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. 2019 Sep 16;14(9):e0222503.
doi: 10.1371/journal.pone.0222503. eCollection 2019.

Genetic diversity and population structure of four Chinese rabbit breeds

Anyong Ren  1 , Kun Du  1 , Xianbo Jia  1 , Rui Yang  2 , Jie Wang  1 , Shi-Yi Chen  1 , Song-Jia Lai  1
Affiliations

Genetic diversity and population structure of four Chinese rabbit breeds

Anyong Ren et al. PLoS One. .

Abstract

There are a few well-known indigenous breeds of Chinese rabbits in Sichuan and Fujian provinces, for which the genetic diversity and population structure have been poorly investigated. In the present study, we successfully employed the restriction-site-associated DNA sequencing (RAD-seq) approach to comprehensively discover genome-wide SNPs of 104 rabbits from four Chinese indigenous breeds: 30 Sichuan White, 34 Tianfu Black, 32 Fujian Yellow and eight Fujian Black. A total of 7,055,440 SNPs were initially obtained, from which 113,973 high-confidence SNPs (read depth ≥ 3, calling rate = 100% and biallelic SNPs) were selected to study the genetic diversity and population structure. The mean polymorphism information content (PIC) and nucleotide diversity (π) of each breed slightly varied with ranging from 0.2000 to 0.2281 and from 0.2678 to 0.2902, respectively. On the whole, Fujian Yellow rabbits showed the highest genetic diversity, which was followed by Tianfu Black and Sichuan White rabbits. The principal component analysis (PCA) revealed that the four breeds were clearly distinguishable. Our results first reveal the genetic differences among these four rabbit breeds in the Sichuan and Fujian provinces and also provide a high-confidence set of genome-wide SNPs for Chinese indigenous rabbits that could be employed for gene linkage and association analyses in the future.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Rabbit pictures from each of the four indigenous breeds in this study.
Fig 2
Fig 2. SNP distribution and nucleotide diversity.
(A) Distribution density of SNPs across 22 chromosomes, in which each block represents a split bin. (B) Substitution types of SNPs in all populations. (C) Distribution density of the nucleotide diversity in four rabbit breeds.
Fig 3
Fig 3. Population structure of the four rabbit breeds.
(A) The plot shows the pairwise Wright’s FST values in the lower triangular area and FIS values in diagonal cells. (B) Plot of pairwise principal components (PC1 and PC2) of four rabbit breeds based on the SNP data.
See this image and copyright information in PMC

References

    1. Monnerot M, Vigne JD, Biju-Duval C, Casane D, Callou C, Hardy C, et al. Rabbit and man: genetic and historic approach. Genet Sel Evol. 1994;26(Suppl 1):1–14.
    1. Graham-Jones O. Natural history of domesticated mammals. Vet J. 2001;161(1):22–3.
    1. Whitman BD. Domestic rabbits & their histories: Breeds of the World. Leathers Publishing; 2004.
    1. Rogel Gaillard C, Ferrand N, Hayes H. Rabbit In: Kole C, Cockett N, editors. genome mapping and genomics in domestic animals.Springer; 2009. p. 165–230.
    1. Long J-R, Qiu X-P, Zeng F-T, Tang L-M, Zhang Y-P. Origin of rabbit (Oryctolagus cuniculus) in China: evidence from mitochondrial DNA control region sequence analysis. Anim Genet. 2003;34(2):82–7. - PubMed

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