Using targeted re-sequencing for identification of candidate genes and SNPs for a QTL affecting the pH value of chicken muscle

Using targeted genetical genomics, a QTL affecting the initial post-mortem pH value of chicken breast muscle (Pectoralis major) on chromosome 1 (GGA1) was recently fine-mapped. Thirteen genes were present in the QTL region of about 1 Mb. In this study, ten birds that were inferred to be homozygous for either the high (QQ) or low (qq) QTL allele were selected for re-sequencing. After enrichment for 1 Mb around the QTL region, > 200 x coverage for the QTL region in each of the ten birds was obtained. We used custom tools to identify putative causal mutations in the mapped QTL region from next generation sequence data. Four non-synonymous SNPs differentiating the two QTL genotype groups were identified within four local genes (PRDX4, EIF2S3, PCYT1B and E1BTD2). These were defined to be most likely candidate SNPs to explain the QTL effect. Moreover, 29 consensus SNPs were detected within gene-related regions (UTR regions and splicing sites) for the QQ birds and 26 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 post-mortem pH value of chicken muscle.