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

Abstract

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.

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

Figure 1

Number of unique single nucleotide polymorphisms (SNPs) per chromosome found in high muscle color (HMC) (A) and low muscle color (LMC) (B). Open bars indicate number of SNPs derived from parental line (RAN), while solid bars indicate number of SNPs, which is not shared with parental line (RAN).

Figure 2

Gene network for genes containing 15 single nucleotide polymorphisms (SNPs) causing amino acid changes. Molecular interactions among important focus molecules are displayed. Gray symbols show the genes found in the list of SNPs while white symbols indicate neighboring genes, which are functionally associated, but not included in the gene list of SNP. Symbols for each molecule are presented according to molecular functions and type of interactions. Gene network image was created by IPA analysis.