Using GWAS and Next Gen Genotype-by-Sequencing to Map Determinants of Pulmonary Hypertension (ascites) in Broilers

We have been using single nucleotide polymorphism (SNP) based mapping to identify gene and chromosomal regions affecting the ascites phenotype in broilers. Ascites or pulmonary hypertension in chickens is a complex, heritable trait affecting fast-growing, meat-type birds. We performed two GWAS (genome wide association study) that consistently showed association with disease phenotype for a region around 70 Mbp on chicken chromosome 2. Further analysis with two SNPs in this region showed association with respect to right ventricular to total ventricular (RVTV) ratios in males among chickens phenotyped as ascites resistant and ascites susceptible. This region contains the CDH6 (Cadherin 6) gene which is involved with thrombosis and renal development, and thus might play a role in the hypertensive response to high altitude conditions we use for phenotyping. Our recent next gen sequencing data identified a region around 127 Mbp where more than 30 SNPs showed markedly different frequencies for ascites resistant and susceptible male chickens. These SNPs are within the CPQ (Carboxypeptidase Q; a.k.a. PGCP, Plasma Glutamate Carboxypeptidase) gene, which has been associated with regulation of hypertension and heart rate in humans and mouse. Thus, our research has identified two regions on chromosome 2 which appear to contribute to this disease in a gender-specific manner. We are now genotyping another 1000 DNA samples using TaqMan assays to further verify association of the CPQ gene region with ascites. Thereafter, our plan is to analyze the transcriptional expression patterns of the CPQ gene from heart and pulmonary arteries for hypoxic and normal birds based on these SNP variants.