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Title: Selection Signature Analysis Implicates the PC1/PCSK1 Region for Chicken Abdominal Fat Content
Contributor(s): Zhang, Hui (author); Hu, Xiaoxiang (author); Wang, Yuxiang (author); Tang, Zhiquan (author); Li, Ning (author); Da, Yang (author); Li, Hui (author); Wang, Zhipeng (author); Zhang, Yuandan  (author); Wang, Shouzhi (author); Wang, Ning (author); Ma, Li (author); Leng, Li (author); Wang, Shengwen (author); Wang, Qigui (author)
Publication Date: 2012
Open Access: Yes
DOI: 10.1371/journal.pone.0040736Open Access Link
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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 PC 1/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, GJD 4-CCNY, NDS T4, NOVA 1, GAL NT9, 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.
Publication Type: Journal Article
Source of Publication: PLoS One, 7(7), p. 1-14
Publisher: Public Library of Science (PLoS)
Place of Publication: United States of America
ISSN: 1932-6203
Field of Research (FOR): 070201 Animal Breeding
110311 Medical Genetics (excl Cancer Genetics)
Socio-Economic Outcome Codes: 860103 Carcass Meat (incl. Fish and Seafood)
Peer Reviewed: Yes
HERDC Category Description: C1 Refereed Article in a Scholarly Journal
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Appears in Collections:Animal Genetics and Breeding Unit (AGBU)
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