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

doi:10.1016/j.isci.2020.101193

Microevolutionary Dynamics of Chicken Genomes under Divergent Selection for Adiposity

iScience. 2020 Jun 26;23(6):101193. doi: 10.1016/j.isci.2020.101193. Epub 2020 May 23.

Authors

Hui Zhang¹, Qiqi Liang², Ning Wang¹, Qigui Wang³, Li Leng¹, Jie Mao², Yuxiang Wang¹, Shouzhi Wang¹, Jiyang Zhang¹, Hao Liang¹, Xun Zhou², Yumao Li¹, Zhiping Cao¹, Peng Luan¹, Zhipeng Wang¹, Hui Yuan¹, Zhiquan Wang⁴, Xuming Zhou⁵, Susan J Lamont⁶, Yang Da⁷, Ruiqiang Li², Shilin Tian⁸, Zhiqiang Du⁹, Hui Li¹⁰

Affiliations

¹ 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.
² Novogene Bioinformatics Institute, Beijing 10089, P. R. China.
³ Chongqing Academy of Animal Science, Chongqing 402460, P. R. China.
⁴ Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, AB T6G 2C8, Canada.
⁵ Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China.
⁶ Department of Animal Science, Iowa State University, Ames 50011, USA.
⁷ Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA.
⁸ Novogene Bioinformatics Institute, Beijing 10089, P. R. China. Electronic address: tianshilin@novogene.com.
⁹ 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. Electronic address: zhqdu@neau.edu.cn.
¹⁰ 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. Electronic address: lihui@neau.edu.cn.

Abstract

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.

Keywords: Biological Sciences; Evolutionary Biology; Genetics; Genomics.