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Asian-Australas J Anim Sci > Accepted Articles
DOI:    [Accepted] Published online August 22, 2017.
Genome re-sequencing to identify SNP markers for muscle color traits in broiler chickens
Hyeonmin R. Kong1, Nicholas B. Anthony1, Kaylee C. Rowland1, Bhuwan Khatri1, Byungwhi C. Kong1,*
University of Arkansas, Fayetteville, United States
Correspondence:  Byungwhi C. Kong, Tel: 4795755494, Fax: 4795757139, Email:
Received: 24 June 2017   • Revised: 8 August 2017   • Accepted: 14 August 2017
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.


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 SNPs showing non-synonymous changes in CDS region were chosen in each line. Bioinformatic analyses to interpret functions genes retaining SNPs was performed using the Ingenuity Pathways Analysis (IPA).


Millions of single nucleotide polymorphisms (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.
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.
Keywords: Muscle color; Genome re-sequencing; SNP markers
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