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

打开文本图片集

中图分类号：S835.2 文献标志码：A 文章编号：0366-6964（2025）07-3199-11

Abstract： This study aimed to explore the phylogenetic relationships between the Jinggang blackpalm 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 12O 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 neighborjoining（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 fewerin 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.

Keywords： Jinggang black-palm goose; Chinese domestic goose; whole-genome SNPs； genetic diversity；germplasm resources ∗ Corresponding author：KANG Dongliu，E-mail： kangdongliu@ sina. com

雁形自（Anseriformes）、鸭科（Anatidae）、雁属（Anser）的家鹅作为我国传统驯养禽类，其驯化历史可追溯至7000 年前的江浙地区[1]。（剩余15563字）