Genetic diversity and population structure of four Chinese rabbit breeds.

Anyong Ren,Rui Yang,Xianbo Jia,Kun Du,Jie Wang,Shi-Yi Chen,Song-Jia Lai,Tzen-Yuh Chiang

doi:10.1371/journal.pone.0222503

Anyong Ren, Rui Yang + Show 6 more

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https://doi.org/10.1371/journal.pone.0222503

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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.

Highlights

Rabbits (Oryctolagus cuniculus) are one of the most recently domesticated animals with an estimated history of approximately 1,400 years [1, 2]
Blood samples were randomly collected from 104 unrelated individuals from four indigenous breeds of Chinese rabbits (Fig 1), including 30 Sichuan White (SW) and 34 Tianfu Black (TB) from Sichuan province, 32 Fujian Yellow (FY) and eight Fujian Black (FB) from Fujian province
Sustainable development of the Chinese rabbit industry significantly depends on a sufficient amount of genetic resources available, especially for these indigenous breeds

Summary

Introduction

Rabbits (Oryctolagus cuniculus) are one of the most recently domesticated animals with an estimated history of approximately 1,400 years [1, 2]. In China, there are approximately 20 indigenous and recently imported rabbit breeds, which are widely kept for their meat, fur and wool [5]. Compared to the indigenous rabbit breeds, these imported breeds are more prevalent in the Chinese rabbit industry because of their better production performances on the important economic traits [6]. These indigenous breeds have superior disease resistance and environmental adaptation [7], and these characteristics make them important for the sustainable development of the rabbit industry in China.

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