The First Crested Duck Genome Reveals Clues to Genetic Compensation and Crest Cushion Formation

Guobin Chang; Xiaoya Yuan; Qixin Guo; Hao Bai; Xiaofang Cao; Meng Liu; Zhixiu Wang; Bichun Li; Shasha Wang; Yong Jiang; Zhiquan Wang; Yang Zhang; Qi Xu; Qianqian Song; Rui Pan; Lingling Qiu; Tiantian Gu; Xinsheng Wu; Yulin Bi; Zhengfeng Cao; Yu Zhang; Yang Chen; Hong Li; Jianfeng Liu; Wangcheng Dai; Guohong Chen

doi:10.1016/j.gpb.2023.08.002

The First Crested Duck Genome Reveals Clues to Genetic Compensation and Crest Cushion Formation

Genomics Proteomics Bioinformatics. 2023 Jun;21(3):483-500. doi: 10.1016/j.gpb.2023.08.002. Epub 2023 Aug 29.

Authors

Guobin Chang¹, Xiaoya Yuan², Qixin Guo², Hao Bai³, Xiaofang Cao⁴, Meng Liu⁴, Zhixiu Wang², Bichun Li², Shasha Wang², Yong Jiang², Zhiquan Wang⁵, Yang Zhang², Qi Xu², Qianqian Song², Rui Pan², Lingling Qiu², Tiantian Gu², Xinsheng Wu², Yulin Bi², Zhengfeng Cao², Yu Zhang², Yang Chen², Hong Li⁴, Jianfeng Liu⁶, Wangcheng Dai⁷, Guohong Chen⁸

Affiliations

¹ Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China.
² Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
³ Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China.
⁴ Novogene Bioinformatics Institute, Beijing 100080, China.
⁵ Department of Agricultural, Food, and Nutritional Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada.
⁶ College of Animal Science and Technology, China Agricultural University, Beijing 100091, China.
⁷ Zhenjiang Tiancheng Agricultural Science and Technology Co., Ltd, Zhenjiang 210034, China.
⁸ Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China. Electronic address: ghchen2019@yzu.edu.cn.

Abstract

The Chinese crested (CC) duck is a unique indigenous waterfowl breed, which has a crest cushion that affects its survival rate. Therefore, the CC duck is an ideal model to investigate the genetic compensation response to maintain genetic stability. In the present study, we first generated a chromosome-level genome of CC ducks. Comparative genomics revealed that genes related to tissue repair, immune function, and tumors were under strong positive selection, indicating that these adaptive changes might enhance cancer resistance and immune response to maintain the genetic stability of CC ducks. We also assembled a Chinese spot-billed (Csp-b) duck genome, and detected the structural variations (SVs) in the genome assemblies of three ducks (i.e., CC duck, Csp-b duck, and Peking duck). Functional analysis revealed that several SVs were related to the immune system of CC ducks, further strongly suggesting that genetic compensation in the anti-tumor and immune systems supports the survival of CC ducks. Moreover, we confirmed that the CC duck originated from the mallard ducks. Finally, we revealed the physiological and genetic basis of crest traits and identified a causative mutation in TAS2R40 that leads to crest formation. Overall, the findings of this study provide new insights into the role of genetic compensation in adaptive evolution.

Keywords: Chinese crested duck; Crest cushion; Genetic compensation; Genome adaptive evolution; Genome assembly.

MeSH terms

Animals
Animals, Domestic* / genetics
Dogs
Ducks* / genetics
Genome
Mutation
Phenotype