Molecular Biology Reports

, Volume 39, Issue 3, pp 3153–3160 | Cite as

Novel SNPs in the PRDM16 gene and their associations with performance traits in chickens

  • Ruili Han
  • Yang Wei
  • Xiangtao Kang
  • Hong Chen
  • Guirong Sun
  • Guoxi Li
  • Yichun Bai
  • Yadong Tian
  • Yanqun Huang


The PR domain containing 16 (PRDM16) is a member of the Prdm family, and is known to regulate cell differentiation. In the present study, DNA pool sequencing methods were employed to screen genetic variations in the chicken PRDM16 gene. The results revealed four novel single nucleotide polymorphisms (SNPs): NC_006108.2: g.92188G>A, XM_417551: c.1161C>T (Ala/Ala, 387aa), c.1233C>T (Ser/Ser, 411aa) and c.1433G>A (Ser/Asn, 478aa). The BglI polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) was used to detect c.1161C>T, while HhaI Forced PCR-RFLP methods were used to detect 1233C>T and c.1433G>A in 964 chickens. The chickens comprised 38 grandparents, 66 F1 parents and 860 F2 birds derived from an F2 resource population of Gushi chickens crossed with Anka broilers. The associations of the polymorphisms in the chicken PRDM16 gene with performance traits were analyzed in the 860 F2 chickens. The results indicated that the three SNPs were significantly associated with growth, fatness and meat quality traits in the chickens. In particular, the polymorphisms of the missense SNP (c.1433G>A) had positive effects on chicken body weight and body size at different stages. It affected also fatness traits significantly. Comparison of the different genotypes of c.1433G>A showed that the GG genotype favored chicken growth and fatness traits.


Chicken PRDM16 gene Single nucleotide polymorphisms (SNP) Association Performance traits 



The work is supported by the National Natural Science Foundation of China (No. 31072023) and the National Agricultural Science, Technology Achievements Transformation Foundation of China (No. 2009GB2D000218), the Earmarked fund for Modern Agro-industry Technology Research System (No. nycytx-41-g05).The authors thank the workers for managerial assistance with the birds; Yimei Sun and Mingming Jin for their help isolating of genomic DNA from 964 blood samples.

Supplementary material

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  1. 1.
    Fumasoni I, Meani N, Rambaldi D, Scafetta G et al (2007) Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates. BMC Evol Biol 7:187PubMedCrossRefGoogle Scholar
  2. 2.
    Baxendale S, Davison C, Muxworthy C, Wolff C et al (2004) The B-cell maturation factor Blimp-1 specifies vertebrate slow-twitch muscle fiber identity in response to Hedgehog signaling. Nat Genet 36:88–93PubMedCrossRefGoogle Scholar
  3. 3.
    Seale P, Kajimura S, Yang W, Chin S et al (2007) Transcriptional control of brown fat determination by PRDM16. Cell Metab 6:38–54PubMedCrossRefGoogle Scholar
  4. 4.
    Seale P, Bjork B, Yang W, Kajimura S et al (2008) PRDM16 controls a brown fat/skeletal muscle switch. Nature 454:961–967PubMedCrossRefGoogle Scholar
  5. 5.
    Valve R, Sivenius K, Miettinen R, Pihlajamaki J et al (1999) Two polymorphisms in the peroxisome proliferator-activated receptor-{gamma} gene are associated with severe overweight among obese women. J Clin Endocrinol Metab 84:3708–3712PubMedCrossRefGoogle Scholar
  6. 6.
    Grindflek E, Hoen N, Sundvold H, Rothschild M et al (2004) Investigation of a peroxisome proliferator-activated receptor gamma haplotype effect on meat quality and carcass traits in pigs. Anim Genet 35:238–241PubMedCrossRefGoogle Scholar
  7. 7.
    Meng H, Zhao J, Li Z, Li H (2005) Single nucleotide polymorphisms on peroxisome proliferator-activated receptor genes associated with fatness traits in chicken. Asian-Australas J Anim Sci 18:1221–1225Google Scholar
  8. 8.
    Toyomizu M, Ueda M, Sato S, Seki Y, Sato K, Akiba Y (2002) Cold-induced mitochondrial uncoupling and expression of chicken UCP and ANT mRNA in chicken skeletal muscle. FEBS Lett 529:313–318PubMedCrossRefGoogle Scholar
  9. 9.
    Mozom J, Emre Y, Bouillaud F, Ricquier D, Criscuolo F (2005) Thermoregulation: What role for UCPs in mammals and birds? Biosci Rep 25:227–249CrossRefGoogle Scholar
  10. 10.
    Hillier L, Miller W, Birney E, Warren W et al (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695–716CrossRefGoogle Scholar
  11. 11.
    Han RL, Lan XY, Zhang LZ, Ren G et al (2010) A novel single-nucleotide polymorphism of the visfatin gene and its associations with performance traits in the chicken. J Appl Genet 51:59–65PubMedCrossRefGoogle Scholar
  12. 12.
    Han RL, Li ZJ, Li MJ, Li JQ et al (2011) Novel 9-bp indel in visfatin gene and its associations with chicken growth. Br Poult Sci 52:52–57PubMedCrossRefGoogle Scholar
  13. 13.
    Chen ZQ, Sun JJ, Jin QJ, Li ZJ et al (2011) Novel SNPs in the caprine stearoyl-CoA desaturase(SCD) and decorin (DCN) genes that are associated with growth traits in Chinese goat breeds. Mol Biol Rep 38:3121–3127PubMedCrossRefGoogle Scholar
  14. 14.
    SPSS Inc. (2004) Statistical Package for the Social Sciences (SPSS) for Windows version 13.0. SPSS Inc., ChicagoGoogle Scholar
  15. 15.
    Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68:978–989PubMedCrossRefGoogle Scholar
  16. 16.
    Lan XY, Lai XS, Li ZJ, Wang J et al (2010) Effects of genetic variability of the carpine homeobox transcription factor HESX1 gene on performance traits. Mol Biol Rep 38:371–377PubMedGoogle Scholar
  17. 17.
    He J, Chen JC, Lu LZ, Tian Y (2011) A novel SNP of liver-type fatty acid-binding protein gene in duck and its associations with the intramuscular fat. Mol Biol Rep. doi:10.1007/s11033-011-0833-z
  18. 18.
    Li ZJ, Chen ZQ, Lan XY, Ma L et al (2010) Two novel cSNPs of weaver gene in Chinese indigenous goat and their associations with milk yield. Mol Biol Rep 37:563–569PubMedCrossRefGoogle Scholar
  19. 19.
    Wang J, Li ZJ, Lan XY, Hua LS et al (2010) Two novel SNPs in the coding region of the bovine PRDM16 gene and its associations with growth traits. Mol Biol Rep 37:571–577PubMedCrossRefGoogle Scholar
  20. 20.
    Niu PX, Zhao SH, Fan B (2009) Identification of gene variation within porcine PRDM16 gene and its association with fat and loin muscle area. S Afr J Ani Sci 39:333–336Google Scholar
  21. 21.
    Chen DX, Jin QJ, Fang XT, Zhang CL et al (2010) Analysis of the polymorphisms in the caprine PRDM16 SHH and SF-1 genes and their association with production traits in goats. Small Rumin Res 93:193–197CrossRefGoogle Scholar
  22. 22.
    Chamary JV, Parmley JL, Hurst LD (2006) Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat Rev Genet 7:98–108PubMedCrossRefGoogle Scholar
  23. 23.
    Plotkin JB, Kudla G (2011) Synonymous but not the same: the causes and consequences of codon bias. Nat Rev Genet 12:32–42PubMedCrossRefGoogle Scholar
  24. 24.
    Ren G, Chen H, Zhang LZ, Lan XY et al (2010) A coding SNP of LHX4 gene is associated with body weight and body length in bovine. Mol Biol Rep 37:417–422PubMedCrossRefGoogle Scholar
  25. 25.
    Li F, Chen H, Lei CZ, Ren G (2010) Novel SNPs of the bovine NUCB2 gene and their association with growth traits in three native Chinese cattle breeds. Mol Biol Rep 37:541–546PubMedCrossRefGoogle Scholar
  26. 26.
    Ryu YC, Kim BC (2005) The relationship between muscle fiber characteristics postmortem metabolic rate and meat quality of pig longissimus dorsi muscle. Meat Sci 71:351–357PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Ruili Han
    • 1
    • 2
  • Yang Wei
    • 1
  • Xiangtao Kang
    • 1
  • Hong Chen
    • 2
  • Guirong Sun
    • 1
  • Guoxi Li
    • 1
  • Yichun Bai
    • 1
  • Yadong Tian
    • 1
  • Yanqun Huang
    • 1
  1. 1.College of Livestock Husbandry and Veterinary EngineeringHenan Research Center of Breeding Resources for Poultry, Henan Agricultural UniversityZhengzhouPeople’s Republic of China
  2. 2.Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and TechnologyNorthwest A&F UniversityYanglingPeople’s Republic of China

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