Skip to main content
SpringerLink
Log in

SNP and haplotype analysis of paired box 3 (PAX3) gene provide evidence for association with growth traits in Chinese cattle

  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

Paired box 3 (PAX3) belongs to the PAX superfamily of transcription factors and plays essential roles in the embryogenesis and postnatal formation of limb musculature through affecting the survival of muscle progenitor cells. By genetic mapping, PAX3 gene is assigned in the interval of quantitative trait loci for body weight on bovine BTA2. The objectives of this study were to detect polymorphisms of PAX3 gene in 1,241 cattle from five breeds and to investigate their effects on growth traits. Initially, three novel single nucleotide polymorphisms (SNPs) were identified by DNA pool sequencing and aCRS-RFLP methods (AC_000159: g.T-580G, g.A4617C and g.79018Ins/del G), which were located at 5′-UTR, exon 4 and intron 6, respectively. A total of eight haplotypes were constructed and the frequency of the three main haplotypes H1 (TAG), H2 (GCG) and H3 (GAG) accounted for over 81.7 % of the total individuals. Statistical analysis revealed that the three SNPs were associated with body height and body length of Nanyang and Chinese Caoyuan cattle at the age of 6 and/or 12 months old (P < 0.05), and consistently significant effects were also found in the haplotype combination analysis on these traits (P < 0.05). This study presented a complete scan of variations within bovine PAX3 gene, which could provide evidence for improving the economic traits of cattle by using these variations as potentially genetic markers in early marker-assisted selection programs.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  1. Heaton MP, Harhay GP, Bennett GL et al (2002) Selection and use of SNP markers for animal identification and paternity analysis in US beef cattle. Mamm Genome 13(5):272–281

    Article  CAS  PubMed  Google Scholar 

  2. Chi N, Epstein JA (2002) Getting your Pax straight: Pax proteins in development and disease. Trends Genet 18(1):41–47

    Article  CAS  PubMed  Google Scholar 

  3. Magli A, Schnettler E, Rinaldi F, Bremer P, Perlingeiro RCR (2013) Functional dissection of Pax3 in paraxial mesoderm development and myogenesis. Stem Cells 31(1):59–70

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  4. Bajard L, Relaix F, Lagha M, Rocancourt D, Daubas P, Buckingham ME (2006) A novel genetic hierarchy functions during hypaxial myogenesis: Pax3 directly activates Myf5 in muscle progenitor cells in the limb. Gene Dev 20(17):2450–2464

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  5. Bober E, Franz T, Arnold HH, Gruss P, Tremblay P (1994) Pax-3 is required for the development of limb muscles: a possible role for the migration of dermomyotomal muscle progenitor cells. Development 120(3):603–612

    CAS  PubMed  Google Scholar 

  6. Relaix F, Rocancourt D, Mansouri A, Buckingham M (2005) A Pax3/Pax7-dependent population of skeletal muscle progenitor cells. Nature 435(7044):948–953

    Article  CAS  PubMed  Google Scholar 

  7. Buckingham M, Relaix F (2007) The role of Pax genes in the development of tissues and organs: Pax3 and Pax7 regulate muscle progenitor cell functions. Annu Rev Cell Dev Biol 23:645–673

    Article  CAS  PubMed  Google Scholar 

  8. Kapoor S, Bindu PS, Taly AB, Sinha S, Gayathri N, Rani SV, Chandak GR, Kumar A (2012) Genetic analysis of an Indian family with members affected with Waardenburg syndrome and Duchenne muscular dystrophy. Mol Vis 18:2022

    PubMed Central  CAS  PubMed  Google Scholar 

  9. Xu Y, Liu J, Lan X, Zhang Y, Lei C, Zhang C, Yang D, Chen H (2011) Consistent effects of single and combined SNP (s) within bovine paired box 7 gene (Pax7) on growth traits. J Genet 90(2):E53–E57

    PubMed  Google Scholar 

  10. Xu Y, Zhou Y, Wang N, Lan X, Zhang C, Lei C, Chen H (2013) Integrating haplotypes and single genetic variability effects of the Pax7 gene on growth traits in two cattle breeds. Genome 56(999):1–7

    CAS  Google Scholar 

  11. Maak S, Neumann K, Swalve H (2006) Identification and analysis of putative regulatory sequences for the MYF5/MYF6 locus in different vertebrate species. Gene 379:141–147

    Article  CAS  PubMed  Google Scholar 

  12. Bhuiyan M, Kim N, Cho Y, Yoon D, Kim K, Jeon J, Lee J (2009) Identification of SNPs in MYOD gene family and their associations with carcass traits in cattle. Livest Sci 126(1):292–297

    Article  Google Scholar 

  13. McClure M, Morsci N, Schnabel R et al (2010) A genome scan for quantitative trait loci influencing carcass, post-natal growth and reproductive traits in commercial Angus cattle. Anim Genet 41(6):597–607

    Article  CAS  PubMed  Google Scholar 

  14. Sambrock J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, New York, pp 49–56

    Google Scholar 

  15. Sham P, Bader JS, Craig I, O’Donovan M, Owen M (2002) DNA pooling: a tool for large-scale association studies. Nat Rev Genet 3(11):862–871

    Article  CAS  PubMed  Google Scholar 

  16. Hu ZL, Fritz ER, Reecy JM (2007) AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond. Nucleic Acids Res 35(suppl 1):D604–D609

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  17. Ott J (1997) Documentation to linkage utility programs. Rockefeller University, New York

    Google Scholar 

  18. Barrett J, Fry B, Maller J, Daly M (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21(2):263–265

    Article  CAS  PubMed  Google Scholar 

  19. Stephens M, Donnelly P (2003) A comparison of bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet 73(5):1162–1169

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  20. Goddard ME, Hayes BJ (2009) Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nat Rev Genet 10(6):381–391

    Article  CAS  PubMed  Google Scholar 

  21. Hayes B, Chamberlain A, McPartlan H, Macleod I, Sethuraman L, Goddard M (2007) Accuracy of marker-assisted selection with single markers and marker haplotypes in cattle. Genet Res 89(4):215

    Article  CAS  PubMed  Google Scholar 

  22. Hayes B, Goddard M (2010) Genome-wide association and genomic selection in animal breeding. Genome 53(11):876–883

    Article  CAS  PubMed  Google Scholar 

  23. Nishimura S, Watanabe T, Mizoshita K, Tatsuda K, Fujita T, Watanabe N, Sugimoto Y, Takasuga A (2012) Genome-wide association study identified three major QTL for carcass weight including the PLAG1-CHCHD7 QTN for stature in Japanese Black cattle. BMC Genet 13(1):40

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  24. Grosz M, MacNeil M (2001) Putative quantitative trait locus affecting birth weight on bovine chromosome 2. J Anim Sci 79(1):68–72

    CAS  PubMed  Google Scholar 

  25. Ron M, Weller J (2007) From QTL to QTN identification in livestock–winning by points rather than knock-out: a review. Anim Genet 38(5):429–439

    Article  CAS  PubMed  Google Scholar 

  26. Greenwood TA, Kelsoe JR (2003) Promoter and intronic variants affect the transcriptional regulation of the human dopamine transporter gene. Genomics 82(5):511–520

    Article  CAS  PubMed  Google Scholar 

  27. Le Hir H, Nott A, Moore MJ (2003) How introns influence and enhance eukaryotic gene expression. Trends Biochem Sci 28(4):215–220

    Article  PubMed  Google Scholar 

  28. Hunt R, Sauna ZE, Ambudkar SV, Gottesman MM, Kimchi-Sarfaty C (2009) Silent (synonymous) SNPs: should we care about them. Methods Mol Biol 578:23–39

    Article  CAS  PubMed  Google Scholar 

  29. Duan J, Wainwright MS, Comeron JM, Saitou N, Sanders AR, Gelernter J, Gejman PV (2003) Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor. Hum Mol Genet 12(3):205–216

    Article  CAS  PubMed  Google Scholar 

  30. Lehnert SA, Reverter A, Byrne KA, Wang Y, Nattrass GS, Hudson NJ, Greenwood PL (2007) Gene expression studies of developing bovine longissimus muscle from two different beef cattle breeds. BMC Dev Biol 7(1):95

    Article  PubMed Central  PubMed  Google Scholar 

  31. Olivier M (2003) A haplotype map of the human genome. Physiol Genomics 13(1):3–9

    Article  CAS  PubMed  Google Scholar 

  32. Scheike TH, Martinussen T, Silver JD (2010) Estimating haplotype effects for survival data. Biometrics 66(3):705–715

    Article  PubMed  Google Scholar 

  33. Bhagavati S, Song X, Siddiqui MAQ (2007) RNAi inhibition of Pax3/7 expression leads to markedly decreased expression of muscle determination genes. Mol Cell Biochem 302(1):257–262

    Article  CAS  PubMed  Google Scholar 

  34. Buchberger A, Freitag D, Arnold HH (2007) A homeo-paired domain-binding motif directs Myf5 expression in progenitor cells of limb muscle. Development 134(6):1171–1180

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This study was supported by the National Natural Science Foundation of China (Grant No. 31272408), Agricultural Science and Technology Innovation Projects of Shaanxi Province (No. 2012NKC01-13), Program of National Beef Cattle Industrial Technology System (CARS-38), National 863 Program of China (No. 2013AA102505).

Author information

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, Yangling, 712100, Shaanxi, China

    Yao Xu, Hanfang Cai, Yang Zhou, Tao Shi, Xianyong Lan, Chuzhao Lei & Hong Chen

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

    Chunlei Zhang

  3. Institute of Animal Husbandry and Veterinary, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China

    Yutang Jia

Authors
  1. Yao Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hanfang Cai
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yang Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Tao Shi
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Xianyong Lan
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Chunlei Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Chuzhao Lei
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Yutang Jia
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Hong Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hong Chen.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 20 kb)

Supplementary material 2 (PDF 62 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Xu, Y., Cai, H., Zhou, Y. et al. SNP and haplotype analysis of paired box 3 (PAX3) gene provide evidence for association with growth traits in Chinese cattle. Mol Biol Rep 41, 4295–4303 (2014). https://doi.org/10.1007/s11033-014-3300-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-014-3300-9

Keywords

Search

Navigation