Genomic characteristics and selection signals of Zhongshan ducks
Hao Chen,
Keyi Luo,
Cong Wang,
Rui Xuan,
Sumei Zheng,
Hongbo Tang,
Yuhang Li,
Yanpeng Xiong,
Yongfei Wu,
Luping Wang,
Jing Ouyang,
Xueming Yan
Affiliations
Hao Chen
Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang 330013, China
Keyi Luo
Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang 330013, China
Cong Wang
Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang 330013, China
Rui Xuan
Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang 330013, China
Sumei Zheng
Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang 330013, China
Hongbo Tang
Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang 330013, China
Yuhang Li
Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang 330013, China
Yanpeng Xiong
Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang 330013, China
Yongfei Wu
Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang 330013, China
Luping Wang
Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang 330013, China
Jing Ouyang
Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang 330013, China
Xueming Yan
Corresponding author.; Jiangxi Key Laboratory of Bioprocess Engineering, College of Life Sciences, Jiangxi Science and Technology Normal University, Nanchang 330013, China
The Zhongshan duck (ZSP) is a duck breed indigenous to China and is known for its moderate body size, strong disease resistance, tender meat, and little subcutaneous fat. However, the genomic basis of such excellent breeding characteristics remains poorly understood. Therefore, we generated whole-genomes of 58 ZSPs and 180 other indigenous Chinese ducks (60 Jinding ducks, 60 Shan Partridge ducks, and 60 Liancheng white ducks) and identified 10 560 032 single nucleotide polymorphisms and 1 334 893 structural variants. Based on genetic diversity and population structure indices, our results confirm that the ZSP is a unique germplasm resource. In addition, three reproduction-related genes (i.e., OAZ, AMH, and RLF) were located in highly differentiated regions between the ZSP and the other three duck breeds (Jinding duck; Liancheng White duck; Shan Partridge duck), suggesting that these genes may have a strong influence on egg production. Among these genes, AMH may have introgressed from an unknown species of the Anatidae family. We also identified other significant genes in the significantly differentiated window (i.e., 1% cut-off), some of which are responsible for growth and development (SEMA5B and MIB1), metabolism (EDEM3 and Xylb), skeletal system morphogenesis (bglap and MGP), and egg shape (ITPR2). These findings highlight the genetic characteristics of the ZSP that shape an array of its morphological traits. Overall, this study should facilitate a more fine-scale approach towards improving the ZSP and other indigenous ducks in China and even all over the world.
