基于全基因组重测序分析豁眼鹅(五龙鹅)遗传多样性和保种效果

doi:10.11843/j.issn.0366-6964.2025.12.019

畜牧兽医学报 ›› 2025, Vol. 56 ›› Issue (12): 6159-6166.doi: 10.11843/j.issn.0366-6964.2025.12.019

基于全基因组重测序分析豁眼鹅(五龙鹅)遗传多样性和保种效果

滕兴怡¹(), 王宝维¹^,², 张名爱¹^,², 孔敏¹^,², 舒音东³, 王丰好⁴, 姜雅静¹, 鲁秀¹, 怀志芳¹, 臧玉婷¹, 黄鲁豫¹, 凡文磊¹^,²^,*()

1. 青岛农业大学动物科技学院, 青岛 266109
2. 青岛农业大学优质水禽研究所, 青岛 266109
3. 昆明市东川区动物疫病预防控制中心, 昆明 654100
4. 莱西市农业农村局, 青岛 266600

收稿日期:2025-04-21 出版日期:2025-12-23 发布日期:2025-12-24
通讯作者: 凡文磊 E-mail:tengxy617@126.com;fanwenlei@qau.edu.cn
作者简介:滕兴怡(2000-)，女，重庆云阳人，硕士生，主要从事动物遗传育种研究，E-mail: tengxy617@126.com
基金资助:
国家自然科学基金青年项目(32202668)；云南省科技厅科技计划项目(202404BP090010)；国家重点研发计划(2023YFD1300305)；国家水禽产业技术体系(CARS-42-14)

The Evaluation of Conservation Efficacy and Population Genetic Diversity in Huoyan Geese (Wulong Geese) Based on Whole-Genome Resequencing

TENG Xingyi¹(), WANG Baowei¹^,², ZHANG Ming'ai¹^,², KONG Min¹^,², SHU Yindong³, WANG Fenghao⁴, JIANG Yajing¹, LU Xiu¹, HUAI Zhifang¹, ZANG Yuting¹, HUANG Luyu¹, FAN Wenlei¹^,²^,*()

1. College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
2. Institute of High Quality Waterfowl, Qingdao Agricultural University, Qingdao 266109, China
3. Dongchuan District Center for Animal Disease Control and Prevention, Kunming 654100, China
4. Bureau of Agriculture and Rural Affairs of Laixi, Qingdao 266600, China

Received:2025-04-21 Online:2025-12-23 Published:2025-12-24
Contact: FAN Wenlei E-mail:tengxy617@126.com;fanwenlei@qau.edu.cn

摘要/Abstract

摘要：

旨在利用全基因组重测序技术分析豁眼鹅(五龙鹅)群体遗传多样性，评估种质资源保护状况，为后续保种工作提供参考。本研究从山东莱阳豁眼鹅(五龙鹅)保种场随机选取了40只公鹅进行全基因组重测序，分析了其遗传多样性、群体遗传结构和连续纯合片段等。结果表明，40只豁眼鹅(五龙鹅)平均测序深度为13×，质控后共鉴定到13 251 291个SNPs位点。群体遗传多样性分析发现，本保种群体平均多态信息含量(PIC)为0.264，平均观察杂合度(Ho)为0.323，平均期望杂合度(He)为0.327，群体近亲系数(F)为0.012。LD衰减分析结果可知，最大R²值为0.47，衰减距离为162 kb。豁眼鹅(五龙鹅)保种群体共检测到309个连续纯合片段(ROH)，基于ROH值计算得出的近交系数(F_ROH)为0.009，表明群体近交程度较低。IBS距离矩阵和G矩阵的结果趋势相似，只有少部分的个体间亲缘关系较近。主成分分析与NJ聚类分析结果同样显示, 保种群总体呈离散状态。总体而言，本次调查的山东莱阳豁眼鹅(五龙鹅)保种场种群遗传多样性良好、近交程度较低，保种效果良好。

关键词: 豁眼鹅, 保种效果, 全基因组重测序, 遗传多样性, 近交

Abstract:

This study aimed to investigate the genetic diversity and inbreeding status of the Huoyan geese (Wulong geese) conservation population using whole-genome resequencing, evaluate the effectiveness of current germplasm conservation strategies, and provide actionable insights for future breeding programs. A total of 40 male Huoyan geese (Wulong geese) were randomly selected from the Shandong Provincial Conservation Farm for whole-genome resequencing. Subsequent analyses included assessments of genetic diversity, population genetic structure, and runs of homozygosity (ROH). The results showed that: a total of 40 slit-eyed geese (Wulong geese) were sequenced with an average depth of 13×, and 13 251 291 SNP loci were identified after quality control. The average polymorphism information content (PIC) of this conservation population was 0.264, the average observed heterozygosity (Ho) was 0.323, and the average expected heterozygosity (He) was 0.327, with an inbreeding coefficient (F) of 0.012. LD decay analysis showed that the maximum R² value was 0.47, with a decay distance of 162 kb. A total of 309 runs of homozygosity (ROH) were detected in the Huoyan Goose (Wulong Goose) conservation population. The inbreeding coefficient (F_ROH) calculated based on ROH was 0.009, indicating a low level of inbreeding within the population. The results of the IBS distance matrix and G matrix showed simi-lar trends, with only a small proportion of individuals exhibiting close kinship. Principal component analysis (PCA) and neighbor-joining (NJ) clustering analysis further confirmed that the conservation population was generally in a dispersed state. Overall, the genetic diversity of the Huoyan goose (Wulong goose) conservation population surveyed in Laiyang was favorable, with a low level of inbreeding, indicating effective conservation efforts.

Key words: Huoyan goose, conservation efficacy, whole-genome resequencing, genetic diversity, inbreeding

中图分类号:

S835.2

滕兴怡, 王宝维, 张名爱, 孔敏, 舒音东, 王丰好, 姜雅静, 鲁秀, 怀志芳, 臧玉婷, 黄鲁豫, 凡文磊. 基于全基因组重测序分析豁眼鹅(五龙鹅)遗传多样性和保种效果[J]. 畜牧兽医学报, 2025, 56(12): 6159-6166.

TENG Xingyi, WANG Baowei, ZHANG Ming'ai, KONG Min, SHU Yindong, WANG Fenghao, JIANG Yajing, LU Xiu, HUAI Zhifang, ZANG Yuting, HUANG Luyu, FAN Wenlei. The Evaluation of Conservation Efficacy and Population Genetic Diversity in Huoyan Geese (Wulong Geese) Based on Whole-Genome Resequencing[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(12): 6159-6166.

图/表 5

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质控数据Quality control data	平均值Mean	标准差Standard deviation	最大值Maximum	最小值Minimum
原始读数 Raw Reads	100 364 393	20 400 921.34	139 238 184	52 561 796
清洁碱基/Gb Clean base	14.99	3.04	20.78	7.85
清洁读数 Clean Reads	100 364 391	20 400 921.72	139 238 184	52 561 794
比对读段数 Mapping Reads	96 489 034.73	19 607 496.35	133 510 422	50 155 861
比对率/% Mapping rate	96	0.65	97	94
测序深度/× Coverage depth	13.02	2.60	17.80	6.83

遗传多样性参数 Genetic diversity parameter	均值±标准差 Mean±SD
观测杂合度 Observed heterozygosity(Ho)	0.323±0.146
期望杂合度 Expected heterozygosity(He)	0.327±0.134
群体近交系数 Inbreeding coefficient(F)	0.012±0.051
多态信息含量 Polymorphism information content(PIC)	0.264±0.093

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基于全基因组重测序分析豁眼鹅(五龙鹅)遗传多样性和保种效果

The Evaluation of Conservation Efficacy and Population Genetic Diversity in Huoyan Geese (Wulong Geese) Based on Whole-Genome Resequencing

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