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

Abstract

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

CLC Number:

S835.2

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.

Figures/Tables 9

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

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