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We conducted a selection signature analysis using the chicken 60k SNP chip in two chicken lines that had been divergently selected for abdominal fat content (AFC) for 11 generations. The selection signature analysis used multiple signals of selection, including long-range allele frequency differences between the lean and fat lines, long-range heterozygosity changes, linkage disequilibrium, haplotype frequencies, and extended haplotype homozygosity. Multiple signals of selection identified ten signatures on chromosomes 1, 2, 4, 5, 11, 15, 20, 26 and Z. The 0.73 Mb  PC1/PCSK1  region of the Z chromosome at 55.43-56.16 Mb was the most heavily selected region. This region had 26 SNP markers and seven genes,  Mar-03 ,  SLC12A2 ,  FBN2 ,  ERAP1 ,  CAST ,  PC1/PCSK1  and  ELL2 , where  PC1/PCSK1  are the chicken/human names for the same gene. The lean and fat lines had two main haplotypes with completely opposite SNP alleles for the 26 SNP markers and were virtually line-specific, and had a recombinant haplotype with nearly equal frequency (0.193 and 0.196) in both lines. Other haplotypes in this region had negligible frequencies. Nine other regions with selection signatures were  PAH-IGF1 ,  TRPC4 ,  GJD4-CCNY ,  NDST4 ,  NOVA1 ,  GALNT9 , the  ESRP2-GALR1  region with five genes, the  SYCP2-CADH4  with six genes, and the  TULP1-KIF21B  with 14 genes. Genome-wide association analysis showed that nearly all regions with evidence of selection signature had SNP effects with genome-wide significance (P<10 –6 ) on abdominal fat weight and percentage. The results of this study provide specific gene targets for the control of chicken AFC and a potential model of AFC in human obesity.

Selection Signature Analysis Implicates the PC1/PCSK1 Region for Chicken Abdominal Fat Content