基于全基因组重测序SNP分析宁蒗高原鸡保种群的群体遗传多样性和群体遗传结构

doi:10.11843/j.issn.0366-6964.2024.12.016

Abstract

Abstract:

In order to better protect and utilize the Ninglang Plateau chickens, the population genetic diversity and population genetic structure of Ninglang Plateau chickens conserved population were explored in this study. Whole-genome resequencing technology was used to detect single-nucleotide polymorphism (SNP) in Ninglang Plateau chickens(n=57), Daweishan Mini chickens(n=20), Dulong chickens(n=10) and Nixi chickens(n=11) populations, and population genetic diversity was analyzed by observing heterozygosity (Ho), expected heterozygosity (He), polymorphic nucleotide ratio (P_N), nucleotide diversity (Pi), and minor allele frequency (Maf), and linkage disequilibrium (LD) decay. Principal component analysis, phylogenetic tree, and population structure analysis were employed to examine the population genetic structure of different breeds. The degree of differentiation between breeds was evaluated using the fixation index (Fst). Additionally, the genetic relatedness within the conservation population of Ninglang Plateau chickens were analyzed using identity by state (IBS), G matrix, and the coefficient of inbreeding (F_ROH). The results showed that the observed heterozygosity (Ho) of the Ninglang Plateau chickens population was 0.212, which was lower than its expected heterozygosity (He) of 0.221, while the Ho values of Daweishan Mini chickens, Dulong chickens, and Nixi chickens were higher than their respective He values, indicating that the genetic diversity of the Ninglang Plateau chickens population was relatively high; LD decay analysis showed that the decay rates of the 4 breeds from fastest to slowest was Ninglang Plateau chickens, Daweishan Mini chickens, Nixi chickens, and Dulong chickens, indicating that Ninglang Plateau chickens population had the highest genetic diversity and the lowest degree of genome selection. The results of principal component analysis and phylogenetic tree showed that Ninglang Plateau chickens were divided into 3 branches. Daweishan Mini chickens exhibited significant genetic divergence from Ninglang Plateau chickens, Dulong chickens, and Nixi chickens. Population structure analysis revealed that the optimal number of clusters was K=2, with Ninglang Plateau chickens exhibiting a complex genetic background, while Dulong chickens and Nixi chickens had relatively similar genetic backgrounds. Population genetic differentiation analysis found moderate levels of differentiation between Ninglang Plateau chickens and Daweishan Mini chickens, Nixi chickens, and Dulong chickens, whereas the genetic differentiation index between Dulong chickens and Nixi chickens was lower; IBS matrix and G matrix analysis revealed that most individuals within the conservation population of Ninglang Plateau chickens were distantly related, with a few individuals showing closer relationships. The results showed that there was a moderate differentiation between Ninglang Plateau chickens and Daweishan Mini chickens, Nixi chickens, and Dulong chickens. The genetic diversity of the Ninglang Plateau chickens breeding population was relatively rich, but there was a trend of inbreeding within the conservation population. Therefore, effective breeding programs should be established, and conservation efforts should be strengthened to avoid inbreeding depression.

Key words: whole genome, Ninglang Plateau chickens, population genetic diversity, population genetic structure

CLC Number:

S831.2

XU Kuowei, LI Zhuohui, LENG Tangjian, XIONG Bao, ZHOU Jielong, GUO Panjiang, WANG Yu, CHEN Fenfen. Analysis of Population Genetic Diversity and Population Genetic Structure of Conservation Population in Ninglang Plateau Chickens Based on Whole-genome Resequencing SNP[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(12): 5498-5510.

Figures/Tables 10

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品种 Breed	观测杂合度(Ho) Observed heterozygosity	期望杂合度(He) Expected heterozygosity	多态标记比例(P_N) Polymorphic marker ratio	核苷酸多态性(Pi) Nucleotide diversity	次等位基因频率(Maf) Minor allele frequency
大围山微型鸡Daweishan	0.232	0.229	0.819 0	4.04×10^-3	0.164
独龙鸡Dulong	0.239	0.225	0.736 7	4.06×10^-3	0.162
尼西鸡Nixi	0.231	0.219	0.730 6	3.83×10^-3	0.158
宁蒗高原鸡Ninglang	0.212	0.221	0.868 3	3.94×10^-3	0.159

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Analysis of Population Genetic Diversity and Population Genetic Structure of Conservation Population in Ninglang Plateau Chickens Based on Whole-genome Resequencing SNP

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