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. 2024 Jun 19:11:1319854.
doi: 10.3389/fvets.2024.1319854. eCollection 2024.

Molecular genetic identification of Wuzhishan ant chicken, a newly discovered resource in China

Lihong Gu  1 , Fanghu Wu  2 , Xinli Zheng  1 , Xiaohui Zhang  2 , Yanmin Chen  3 , Lizhi Lu  4 , Xiangxiang Liu  3 , Shuhui Mo  3 , Zhe Chao  1 , Zhongchun He  1 , Yuanyuan Shang  2 , Dong Wei  5 , Sheng Wei  5 , Youyi Chen  3 , Tieshan Xu  6
Affiliations

Molecular genetic identification of Wuzhishan ant chicken, a newly discovered resource in China

Lihong Gu et al. Front Vet Sci. .

Abstract

Introduction: The Wuzhishan ant (MY) chicken exhibits significant differences from other chicken breeds. However, the molecular genetic relationship between the MY breed and other chicken breeds has not been assessed.

Methods: Whole-genome resequencing was used to compare genetic diversity, nucleotide diversity, the fixation index, the linkage disequilibrium coefficient, and phylogenetic tree relationships between the MY breed and the Wenchang (WC), Danzhou (DZ), Bawangling (BW), and Longsheng Feng (LF) breeds.

Results: A total of 21,586,378 singlenucleotide polymorphisms and 4,253,341 insertions/deletions were screened out among the five breeds. The MY breed had the second highest genomic genetic diversity and nucleotide diversity and the lowest LD coefficient among the five breeds. Moreover, the phylogenetic tree analysis showed that individual birds of each breed clustered together with those of their respective breeds.

Discussion: Our data indicated that the MY breed is distinct from the other breeds and can be considered a new genetic resource.

Keywords: Wuzhishan ant chicken; genetic diversity; genetic resource; genetic structure; whole-genome resequencing.

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Conflict of interest statement

DW and SW were affiliated to Wuzhishan Ant Chicken Cooperative. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Distribution map of the five breeds. LF, Longsheng Feng chickens; BW, Bawangling chickens; DZ, Danzhou chickens; WC, Wenchang chickens; MY, Wuzhishan ant chickens.
Figure 2
Figure 2
Single-nucleotide polymorphism (SNP) and insertion/deletion (InDel) screening results. (A) Statistical map of the SNPs. (B) Statistical map of SNP positions. (C) Statistical map of InDel positions. (D) Statistical map of InDel functional annotations in coding sequence (CDS) regions.
Figure 3
Figure 3
Manhattan plot of nucleotide diversity (π) distribution. The horizontal axis indicates the position of the genome, and the vertical coordinate indicates the π value of the windows. Chrom, chromosome.
Figure 4
Figure 4
Linkage disequilibrium decay plot. LF, Longsheng Feng chickens; BW, Bawangling chickens; DZ, Danzhou chickens; WC, Wenchang chickens; MY, Wuzhishan ant chickens.
Figure 5
Figure 5
Principal component analysis of the five chicken breeds. (A) PC1/PC2. (B) PC1/PC3. (C) PC2/PC3. (D) 3D PCA Scatter Plot. LF, Longsheng Feng chickens; BW, Bawangling chickens; DZ, Danzhou chickens; WC, Wenchang chickens; MY, Wuzhishan ant chickens.
Figure 6
Figure 6
Phylogenetic tree of five chicken breeds. The “group” label indicates the different chicken breeds. The number 0.007 indicates that the branch of this length represents a genetic variation of 0.007 in the genome.
Figure 7
Figure 7
Histogram of the genetic composition of the samples. Each color represents a cluster within each K value.
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References

    1. China National Commission of Animal Genetic Resources . Animal genetic resources in China Poultrys [M]. Beijing: China Agriculture Press; (2011).
    1. Mcmahon BJ, Teeling EC, Höglund J. How and why should we implement genomics into conservation? [J]. Evol Appl. (2014) 7:999–1007. doi: 10.1111/eva.12193, PMID: - DOI - PMC - PubMed
    1. Lopes MS, Mendonça D, Rojer H, Cabral VÃ3, Bettencourt SÃX, da Câmara Machado A. Morphological and genetic characterization of an emerging Azorean horse breed: the Terceira pony [J]. Front Genet. (2015) 6:62. doi: 10.3389/fgene.2015.00062 - DOI - PMC - PubMed
    1. Andersson L, Georges M. Domestic-animal genomics: deciphering the genetics of complex traits [J]. Nat Rev Genet. (2004) 5:202–12. doi: 10.1038/nrg1294, PMID: - DOI - PubMed
    1. Gu LH. Performance study of Wuzhishan ant chicken germplasm [J]. Chin Livest Poult Breed. (2022) 18:5–7+3.