Journal Article

genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms

Wilson, Richard K, Zheng, Weimou, Yang, Xu, Huang, Xiangang, Zheng, Hongkun, Bovenhuis, Henk, Lin, Wei, Liu, Bin, Chen, Chen, Zhang, Zhenpeng, Huang, Yanqing, Sun, Yongqiao, Burt, David W, Ni, Peixiang, Hao, Bailin, Gordon, Laurie, Xie, Fei, Wahlberg, Per, Xi, Yan, Hu, Songnian, Kaiser, Pete, Walker, Brian A, Zhang, Jianguo, de Koning, Dirk-Jan, Young, John R, Lamont, Susan J, Li, Guoqing, Zhang, Yong, Rothwell, Lisa, Aerts, Andrea, Zhou, Jun, Li, Wenjie, Li, Ruiqiang, Qi, Qiuhui, Zhang, Jingjing, Li, Shengting, Rogers, Sally, Wang, Jianjun, Hunt, Henry, Zhao, Wenming, Cheng, Hans H, Li, Guangyuan, Glavina, Tijana, Zhou, Yan, Li, Ning, Zhang, Yunze, Zhao, Yiqiang, Wei, Dong, Tong, Wei, Groenen, Martien A M, Yang, Zheng, Wong, Gane Ka-Shu, Yang, Shiaw-Pyng, Wang, Xiaoling, Yu, Yingpu, Wang, Pei, Hocking, Paul M, Li, Songgang, Law, Andy, Morrice, David, Hillier, Ladeana W, Bumstead, Nat, van der Poel, Jan J, Ye, Chen, Ellegren, Hans, Lan, Fengdi, Ye, Jia, van Hateren, Andy, Li, Heng, Zhang, Xiaowei, Dai, Mingtao, He, Dandan, Li, Dawei, Shi, Jianping, Dong, Le, Lucas, Susan, He, Ximiao, Chen, Jie, Wang, Miaoheng, Warren, Wesley C, Kaufman, Jim, Ba

2004

Overview

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds (a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic linesin contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases.

• Publisher: Nature Publishing Group UK,Nature Publishing,Nature Publishing Group
• Subject: Alleles / Amino Acid Sequence / Animals / Animals, Domestic - classification / Animals, Domestic - genetics / Biologi / Biological and medical sciences / Biology / Birds / broiler chickens / Cell and molecular biology / Cell- och molekylärbiologi / chicken breeds / Chickens / Chickens - classification / Chickens - genetics / Chickens/classification/genetics / Chromosomes - genetics / Classical genetics, quantitative genetics, hybrids / Comparative Study / Domestic animals / Domestication / Female / Fundamental and applied biological sciences. Psychology / Gallus gallus / Gene expression / Genetic diversity / genetic variation / Genetics / Genetics of eukaryotes. Biological and molecular evolution / Genetik / Genome / Genomics / haplotypes / Haplotypes - genetics / Humanities and Social Sciences / Humans / laying hens / Molecular Sequence Data / multidisciplinary / NATURAL SCIENCES / NATURVETENSKAP / Ornithine Carbamoyltransferase - chemistry / Physical Chromosome Mapping / Polymorphism, Single Nucleotide - genetics / Science / Science (multidisciplinary) / Selection (Genetics) / Selection, Genetic / single nucleotide polymorphism / Vertebrata