基于全基因组重测序分析道州灰鹅保种效果

doi:10.11843/j.issn.0366-6964.2025.02.015

摘要/Abstract

摘要：

旨在研究道州灰鹅保种场鹅群的遗传结构、遗传多样性和亲缘关系，为后续道州灰鹅的保种工作提供参考。道州灰鹅保种场采用单父本家系轮配的保种模式进行保种，共49个家系，每个家系中取一只200日龄左右的健康公鹅，采静脉血进行DNA抽提，对DNA样品进行全基因组重测序，根据每个家系公鹅的重测序数据，利用生物信息学软件对群体遗传结构和遗传多样性进行分析与评价。结果，共检测到道州灰鹅保种群体的SNPs位点15 245 050个，在过滤质控后得到SNPs位点14 628 485个。群体遗传多样性分析结果显示，群体的平均观测杂合度(Ho)为0.280，平均期望杂合度(He)为0.288，群体近亲系数(Fis)为0.070，平均多态信息含量(PIC)为0.262，基因多样性指数(Nei)为0.331。道州灰鹅保种群体共检测到802个连续纯合片段(ROH)，基于ROH值计算得出的近交系数为0.010，近交程度较低。IBS距离矩阵、G矩阵的结果相似，只有少部分的个体间亲缘关系较近。群体渗透分析与主成分分析结果同样显示，大部分个体聚类为一个亚群，少部分个体聚类为2个小亚群。通过群体分化指数(Fst)的计算结果，2个小的亚群之间出现了中等程度的分化。总体而言，道州灰鹅保种群体的遗传多样性较为丰富，近交水平较低，保种效果优良，建议减少亲缘关系过于接近的家系间的配种，以保持遗传多样性和群体的长期健康。

关键词: 重测序, 道州灰鹅, 遗传结构

Abstract:

This study aimed to investigate the genetic structure, diversity, and kinship of geese at the Daozhou gray goose conservation farm to guide future conservation efforts.The Daozhou gray goose conservation farm used a single-sire family rotation model, involving 49 families. A healthy 200-day-old male goose from each family was selected for DNA extraction via venous blood sampling. The DNA samples were subjected to whole-genome resequencing, and the resulting data were analyzed using bioinformatics software to assess the genetic structure and diversity of the population.A total of 15 245 050 SNPs were detected in the Daozhou gray goose conservation population, reducing to 14 628 485 after quality control. Genetic diversity analysis revealed an average observed heterozygosity (Ho) of 0.280, expected heterozygosity (He) of 0.288, inbreeding coefficient (Fis) of 0.070, average polymorphism information content (PIC) of 0.262, and gene diversity index (Nei) of 0.331. A total of 802 runs of homozygosity (ROH) were identified, with an inbreeding coefficient of 0.010, indicating low inbreeding levels. IBS distance matrix and G-matrix results showed that only a few individuals had close kinship. Population admixture and principal component analysis indicated that most individuals clustered into one subpopulation, while a few formed two small subpopulations. Fst calculation result showed moderate differentiation between the two smaller subpopulations.In summary, the conserved population of Daozhou gray goose exhibits relatively rich genetic diversity and a low level of inbreeding, reflecting good conservation outcomes. It is recommended to decrease breeding between family lines with excessively close kinship relationships in order to maintain genetic diversity and ensure the long-term health of the population.

Key words: resequencing, Daozhou gray goose, genetic structure

中图分类号:

S835.2

万伟粲, 何旭, 刘洋, 马玉勇, 蒋玉章, 戴求仲, 燕海峰, 蒋桂韬, 李闯. 基于全基因组重测序分析道州灰鹅保种效果[J]. 畜牧兽医学报, 2025, 56(2): 633-642.

WAN Weican, HE Xu, LIU Yang, MA Yuyong, JIANG Yuzhang, DAI Qiuzhong, YAN Haifeng, JIANG Guitao, LI Chuang. Evaluation of Daozhou Gray Goose Conservation Based on Whole Genome Resequencing Analysis[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(2): 633-642.

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遗传多样性指标 Genetic diversity index	均值±标准差 Mean±SD
观测杂合度Ho	0.280±0.004
期望杂合度He	0.288±0.026
群体近亲系数Fis	0.070±0.050
多态信息含量PIC	0.262±0.092
基因多样性指数Nei	0.331±0.193

分群 Group	亚群1 Subgroup 1	亚群2 Subgroup 2	亚群3 Subgroup 3
亚群1 Subgroup 1	/	0.037 4	0.100 8
亚群2 Subgroup 2	/	/	0.026 7

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