iScience (Jun 2020)
Microevolutionary Dynamics of Chicken Genomes under Divergent Selection for Adiposity
- Hui Zhang,
- Qiqi Liang,
- Ning Wang,
- Qigui Wang,
- Li Leng,
- Jie Mao,
- Yuxiang Wang,
- Shouzhi Wang,
- Jiyang Zhang,
- Hao Liang,
- Xun Zhou,
- Yumao Li,
- Zhiping Cao,
- Peng Luan,
- Zhipeng Wang,
- Hui Yuan,
- Zhiquan Wang,
- Xuming Zhou,
- Susan J. Lamont,
- Yang Da,
- Ruiqiang Li,
- Shilin Tian,
- Zhiqiang Du,
- Hui Li
Affiliations
- Hui Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
- Qiqi Liang
- Novogene Bioinformatics Institute, Beijing 10089, P. R. China
- Ning Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
- Qigui Wang
- Chongqing Academy of Animal Science, Chongqing 402460, P. R. China
- Li Leng
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
- Jie Mao
- Novogene Bioinformatics Institute, Beijing 10089, P. R. China
- Yuxiang Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
- Shouzhi Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
- Jiyang Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
- Hao Liang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
- Xun Zhou
- Novogene Bioinformatics Institute, Beijing 10089, P. R. China
- Yumao Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
- Zhiping Cao
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
- Peng Luan
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
- Zhipeng Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
- Hui Yuan
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China
- Zhiquan Wang
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, AB T6G 2C8, Canada
- Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
- Susan J. Lamont
- Department of Animal Science, Iowa State University, Ames 50011, USA
- Yang Da
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA
- Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing 10089, P. R. China
- Shilin Tian
- Novogene Bioinformatics Institute, Beijing 10089, P. R. China; Corresponding author
- Zhiqiang Du
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China; Corresponding author
- Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs; Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province; College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, P. R. China; Corresponding author
- Journal volume & issue
-
Vol. 23,
no. 6
p. 101193
Abstract
Summary: Decades of artificial selection have significantly improved performance and efficiency of animal production systems. However, little is known about the microevolution of genomes due to intensive breeding. Using whole-genome sequencing, we document dynamic changes of chicken genomes under divergent selection on adiposity over 19 generations. Directional selection reduced within-line but increased between-line genomic differences. We observed that artificial selection tended to result in recruitment of preexisting variations of genes related to adipose tissue growth. In addition, novel mutations contributed to divergence of phenotypes under selection but contributed significantly less than preexisting genomic variants. Integration of 15 generations genome sequencing, genome-wide association study, and multi-omics data further identified that genes involved in signaling pathways important to adipogenesis, such as autophagy and lysosome (URI1, MBL2), neural system (CHAT), and endocrine (PCSK1) pathways, were under strong selection. Our study provides insights into the microevolutionary dynamics of domestic animal genomes under artificial selection.
