Identification of Copy Number Variations Associated with Ascites Phenotype in Broilers

We have been mapping chromosomal regions associated with resistance or susceptibility to pulmonary hypertension syndrome or ascites, using three experimental lines divergently selected for ascites phenotype. Previous Genome Wide Association Studies (GWAS) based on Single Nucleotide Polymorphisms (SNPs) have identified regions on chromosomes 2, 9 and Z. Despite several GWAS and further genotyping we have not identified any major genes for ascites phenotype. We have now begun a screen for differentially represented Copy Number Variations (CNVs) in ascites resistant and susceptible birds from the relaxed, REL, line. DNA samples from resistant and susceptible birds were purified, quantified and pooled in two pools of 10 DNAs from each phenotype for both genders. Eight pools (2pools x 2phenotypes x 2genders) were generated, each pool was submitted for bar-coded library generation, and 2x125 paired end reads on Illumina HiSeq 2500 and with 25X genome coverage. The sequence reads were mapped onto Galgal5 using Bowtie for initial CNV mapping cn.mops (R package). Further mapping to chromosome Z was done using NGen and ArrayStar (DNAStar ver 13). CNVs reports were used to identify genes affected and pathway analysis using KEGG and NCBI. The regions we have identified will need to be further validated using, qPCR assays in a larger catalog of DNAs.