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
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.
2. Graham-Jones O. Natural history of domesticated mammals. Vet J. 2001;161(1):22–3.
3. Whitman BD. Domestic rabbits & their histories: Breeds of the World. Leathers Publishing. 2004.
4. 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.
5. 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. 12648090
6. Ban Z, Liu R, Xiao C, Wu Y, Liu S. Feasibility study on calculating Heterosis by genetic structure of strains. Chinese Journal of Rabbit Farming. 1996;1:15–21 (in Chinese).
7. Wan X, Mao L, Li T, Qin L, Pan Y, Li B, et al. IL-10 gene polymorphisms and their association with immune traits in four rabbit populations. J Vet Med Sci. 2014;76(3):369–75. doi: 10.1292/jvms.13-0304 24240540
8. Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA. Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res. 2007;17(2):240–8. doi: 10.1101/gr.5681207 17189378
9. Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet. 2011;12(7):499–510. doi: 10.1038/nrg3012 21681211
10. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, et al. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One. 2008;3(10):e3376. doi: 10.1371/journal.pone.0003376 18852878
11. Wang W, Yan H, Yu J, Yi J, Qu Y, Fu M, et al. Discovery of genome-wide SNPs by RAD-seq and the genetic diversity of captive hog deer (Axis porcinus). PLoS One. 2017;12(3):e0174299. doi: 10.1371/journal.pone.0174299 28323863
12. Rodriguez-Ezpeleta N, Alvarez P, Irigoien X. Genetic diversity and connectivity in maurolicus muelleri in the Bay of Biscay inferred from thousands of SNP markers. Front Genet. 2017;8:195. doi: 10.3389/fgene.2017.00195 29234350
13. Kang J, Ma X, He S. Population genetics analysis of the Nujiang catfish Creteuchiloglanis macropterus through a genome-wide single nucleotide polymorphisms resource generated by RAD-seq. Sci Rep. 2017;7(1):2813. doi: 10.1038/s41598-017-02853-3 28588195
14. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884–i90. doi: 10.1093/bioinformatics/bty560 30423086
15. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754–60. doi: 10.1093/bioinformatics/btp324 19451168
16. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297–303. doi: 10.1101/gr.107524.110 20644199
17. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43(5):491–8. doi: 10.1038/ng.806 21478889
18. Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, et al. From FastQ data to high‐confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics. 2013;11(1110):1–33.
19. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156–8. doi: 10.1093/bioinformatics/btr330 21653522
20. Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA. Stacks: an analysis tool set for population genomics. Mol Ecol. 2013;22(11):3124–40. doi: 10.1111/mec.12354 23701397
21. Chen SY, Deng F, Huang Y, Li C, Liu L, Jia X, et al. PopSc: computing toolkit for basic statistics of molecular population genetics simultaneously implemented in web-based calculator, Python and R. PLoS One. 2016;11(10):e0165434. doi: 10.1371/journal.pone.0165434 27792763
22. Yang J, Lee SH, Goddard ME, Visscher PM. GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet. 2011;88(1):76–82. doi: 10.1016/j.ajhg.2010.11.011 21167468
23. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81(3):559–75. doi: 10.1086/519795 17701901
24. Ginestet C. ggplot2: elegant graphics for data analysis. J R Stat Soc. 2011;174(1):245–6.
25. Wu L, Gu R, Li X, editors. The international competitiveness of China’s rabbit meat industry. Proc 10 th World Rabbit Congress, Egypt, Sharm El-Sheikh; 2012.
26. Xie X-L, Chen D-L, Chen Y-F, Sun S-K, Sang L, Wu X-S, et al. Determination of genetic characteristics of Minxinan black rabbit population using microsatellite markers. Fujian Journal of Agricultural Sciences. 2012;33(1):37–42 (in Chinese).
27. Rong M, Yang F-H, Xing X-M, Sun H-M, Zhao J-P. The genetic diversity of Chinese rabbit by using microsatellite DNA markers. Chinese Journal of Animal Science. 2008;44(7):1–5 (in Chinese).
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