose mutations were associated with myelodysplastic syndrome (MDS) and leukemogenesis in human and murine model of leukemia. To date, no polymorphisms of PRDM16 gene in bovine had been reported. Herein, PCR-SSCP and DNA sequencing methods were employed to screen the genetic variation within PRDM16 gene in 1031 Chinese indigenous bovine. The results revealed two novel silent mutations: XM_001788152: m.1641T>C (547aa), 1881G>A (627aa). Hence, we described the PvuII and HaeIII forced PCR–RFLP methods for detecting these mutations, respectively. In the forced PCR–RFLP analysis with PvuII, the frequencies of bovine PRDM16-C allele varied from 0.044 to 0.506 in four Chinese native breeds. In the forced PCR–RFLP analysis with HaeIII, the frequencies of bovine PRDM16-G allele were 0.474, 0.494, 0.576 and 0.906 for Jiaxian (JX), Nanyang (NY), Qinchuan (QC) and Chinese Holstein (CH) population. Significant statistical differences between genotypic frequencies implied that both of the polymorphic loci were significantly associated with cattle breeds by the chi square test (χ2 = 190.058, P < 0.001 and χ2 = 118.239, P < 0.001 for PvuII; χ2 = 209.842, P < 0.001 and χ2 = 108.711, P < 0.001 for HaeIII). The associations of the PvuII and HaeIII forced PCR–RFLPs of bovine PRDM16 loci with growth traits were analyzed in Nanyang breed. The two SNPs were associated with body weight and average daily gain in Nanyang aged 12 months, individuals with genotype TT and AA showed significantly better body weight (P < 0.05) and average daily gain (P < 0.01) at 12 months, respectively.

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References

  1. Jenuwein T (2001) Re-SET-ting heterochromatin by histone methyltransferases. Trends Cell Biol 11:266–273

    Article  CAS  PubMed  Google Scholar 

  2. Reid AG, Nacheva EP (2004) A potential role for PRDM12 in the pathogenesis of chronic myeloid leukaemia with derivative chromosome 9 deletion. Leukemia 18:178–180

    Article  CAS  PubMed  Google Scholar 

  3. Pasqualucci L, Compagno M, Houldsworth J et al (2006) Inactivation of the PRDM1/BLIMP1 gene in diffuse large B cell lymphoma. J Exp Med 203:311–317

    Article  CAS  PubMed  Google Scholar 

  4. Tam W, Gomez M, Chadburn A et al (2006) Mutational analysis of PRDM1 indicates a tumor-suppressor role in diffuse large B-cell lymphomas. Blood 107:4090–4100

    Article  CAS  PubMed  Google Scholar 

  5. Nishikawa N, Toyota M, Suzuki H et al (2007) Gene amplification and overexpression of PRDM14 in breast cancers. Cancer Res 67:9649–9657

    Article  CAS  PubMed  Google Scholar 

  6. Davis CA, Haberland M, Arnold MA et al (2006) PRISM/PRDM6, a transcriptional repressor that promotes the proliferative gene program in smooth muscle cells. Mol Cell Biol 26:2626–2636

    Article  CAS  PubMed  Google Scholar 

  7. Fumasoni I, Meani N, Rambaldi D et al (2007) Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates. BMC Evol Biol 7:187

    Article  PubMed  Google Scholar 

  8. Kinameri E, Inoue T, Aruga J et al (2008) Prdm proto-oncogene transcription factor family expression and interaction with the Notch-Hes pathway in mouse neurogenesis. PLoS ONE 3:e3859

    Article  PubMed  Google Scholar 

  9. Warner DR, Horn KH, Mudd L et al (2007) PRDM16/MEL1: a novel Smad binding protein, expressed in murine embryonic orofacial tissue. Biochim Biophys Acta 1773:814–820

    Article  CAS  PubMed  Google Scholar 

  10. Seale P, Kajimura S, Yang W et al (2007) Transcriptional control of brown fat determination by PRDM16. Cell Metab 6:38–54

    Article  CAS  PubMed  Google Scholar 

  11. Seale P, Bjork B, Yang WL et al (2008) PRDM16 controls a brown fat/skeletal muscle switch. Nature 454:961-U27

    Google Scholar 

  12. Kajimura S, Seale P, Tomaru T et al (2008) Regulation of the brown and white fat gene programs through a PRDM16/CtBP transcriptional complex. Genes Dev 22:1397–1409

    Article  CAS  PubMed  Google Scholar 

  13. Xiao ZJ, Zhang MR, Liu XP et al (2006) MEL1S, not MEL1, is overexpressed in myelodysplastic syndromes patients with t(1;3)(p36;q21). Leuk Res 30:332–334

    Article  CAS  PubMed  Google Scholar 

  14. Shing DC, Trubia M, Marchesi F et al (2007) Overexpression of sPRDM16 coupled with loss of p53 induces myeloid leukemias in mice. J Clin Invest 117:3696–3707

    CAS  PubMed  Google Scholar 

  15. Ott MG, Schmidt M, Schwarzwaelder K et al (2006) Correction of X-linked chronic granulomatous disease by gene therapy, augmented by insertional activation of MDS1-EVI1, PRDM16 or SETBP1. Nat Med 12:401–409

    Article  CAS  PubMed  Google Scholar 

  16. Rosado EL, Bressan J, Martins MF et al (2007) Polymorphism in the PPARgamma2 and beta2-adrenergic genes and diet lipid effects on body composition, energy expenditure and eating behavior of obese women. Appetite 49:635–643

    Article  CAS  PubMed  Google Scholar 

  17. Walczak R, Tontonoz P, Edward AD (2003) PPAR[gamma] signaling in adipose tissue development. In: Handbook of cell signaling, pp. 39–46. Academic Press, Burlington

  18. Rhee EJ, Oh KW, Lee WY et al (2006) Effects of two common polymorphisms of peroxisome proliferator-activated receptor-[gamma] gene on metabolic syndrome. Arch Med Res 37:86–94

    Article  CAS  PubMed  Google Scholar 

  19. Yang LL, Hua Q, Liu RK et al (2009) Association between two common polymorphisms of PPAR[gamma] gene and metabolic syndrome families in a Chinese population. Arch Med Res 40:89–96

    Article  CAS  PubMed  Google Scholar 

  20. Sambrook J, Russell DW (2002) Molecular cloning a laboratory manual, 3rd edn. Science Beijing (Translated by Huang Pei Tang)

  21. Lan XY, Pan CY, Chen H et al (2007) An AluI PCR–RFLP detecting a silent allele at the goat POU1F1 locus and its association with production traits. Small Rumin Res 73:8–12

    Article  Google Scholar 

  22. Nei M, Roychoudhury AK (1974) Sampling variances of heterozygosity and genetic distance. Genetics 76:379–390

    CAS  PubMed  Google Scholar 

  23. Komar AA (2007) Silent SNPs: impact on gene function and phenotype. Pharmacogenomics 8:1075–1080

    Article  CAS  PubMed  Google Scholar 

  24. Kimchi-Sarfaty C, Oh JM, Kim IW et al (2007) A “silent” polymorphism in the MDR1 gene changes substrate specificity. Science 315:525–528

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

This study was supported by the National 863 Program of China (No. 2006AA10Z197, 2008AA101010), National Natural Science Foundation of China (No.30771544), National Key Technology R&D Program (No. 2006BAD01A10-5), Keystone Project of transfergene in China (2009ZX08009-157B, 2008ZX08007-002), “13115” Sci-Tech Innovation Program of Shaanxi Province (2008ZDKG-11), Program of National Beef Cattle Industrial Technology System.

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Authors and Affiliations

  1. College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, No. 22 Xinong Road, 712100, Yangling, Shaanxi, China

    J. Wang, Z. J. Li, X. Y. Lan, L. S. Hua, Y. T. Huai, Y. Z. Huang, L. Ma, M. Zhao, Y. J. Jing & H. Chen

  2. Institute of Cellular and Molecular Biology, Xuzhou Normal University, 221116, Xuzhou, Jiangsu, China

    H. Chen

  3. Research Center of Cattle Engineering Technology in Henan, 450003, Zhengzhou, Henan, China

    J. Q. Wang

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  1. J. Wang
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  2. Z. J. Li
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  3. X. Y. Lan
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  4. L. S. Hua
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  5. Y. T. Huai
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  9. Y. J. Jing
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  10. H. Chen
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Correspondence to H. Chen.

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Wang, J., Li, Z.J., Lan, X.Y. et al. Two novel SNPs in the coding region of the bovine PRDM16 gene and its associations with growth traits. Mol Biol Rep 37, 571–577 (2010). https://doi.org/10.1007/s11033-009-9816-8

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  • DOI: https://doi.org/10.1007/s11033-009-9816-8

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