Abstract
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.
Highlights
The chicken (Gallus gallus) is an important model organism that bridges the evolutionary gap between mammals and other vertebrates [1]
Abdominal fat weight (AFW) can be measured directly, and experiments could be designed to identify genetic variants associated with abdominal fat content (AFC)
Heterozygosity and allele frequency differences (AFD) measures were used for the first screening of selection signatures, and linkage disequilibrium (LD), haplotype frequencies and extended haplotype homozygosity (EHH) were analyzed as additional evidence of selection signatures and as indications of whether selection had occurred in one line or both lines
Summary
The chicken (Gallus gallus) is an important model organism that bridges the evolutionary gap between mammals and other vertebrates [1]. Research on human obesity typically uses body mass index (BMI) as the phenotypic measure of obesity [2,3,4,5,6,7,8,9,10,11,12]. BMI is affected by variations in the entire body, including bones, muscles and body fat, and is not specific for abdominal fat, a major problem in obese people. Abdominal fat weight (AFW) can be measured directly, and experiments could be designed to identify genetic variants associated with abdominal fat content (AFC). The results from this type of experiment may provide useful comparative information for human obesity research and lead to genetic improvement for reduced abdominal fat in chickens
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