ArticleAsian-Australasian journal of animal sciences2018
Genome re-sequencing to identify single nucleotide polymorphism markers for muscle color traits in broiler chickens.
Article in Asian-Australasian journal of animal sciences, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 9 citations in OpenAlex.
- Causal variants in animal genomes: approaches to identification, phenotypic impact, and implications for selective breeding.BMC genomics · 2026Review
- Bioinformatic approach to identifying causative missense polymorphisms in animal genomes.BMC genomics · 2024Article
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- Bovine viral diarrhoea virus loses quasispecies diversity rapidly in culture.Microbial genomics · 2020Article
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5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
objectiveMeat 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.
methodsWhole 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).
resultsMillions 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.
conclusionIn 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.
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