Abstract:

Aims: The Zhongshan Partridge Duck is the only local duck breed in Guangdong Province and represents the most iconic rare genetic resource in Zhongshan City. However, current research lacks a comprehensive understanding of the genetic diversity and genetic structure of Zhongshan Partridge Duck, limiting protection and resource utilization.The primary objectives of this study are to systematically analyze the genetic diversity and population structure of the Zhongshan Partridge Duck using whole-genome resequencing technology, evaluate the conservation effectiveness of its captive breeding programs in maintaining genetic integrity, and propose scientifically informed strategies for the protection of this genetic resource. This work establishes a critical theoretical foundation and provides empirical evidence to advance the conservation of Zhongshan Partridge Duck germplasm resources. 

Methods: We collected 91 samples from seven duck populations in Guangdong and Guangxi provinces and obtained resequencing data for 388 samples from 19 additional populations through the NCBI public database, generating a combined dataset of 479 individuals representing 22 duck breeds. Population-level variant detection was conducted using the GenomicsDB method in GATK software. Genetic diversity parameters—including effective number of alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He), polymorphism information content (PIC), and nucleotide diversity (π)—were systematically calculated for all 22 populations using VCFtools. Population structure was evaluated through neighbor-joining (NJ) tree construction, principal component analysis (PCA), and Bayesian clustering analysis (STRUCTURE). Gene flow dynamics between the Zhongshan Partridge Duck and other breeds were subsequently investigated using Treemix analysis. 

Results: Genetic diversity assessments revealed that the Zhongshan Partridge Duck population exhibits relatively elevated genetic diversity among the 22 analyzed breeds (Ne = 3.8656, Ho = 0.3382, He = 0.3313). Notably, its observed heterozygosity (Ho) ranked highest across all breeds, while its expected heterozygosity (He) occupied the seventh position, still reflecting a substantial level of genetic variation. Population genetic structure analyses, including phylogenetic tree reconstruction and principal component analysis (PCA), demonstrated close clustering of the Zhongshan Partridge Duck with the Pekin Duck, Wenshi Partridge Duck, and Maple Leaf Duck. Admixture analysis identified the Zhongshan Partridge Duck as a distinct genetic cluster characterized by a single ancestral component at K=10. Treemix analysis with Zhongshan Partridge Duck designated as the outgroup failed to detect significant gene flow from other breeds into this population. Analyses utilizing the Mallard (Anas platyrhynchos) as the outgroup revealed only one migration event associated with the Zhongshan Partridge Duck, originating from the ancestral node of the Yulin Partridge Duck prior to its divergence. 

Conclusion: Population fluctuations constitute a critical determinant of genetic diversity in avian conservation genetics. Despite undergoing historical demographic bottlenecks characterized by severe population contractions, the Zhongshan Partridge Duck retains comparatively elevated genomic diversity, a conservation outcome attributable to coordinated ex situ management protocols implemented through the collaborative efforts of the Zhongshan Agricultural Technology Extension Center and South China Agricultural University. Population genomic structure analyses substantiate the conservation efficacy of the Wugui Mountain Conservation Farm, demonstrating successful maintenance of ancestral allelic variation. This investigation delineates the extant genetic architecture and population stratification patterns of the Zhongshan Partridge Duck, formulates empirically grounded strategies for conserving its evolutionary significant units (ESUs), and establishes a genomic-informed paradigm for safeguarding this agriculturally vital germplasm resource.

Key words: genetic diversity, population genetic structure, Zhongshan duck, gene flow analysis, whole-genome resequencing