Genome re-sequencing to identify single nucleotide polymorphism markers for muscle color traits in broiler chickens

  • Kong, H.R. (Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas) ;
  • Anthony, N.B. (Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas) ;
  • Rowland, K.C. (Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas) ;
  • Khatri, B. (Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas) ;
  • Kong, B.C. (Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas)
  • Received : 2017.06.24
  • Accepted : 2017.08.14
  • Published : 2018.01.01


Objective: Meat quality including muscle color in chickens is an important trait and continuous selective pressures for fast growth and high yield have negatively impacted this trait. This study was conducted to investigate genetic variations responsible for regulating muscle color. Methods: Whole genome re-sequencing analysis using Illumina HiSeq paired end read method was performed with pooled DNA samples isolated from two broiler chicken lines divergently selected for muscle color (high muscle color [HMC] and low muscle color [LMC]) along with their random bred control line (RAN). Sequencing read data was aligned to the chicken reference genome sequence for Red Jungle Fowl (Galgal4) using reference based genome alignment with NGen program of the Lasergene software package. The potential causal single nucleotide polymorphisms (SNPs) showing non-synonymous changes in coding DNA sequence regions were chosen in each line. Bioinformatic analyses to interpret functions of genes retaining SNPs were performed using the ingenuity pathways analysis (IPA). Results: Millions of SNPs were identified and totally 2,884 SNPs (1,307 for HMC and 1,577 for LMC) showing >75% SNP rates could induce non-synonymous mutations in amino acid sequences. Of those, SNPs showing over 10 read depths yielded 15 more reliable SNPs including 1 for HMC and 14 for LMC. The IPA analyses suggested that meat color in chickens appeared to be associated with chromosomal DNA stability, the functions of ubiquitylation (UBC) and quality and quantity of various subtypes of collagens. Conclusion: In this study, various potential genetic markers showing amino acid changes were identified in differential meat color lines, that can be used for further animal selection strategy.


Muscle Color;Genome Re-sequencing;Single Nucleotide Polymorphism Markers;Chickens


Supported by : Arkansas Bioscience Institute


  1. Dransfield E, Sosnicki AA. Relationship between muscle growth and poultry meat quality. Poult Sci 1999; 78:743-6.
  2. Chicken QTLdb [Internet]. Ames, IA, USA: NAGRP Bioinformatics Team [2017 June 15]. Available from:
  3. Fan B, Du ZQ, Gorbach DM, Rothschild MF. Development and application of high-density SNP arrays in genomic studies of domestic animals. Yi Chuan Xue Bao 2010;23:833-47.
  4. Sun Y, Zhao G, Liu R, et al. The identification of 14 new genes for meat quality traits in chicken using a genome-wide association study. BMC Genomics 2013;14:458.
  5. Harford ID, Pavlidis HO, Anthony NB. Divergent selection for muscle color in broilers. Poult Sci 2014;93:1059-66.
  6. Jang HM, Erf GF, Rowland KC, Kong BW. Genome resequencing and bioinformatic analysis of SNP containing candidate genes in the autoimmune vitiligo Smyth line chicken model. BMC Genomics 2014;15:707.
  7. Kong BW, Lee JY, Bottje WG, et al. Genome-wide differential gene expression in immortalized DF-1 chicken embryo fibroblast cell line. BMC Genomics 2011;12:571.
  8. Shiloh Y, Ziv Y. The ATM protein kinase: regulating the cellular response to genotoxic stress, and more. Nat Rev Mol Cell Biol 2013;14: 197-210.
  9. Metcalfe JA, Parkhill J, Campbell L, et al. Accelerated telomere shortening in ataxia telangiectasia. Nat Genet 1996;13:350-3.
  10. Lieber MR, Ma Y, Pannicke U, Schwarz K. Mechanism and regulation of human non-homologous DNA end-joining. Nat Rev Mol Cell Biol 2003;4:712-20.
  11. Anai M, Shojima N, Katagiri H, et al. A novel protein kinase B (PKB)/AKT-binding protein enhances PKB kinase activity and regulates DNA synthesis. J Biol Chem 2005;280:18525-35.
  12. Danielsen JM, Sylvestersen KB, Bekker-Jensen S, et al. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. Mol Cell Proteomics 2011;10:M110.003590.
  13. Emanuele MJ, Elia AE, Xu Q, et al. Global identification of modular cullin-RING ligase substrates. Cell 2011;147:459-74.
  14. Kim W, Bennett EJ, Huttlin EL, et al. Systematic and quantitative assessment of the ubiquitin-modified proteome. Mol Cell 2011;44:325-40.
  15. Wagner SA, Beli P, Weinert BT, et al. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Mol Cell Proteomics 2011;10:M111.013284.
  16. Modderman PW, Admiraal LG, Sonnenberg A, von dem Borne AE. Glycoproteins V and Ib-IX form a noncovalent complex in the platelet membrane. J Biol Chem 1992;267:364-9.
  17. McCormick RJ. Extracellular modifications to muscle collagen: implications for meat quality. Poult Sci 1999;78:785-91.
  18. Gowe RS, Robertson A, Latter BDH. Environment and poultry breeding problems 5. The design of poultry control strains. Poult Sci 1959;38:462-71.