Genetic basis and identification of candidate genes for wooden breast and white striping in commercial broiler chickens

Abstract

Wooden breast (WB) and white striping (WS) are highly prevalent and economically damaging muscle disorders of modern commercial broiler chickens characterized respectively by palpable firmness and fatty white striations running parallel to the muscle fiber. High feed efficiency and rapid growth, especially of the breast muscle, are believed to contribute to development of such muscle defects; however, their etiology remains poorly understood. To gain insight into the genetic basis of these myopathies, a genome-wide association study was conducted using a commercial crossbred broiler population (n = 1193). Heritability was estimated at 0.5 for WB and WS with high genetic correlation between them (0.88). GWAS revealed 28 quantitative trait loci (QTL) on five chromosomes for WB and 6 QTL on one chromosome for WS, with the majority of QTL for both myopathies located in a ~ 8 Mb region of chromosome 5. This region has highly conserved synteny with a portion of human chromosome 11 containing a cluster of imprinted genes associated with growth and metabolic disorders such as type 2 diabetes and Beckwith-Wiedemann syndrome. Candidate genes include potassium voltage-gated channel subfamily Q member 1 (KCNQ1), involved in insulin secretion and cardiac electrical activity, lymphocyte-specific protein 1 (LSP1), involved in inflammation and immune response.

Figure 1

Genome-wide association results for wooden breast (WB) score using multi-marker (BayesB) and single-SNP (mixed linear model) analyses. (Top Left) Percentage of genetic variance explained by 1-Mb regions across the genome for WB score. (Top Right) Distribution of WB scores across progeny used in genome-wide association analyses; dark red = male, light red = female. (Bottom Left) Manhattan plot of single-SNP results showing the − log10(p-value) of SNPs ordered by chromosome and position. (Bottom Right) Quantile–quantile plot of p-values from single-SNP results of WB score. Solid and dashed lines indicate significant and suggestive thresholds, respectively, for each model.

Figure 2

Genome-wide association results for white striping (WS) score using multi-marker (BayesB) and single-SNP (mixed linear model) analyses. (Top Left) Percentage of genetic variance explained by 1-Mb regions across the genome for WS score. (Top Right) Distribution of WS scores across progeny used in genome-wide association analyses; dark blue = male, light blue = female. (Bottom Left) Manhattan plot of single-SNP results showing the − log10(p-value) of SNPs ordered by chromosome and position. (Bottom Right) Quantile–quantile plot of p-values from single-SNP results of WS score. Solid and dashed lines indicate significant and suggestive thresholds, respectively, for each model.

Figure 3

Gene landscape of QTL-rich region between 8.0 Mb and 16.5 Mb on chicken chromosome 5. Mirrored Manhattan plot shows SNPs with significance thresholds indicated by color; dark red = significant, orange = suggestive.

Figure 4

Conserved synteny between chickens and humans. The wooden breast QTL-rich region of chicken chromosome 5 (GGA5) has highly conserved synteny with human chromosome 11 (HSA11), especially compared to homologous regions in the mouse genome on chromosomes 2 (MMU2) and 7 (MMU7). In humans, this area is associated with a high number of growth and metabolic disorders, which are highlighted here based on existing knowledge of wooden breast and white striping, including a hypothesis suggesting dysregulation of lipid and glucose metabolism as an important underlying factor in development of the myopathies. The scatter plot on GGA5 represents GWAS results from the present study with significant SNPs in red. Red bands on GGA5 indicate previously identified selective sweeps in commercial purebred broiler lines that are susceptible to wooden breast with overlapping selective sweep regions in dark red. The centromere (pink) and G-banding (grey and white) are shown on HSA11 to improve visualization. Defic: deficiency, ID: insulin-dependent, NID: non-insulin-dependent, PN: permanent neonatal, TN: transient neonatal.