全基因组SNPs揭示井冈黑掌鹅种质资源特性与遗传多样性特征

doi:10.11843/j.issn.0366-6964.2025.07.015

畜牧兽医学报 ›› 2025, Vol. 56 ›› Issue (7): 3199-3209.doi: 10.11843/j.issn.0366-6964.2025.07.015

全基因组SNPs揭示井冈黑掌鹅种质资源特性与遗传多样性特征

缪俊杰¹^,²(), 张日泉³, 吴厚义³, 游新明³, 黄奕雯¹, 黄小英³, 郭震洋⁴, 刘建林⁵, 肖卫华⁶, 郭田华⁶, 陈浩², 康冬柳¹^,*()

1. 吉安市农业农村产业发展服务中心，吉安 343000
2. 江西科技师范大学生命科学学院，南昌 330013
3. 吉安市畜禽良种场，吉安 343000
4. 万安县农业产业发展服务中心，万安 343800
5. 吉安市青原区农业农村局，吉安 343000
6. 遂川县农业产业发展服务中心，遂川 343900

收稿日期:2024-12-26 出版日期:2025-07-23 发布日期:2025-07-25
通讯作者: 康冬柳 E-mail:1171708961@qq.com;kangdongliu@sina.com
作者简介:缪俊杰(2001-)，男，江西赣州人，硕士生，主要从事鹅与鸭等水禽的群体遗传学、基因组学、复杂性状遗传解析等相关方面研究，E-mail: 1171708961@qq.com
基金资助:
国家自然科学基金地区项目(32460141); 江西省自然科学基金面上项目(20232BAB205059);江西科技师范大学青年拔尖人才项目(2023QNBJRC004)

Genome-Wide SNP Analysis Revealed the Characteristics of Germplasm Resources and Genetic Diversity of Jinggang Black-Palm Geese

MIAO Junjie¹^,²(), ZHANG Riquan³, WU Houyi³, YOU Xinming³, HUANG Yiwen¹, HUANG Xiaoying³, GUO Zhenyang⁴, LIU Jianlin⁵, XIAO Weihua⁶, GUO Tianhua⁶, CHEN Hao², KANG Dongliu¹^,*()

1. Ji'an Agricultural and Rural Industry Development Service Center, Ji'an 343000, China
2. College of Life Sciences, Jiangxi Normal University of Science and Technology, Nanchang 330013, China
3. Ji'an Livestock and Poultry Breeding Farm, Ji'an 343000, China
4. Wan'an County Agricultural Industry Development Service Center, Wan'an 343800, China
5. Qingyuan District Agricultural and Rural Bureau, Ji'an 343000, China
6. Suichuan County Agricultural Industry Development Service Center, Suichuan 343900, China

Received:2024-12-26 Online:2025-07-23 Published:2025-07-25
Contact: KANG Dongliu E-mail:1171708961@qq.com;kangdongliu@sina.com

摘要/Abstract

摘要：

旨在基于全基因组SNPs数据探讨井冈黑掌鹅(Jinggang black-palm goose，JGG)与中国不同地域地方鹅之间的系统发育关系，解析中国家鹅及JGG的遗传多样性和遗传结构，为中国家鹅资源的鉴定与保护提供理论基础。本研究基于81只井冈黑掌鹅和6个地方家鹅品种的120只个体的基因组重测序数据(12×)，使用GATK和SnpEff软件对重测序基因组的单核苷酸多态性(single nucleotide polymorphism, SNP)进行检测与注释。基于常染色体SNP，构建系统进化树(neighbour-joining tree, NJ tree)，进行主成分分析(principal component analysis, PCA)聚类和Admixture分析，评估中国家鹅的群体结构和遗传多样性。研究结果显示，JGG群体中检测到5 955 261个SNPs，变异主要富集在基因间区(46.39%)和内含子区(34.56%)，外显子区(1.38%)变异较少。NJ tree、PCA和Admixture的结果显示，JGG种群单独聚类，其遗传分化受地理隔离、体型和羽色选育的驱动，显示出与兴国灰鹅、丰城灰鹅以及狮头鹅较近的亲缘关系。JGG的遗传多样性较低，常见SNP为3 414 168个，多肽位点比例(proportion of polypeptide sites, Pn)、期望杂合度(expected heterozygosity, He)、实际杂合度(observed heterozygosity, Ho)、近交系数(inbreeding coefficient, F)、种群内遗传距离(intra-population genetic distance，DST)以及纯合性片段长度(runs of homozygosity，ROH)分别为0.83、0.26、0.23、0.33±0.09、0.224±0.022和12.87±8.27。该研究结果系统解析了中国家鹅及井冈黑掌鹅的群体遗传结构和基因组特征，结果表明井冈黑掌鹅作为独立的地方品种鹅，其遗传分化主要受地理隔离和表型选育的影响，但其遗传多样较低，种群特征存在丧失的风险，亟需加强对该地方品种的保护与利用。

关键词: 井冈黑掌鹅, 中国家鹅, 全基因组SNPs, 遗传多样性, 种质资源

Abstract:

This study aimed to explore the phylogenetic relationships between the Jinggang black-palm goose (JGG) and various local goose breeds across China based on whole-genome SNP data, and to analyze the genetic diversity and genetic structure of Chinese geese and JGG, providing a theoretical foundation for the identification and conservation of Chinese goose resources. Genome resequencing data (12×coverage) from 81 Jinggang black-palm geese and 120 individuals of 6 local goose breeds were analyzed. Single nucleotide polymorphisms (SNPs) detection and annotation were conducted on autosomal regions using GATK and SnpEff softwares. A neighbor-joining (NJ) tree, principal component analysis (PCA), and Admixture analysis were performed to assess their population structure and genetic diversity. The JGG population harbored 5 955 261 SNPs, predominantly in intergenic (46.39%) and intronic regions (34.56%), with fewer in exonic regions (1.38%). Consistently, NJ tree, PCA, and Admixture analyses revealed distinct clustering of JGG, showing closer genetic affinity to Xingguo grey geese, Fengcheng grey geese, and Lionhead goose, driven by geographic isolation and artificial selection for body size and plumage traits. JGG exhibited low genetic diversity, with 3 414 168 common SNPs. Key parameters included: proportion of polymorphic sites (Pn=0.83), expected heterozygosity (He=0.26), observed heterozygosity (Ho=0.23), inbreeding coefficient (F=0.33±0.09), intra-population genetic distance (DST=0.224±0.022), and runs of homozygosity (ROH=12.87±8.27). This study systematically elucidates the population genetic structure and genomic characteristics of Chinese geese and JGG. As an independent local breed, JGG's genetic differentiation is shaped by geographic isolation and phenotypic selection, yet its low genetic diversity poses a risk of trait loss, highlighting the imperative for enhanced conservation and utilization efforts.

Key words: Jinggang black-palm goose, Chinese domestic goose, whole-genome SNPs, genetic diversity, germplasm resources

中图分类号:

S835.2

缪俊杰, 张日泉, 吴厚义, 游新明, 黄奕雯, 黄小英, 郭震洋, 刘建林, 肖卫华, 郭田华, 陈浩, 康冬柳. 全基因组SNPs揭示井冈黑掌鹅种质资源特性与遗传多样性特征[J]. 畜牧兽医学报, 2025, 56(7): 3199-3209.

MIAO Junjie, ZHANG Riquan, WU Houyi, YOU Xinming, HUANG Yiwen, HUANG Xiaoying, GUO Zhenyang, LIU Jianlin, XIAO Weihua, GUO Tianhua, CHEN Hao, KANG Dongliu. Genome-Wide SNP Analysis Revealed the Characteristics of Germplasm Resources and Genetic Diversity of Jinggang Black-Palm Geese[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(7): 3199-3209.

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品种 Breed	品种代号 Breed code	样本量 Sample size	原产地 Origin region	体型 Body type
定安鹅Dingan goose	DAG	20	海南定安	中等体型
丰城灰鹅Fengcheng grey goose	FCG	20	江西丰城	中等体型
井冈黑掌鹅Jinggang black-palm goose	JGG	81	江西吉安	大体型
马岗鹅Magang goose	MGG	20	广东开平	中等体型
狮头鹅Shitou goose	STG	20	广东饶平	大体型
乌鬃鹅Wuzong goose	WZG	20	广东清远	小体型
兴国灰鹅Xingguo grey goose	XGG	20	江西兴国	中等体型
总计Total		201

品种 Breed	缩写 Breed code	数量 Sample size	CSNPs	Pn	He	Ho	F	DST	ROH
定安鹅Dingan goose	DAG	20	3 967 550	0.93	0.30	0.27	0.16±0.04	0.260±0.012	5.411±3.194
丰城灰鹅 Fengcheng grey goose	FCG	20	3 956 616	0.93	0.30	0.27	0.16±0.05	0.259±0.004	4.583±1.019
井冈黑掌鹅 Jinggang black-palm goose	JGG	20	3 414 168	0.83	0.26	0.23	0.33±0.09	0.224±0.022	12.874±8.273
马岗鹅Magang goose	MGG	20	3 799 547	0.91	0.29	0.26	0.22±0.11	0.252±0.006	6.791±1.506
狮头鹅Shitou goose	STG	20	3 653 824	0.86	0.27	0.25	0.24±0.09	0.237±0.005	9.013±2.019
乌鬃鹅Wuzong goose	WZG	20	3 550 844	0.79	0.26	0.26	0.22±0.03	0.216±0.014	13.298±2.942
兴国灰鹅 Xingguo grey goose	XGG	20	3 931 859	0.94	0.30	0.29	0.10±0.05	0.252±0.007	4.909±1.148
总计Total		140

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全基因组SNPs揭示井冈黑掌鹅种质资源特性与遗传多样性特征

Genome-Wide SNP Analysis Revealed the Characteristics of Germplasm Resources and Genetic Diversity of Jinggang Black-Palm Geese

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