Peishi Feng1,2, Tao Zeng2, Hua Yang3, Guohong Chen4, Jinping Du5, Li Chen2, Junda Shen2, Zhenrong Tao2, Ping Wang6, Lin Yang7, Lizhi Lu8. 1. College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China. 2. Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China. 3. Institute of Quality and Standards for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China. 4. College of Animal Science and Technology, Yangzhou University, Yangzhou, China. 5. Institute of Animal Husbandry and Veterinary Science, Hubei Academy of Agricultural Science, Wuhan, China. 6. College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China. wangping45@zjut.edu.cn. 7. College of Animal Science, South China Agricultural University, Guangzhou, China. ylin@scau.edu.cn. 8. Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China. lulizhibox@163.com.
Abstract
BACKGROUND: Duck is an ancient domesticated animal with high economic value, used for its meat, eggs, and feathers. However, the origin of indigenous Chinese ducks remains elusive. To address this question, we performed whole-genome resequencing to first explore the genetic relationship among variants of these domestic ducks with their potential wild ancestors in eastern China, as well as understand how the their genomes were shaped by different natural and artificial selective pressures. RESULTS: Here, we report the resequencing of 60 ducks from Chinese spot-billed ducks (Anas zonorhyncha), mallards (Anas platyrhnchos), Fenghua ducks, Shaoxing ducks, Shanma ducks and Cherry Valley Pekin ducks of eastern China (ten from each population) at an average effective sequencing depth of ~ 6× per individual. The results of population and demographic analysis revealed a deep phylogenetic split between wild (Chinese spot-billed ducks and mallards) and domestic ducks. By applying selective sweep analysis, we identified that several candidate genes, important pathways and GO categories associated with artificial selection were functionally related to cellular adhesion, type 2 diabetes, lipid metabolism, the cell cycle, liver cell proliferation, and muscle functioning in domestic ducks. CONCLUSION: Genetic structure analysis showed a close genetic relationship of Chinese spot-billed ducks and mallards, which supported that Chinese spot-billed ducks contributed to the breeding of domestic ducks. During the long history of artificial selection, domestic ducks have developed a complex biological adaptation to captivity.
BACKGROUND: Duck is an ancient domesticated animal with high economic value, used for its meat, eggs, and feathers. However, the origin of indigenous Chineseducks remains elusive. To address this question, we performed whole-genome resequencing to first explore the genetic relationship among variants of these domestic ducks with their potential wild ancestors in eastern China, as well as understand how the their genomes were shaped by different natural and artificial selective pressures. RESULTS: Here, we report the resequencing of 60 ducks from Chinese spot-billed ducks (Anas zonorhyncha), mallards (Anas platyrhnchos), Fenghua ducks, Shaoxing ducks, Shanma ducks and Cherry Valley Pekin ducks of eastern China (ten from each population) at an average effective sequencing depth of ~ 6× per individual. The results of population and demographic analysis revealed a deep phylogenetic split between wild (Chinese spot-billed ducks and mallards) and domestic ducks. By applying selective sweep analysis, we identified that several candidate genes, important pathways and GO categories associated with artificial selection were functionally related to cellular adhesion, type 2 diabetes, lipid metabolism, the cell cycle, liver cell proliferation, and muscle functioning in domestic ducks. CONCLUSION: Genetic structure analysis showed a close genetic relationship of Chinese spot-billed ducks and mallards, which supported that Chinese spot-billed ducks contributed to the breeding of domestic ducks. During the long history of artificial selection, domestic ducks have developed a complex biological adaptation to captivity.
Entities:
Keywords:
Adaptation; Artificial selection; Domestication; Duck; Insulin signaling pathway; Population history
Authors: Carl-Johan Rubin; Michael C Zody; Jonas Eriksson; Jennifer R S Meadows; Ellen Sherwood; Matthew T Webster; Lin Jiang; Max Ingman; Ted Sharpe; Sojeong Ka; Finn Hallböök; Francois Besnier; Orjan Carlborg; Bertrand Bed'hom; Michèle Tixier-Boichard; Per Jensen; Paul Siegel; Kerstin Lindblad-Toh; Leif Andersson Journal: Nature Date: 2010-03-10 Impact factor: 49.962