中山麻鸭是广东省唯一的地方鸭种, 是中山市最具代表性珍稀遗传资源。然而, 目前缺乏对中山麻鸭遗传多样性与遗传结构的全面认识, 限制了对中山麻鸭资源的保护与利用。本研究旨在利用全基因组重测序技术, 系统分析中山麻鸭的遗传多样性和遗传结构, 评估中山麻鸭保种场的保种效果, 并提出相应的遗传资源保护策略。本研究以包括中山麻鸭在内的22个鸭品种479个个体作为研究对象, 基于全基因组重测序技术, 进行群体遗传多样性与遗传结构相关分析。遗传多样性估算结果表明, 22个鸭品种的群体中中山麻鸭群体遗传多样性水平较高(Ne = 3.8656, Ho = 0.3382, He = 0.3313), 其中观测杂合度(Ho)在22个品种中是最高的, 期望杂合度(He)在22个品种中位于第7位也处于较高的水平。群体遗传结构研究中进化树与主成分分析结果均显示, 中山麻鸭与北京鸭、温氏麻鸭、枫叶鸭聚类较近。Admixture分析结果显示, 当K = 10时, 中山麻鸭遗传结构变得单一, 仅有一个祖先的遗传成分。最后以中山麻鸭为外群进行TreeMix分析, 结果中没有发现基因流从其他品种流向中山麻鸭, 以绿头野鸭为外群进行TreeMix分析, 结果显示也仅有从玉林麻鸭分化节点前到中山麻鸭这一次迁移事件与中山麻鸭相关。本研究明晰了中山麻鸭群体遗传多样性和遗传结构, 并提出了中山麻鸭遗传资源的保护策略, 有望能为中山麻鸭种质资源的保护提供理论基础与科学依据。

Aims: The Zhongshan partridge duck is the only local duck breed in Guangdong Province and represents the most representative rare genetic resource in Zhongshan City. However, current research lacks a comprehensive understanding of the genetic diversity and genetic structure of Zhongshan partridge duck populations, 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 populations 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.

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 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 genetic structure was evaluated through neighbor-joining (NJ) tree construction, principal component analysis (PCA), and Bayesian clustering analysis. 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 exhibited relatively elevated genetic diversity among the 22 analyzed breeds (Ne = 3.8656, Ho = 0.3382, He = 0.3313). Notably, its Ho ranked highest across all breeds, while its 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 Beijing 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.