Genetic diversity and population structure of four Chinese rabbit breeds
Autoři:
Anyong Ren aff001; Kun Du aff001; Xianbo Jia aff001; Rui Yang aff002; Jie Wang aff001; Shi-Yi Chen aff001; Song-Jia Lai aff001
Působiště autorů:
Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
aff001; Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
aff002
Vyšlo v časopise:
PLoS ONE 14(9)
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pone.0222503
Souhrn
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.
Klíčová slova:
Biology and life sciences – Organisms – Eukaryota – Animals – Vertebrates – Amniotes – Mammals – Leporids – Evolutionary biology – Genetics – Population genetics – Conservation genetics – Heredity – Heterozygosity – Molecular genetics – Genomics – Animal genomics – Population biology – Ecology – Ecological metrics – Species diversity – Conservation biology – Molecular biology – Molecular biology techniques – Research and analysis methods – Animal studies – Experimental organism systems – Animal models – Rabbits – Sequencing techniques – DNA sequencing – Ecology and environmental sciences – Conservation science
Zdroje
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