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

Zhang, Hui; Hu, Xiaoxiang; Wang, Yuxiang; Tang, Zhiquan; Li, Ning; Da, Yang; Li, Hui; Wang, Zhipeng; Zhang, Yuandan; Wang, Shouzhi; Wang, Ning; Ma, Li; Leng, Li; Wang, Shengwen; Wang, Qigui

doi:10.1371/journal.pone.0040736

Author(s)

Zhang, Hui

Hu, Xiaoxiang

Wang, Yuxiang

Tang, Zhiquan

Li, Ning

Da, Yang

Li, Hui

Wang, Zhipeng

Zhang, Yuandan

Wang, Shouzhi

Wang, Ning

Ma, Li

Leng, Li

Wang, Shengwen

Wang, Qigui

Publication Date

2012

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.

Citation

PLoS One, 7(7), p. 1-14

ISSN

1932-6203

Link

https://hdl.handle.net/1959.11/14289

Language

en

Publisher

Public Library of Science

Title

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

Type of document

Journal Article

Entity Type

Publication

Author(s)	Zhang, Hui Hu, Xiaoxiang Wang, Yuxiang Tang, Zhiquan Li, Ning Da, Yang Li, Hui Wang, Zhipeng Zhang, Yuandan Wang, Shouzhi Wang, Ning Ma, Li Leng, Li Wang, Shengwen Wang, Qigui
Publication Date	2012
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.
Citation	PLoS One, 7(7), p. 1-14
ISSN	1932-6203
Link	https://hdl.handle.net/1959.11/14289
Language	en
Publisher	Public Library of Science
Title	Selection Signature Analysis Implicates the PC1/PCSK1 Region for Chicken Abdominal Fat Content
Type of document	Journal Article
Entity Type	Publication

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

Files: