Using Targeted Resequencing for Identification of Candidate Genes and SNPs for a QTL Affecting the pH Value of Chicken Meat.
Using targeted genetical genomics, a quantitative trait locus (QTL) affecting the initial postmortem pH value of chicken breast muscle (Pectoralis major) on chromosome 1 (GGA1) recently was fine-mapped. Thirteen genes were present in the QTL region of approximately 1 Mb. In this study, 10 birds that were inferred to be homozygous for either the high (QQ) or low (qq) QTL allele were selected for resequencing. After enrichment for 1 Mb around the QTL region, >500 × coverage for the QTL region in each of the 10 birds was obtained. In total 5056 single-nucleotide polymorphisms (SNPs) were identified for which the genotypes were consistent with one of the QTL genotypes. We used custom tools to identify putative causal mutations in the mapped QTL region from these SNPs. Four nonsynonymous SNPs differentiating the two QTL genotype groups were identified within four local genes (PRDX4, EIF2S3, PCYT1B, and E1BTD2). Although these are likely candidate SNPs to explain the QTL effect, 54 additional consensus SNPs were detected within gene-related regions (untranslated regions, splicing sites CpG island, and promoter regions) for the QQ birds and 71 for the qq birds. These could also play a role explaining the observed QTL effect. The results provide an important step for prioritizing among a large amount of candidate mutations and significantly contribute to the understanding of the genetic mechanisms affecting the initial postmortem pH value of chicken muscle.
Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden.
Xidan
X
Li
Department of Ecology and Genetics, Plant Ecology and Evolution, Uppsala University, SE-752 36 Uppsala, Sweden.
Xiaodong
X
Liu
INRA, UR83 Recherches Avicoles, Nouzilly, 37380, France, Roslin Institute and R(D)SVS, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom.
Javad
J
Nadaf
INRA, UR83 Recherches Avicoles, Nouzilly, 37380, France.
Elisabeth
E
Le Bihan-Duval
INRA, UR83 Recherches Avicoles, Nouzilly, 37380, France.
Cécile
C
Berri
Roslin Institute and R(D)SVS, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom.
Ian
I
Dunn
Roslin Institute and R(D)SVS, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom.
Richard
R
Talbot
Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden, Roslin Institute and R(D)SVS, University of Edinburgh, Midlothian, EH25 9RG, United Kingdom dj.de-koning@slu.se.
Dirk-Jan
DJ
De Koning
D000818:Animals; D002645:Chickens / Q000235:genetics*; D018899:CpG Islands; D056726:Genetic Association Studies; D059014:High-Throughput Nucleotide Sequencing; D006863:Hydrogen-Ion Concentration; D008460:Meat / Q000592:standards*; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D022821:RNA Splice Sites; D020506:Untranslated Regions
D022821:RNA Splice Sites; D020506:Untranslated Regions
QTL; SNPs; chicken muscle; next-generation sequencing; nonsynonymous SNPs; pH values