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. 2025 Jan;104(1):104509.
doi: 10.1016/j.psj.2024.104509. Epub 2024 Nov 5.

Research note: Whole-genome sequencing revealed genomic diversity dynamics in duck conserved populations

Yu-Ze Yang  1 , Zhong-Tao Yin  2 , Xiao-Ran Lin  3 , Chun-Ying Zhao  3 , Fang-Xi Yang  4 , Fei-Fan Chen  2 , Zhuo-Cheng Hou  5
Affiliations

Research note: Whole-genome sequencing revealed genomic diversity dynamics in duck conserved populations

Yu-Ze Yang et al. Poult Sci. 2025 Jan.

Abstract

The purpose of this study was to comprehensively analyze the genetic diversity of the Pekin duck conserved population with five generations and to evaluate the effectiveness of the current conservation strategy. In total, 277 Pekin duck conserved individuals and 40 Mallards as ancestral controls were collected. Each duck was sequenced at about 10X whole-genome coverage, while over 7.4 million single nucleotide polymorphisms (SNPs) in total were detected for genetic diversity analysis. Both the expected heterozygosity and observed heterozygosity values exceeded 0.3. The genetic differentiation (FST) values ranged from 0.007 to 0.039, and the Polymorphism information content (PIC) values ranged from 0.29 to 0.34. These results indicate no significant differentiation between generations, and the genetic diversity remains high. In particular, the inbreeding coefficient has been strictly controlled and has not increased rapidly during the conservation. Overall, the inbreeding coefficient of the conserved Pekin duck population was higher than that of its wild ancestors, indicating that domestication has resulted in reduced genetic diversity. This is the first report using whole genome resequencing data to systematically evaluate the genomic dynamics across several generations in ducks. The results show that the strategy of free mating and random seed retention within sire families is effective for maintaining the genetic diversity of the conserved Pekin duck population.

Keywords: Conservation strategy; Conserved population; Duck; Genetic diversity.

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Conflict of interest statement

Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could appear to influence the work reported in this paper.

Figures

Fig 1
Fig. 1
The genetic structure of Mallard and Pekin duck conserved populations. (A) Neighbor-joining tree constructed using genetic sharing distances. (B) Population structures of conserved populations revealed through principal component analysis. (C) An admixture plot for sub-populations analyzed based on Mallard and Pekin duck conserved populations across five generations.
Fig 2
Fig. 2
The genetic diversity of Mallard and Pekin duck conserved populations. (A) Nucleotide diversity (π) and FST across the sub-populations. The value in each circle represents the nucleotide diversity of the respective population, and the value on each line indicates genetic differentiation between the two populations. (B) Linkage disequilibrium between generations and breeds as a function of inter-SNP distance. The allelic richness. (C), polymorphism information content(D), expected heterozygosity (E), and observed heterozygosity (F) value for Pekin duck conserved populations with 5 generations. (G) The average length of ROH in Mallards and Pekin ducks. (H) The inbreeding coefficient is based on ROH in Mallards and Pekin conserved populations.
See this image and copyright information in PMC

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