Asian-Australasian Journal of Animal Sciences

  • 제33권9호
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  • Pages.1378-1386
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  • 2020
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  • 1011-2367(pISSN)
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  • 1976-5517(eISSN)
아세아태평양축산학회 (Asian Australasian Association of Animal Production Societies)
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Detection of copy number variation and selection signatures on the X chromosome in Chinese indigenous sheep with different types of tail

  • Zhu, Caiye (College of Animal Science and Technology, Gansu Agricultural University) ;
  • Li, Mingna (College of Animal Science and Technology, Gansu Agricultural University) ;
  • Qin, Shizhen (College of Animal Science and Technology, Gansu Agricultural University) ;
  • Zhao, Fuping (National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences) ;
  • Fang, Suli (College of Animal Science and Technology, Gansu Agricultural University)
  • 투고 : 2018.09.05
  • 심사 : 2019.06.17
  • 발행 : 2020.09.01
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초록

Objective: Chinese indigenous sheep breeds can be classified into the following three categories by their tail morphology: fat-tailed, fat-rumped and thin-tailed sheep. The typical sheep breeds corresponding to fat-tailed, fat-rumped, and thin-tailed sheep are large-tailed Han, Altay, and Tibetan sheep, respectively. Detection of copy number variation (CNV) and selection signatures provides information on the genetic mechanisms underlying the phenotypic differences of the different sheep types. Methods: In this study, PennCNV software and F-statistics (FST) were implemented to detect CNV and selection signatures, respectively, on the X chromosome in three Chinese indigenous sheep breeds using ovine high-density 600K single nucleotide polymorphism arrays. Results: In large-tailed Han, Altay, and Tibetan sheep, respectively, a total of six, four and 22 CNV regions (CNVRs) with lengths of 1.23, 0.93, and 7.02 Mb were identified on the X chromosome. In addition, 49, 34, and 55 candidate selection regions with respective lengths of 27.49, 16.47, and 25.42 Mb were identified in large-tailed Han, Altay, and Tibetan sheep, respectively. The bioinformatics analysis results indicated several genes in these regions were associated with fat, including dehydrogenase/reductase X-linked, calcium voltage-gated channel subunit alpha1 F, and patatin like phospholipase domain containing 4. In addition, three other genes were identified from this analysis: the family with sequence similarity 58 member A gene was associated with energy metabolism, the serine/arginine-rich protein specific kinase 3 gene was associated with skeletal muscle development, and the interleukin 2 receptor subunit gamma gene was associated with the immune system. Conclusion: The results of this study indicated CNVRs and selection regions on the X chromosome of Chinese indigenous sheep contained several genes associated with various heritable traits.

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참고문헌

  1. Safdarian M, Zamiri MJ, Hashemi M, Noorolahi H. Relationships of fat-tail dimensions with fat-tail weight and carcass characteristics at different slaughter weights of Torki-Ghashghaii sheep. Meat Sci 2008;80:686-9. https://doi.org/10.1016/j.meatsci.2008.03.007
  2. Hossein MM, Ardeshir NJ, Mohammad MS, Dodds KG, Mcewan JC. Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition. BMC Genet 2012;13:10. https://doi.org/10.1186/1471-2156-13-10
  3. Mills RE, Walter K, Stewart C, et al. Mapping copy number variation by population-scale genome sequencing. Nature 2011;470:59-65. https://doi.org/10.1038/nature09708
  4. Stankiewicz P, Lupski JR. Structural variation in the human genome and its role in disease. Annu Rev Med 2010;61:437-55. https://doi.org/10.1146/annurev-med-100708-204735
  5. Giuffra E, Törnsten A, Marklund S, et al. A large duplication associated with dominant white color in pigs originated by homologous recombination between LINE elements flanking KIT. Mamm Genome 2002;13:569-77. https://doi.org/10.1007/s00335-002-2184-5
  6. Zhu C, Fan H, Yuan Z, et al. Detection of selection signatures on the X chromosome in three sheep breeds. Int J Mol Sci 2015;16:20360-74. https://doi.org/10.3390/ijms160920360
  7. Stainton JJ, Haley CS, Charlesworth B, Kranis A, Watson K, Wiener P. Detecting signatures of selection in nine distinct lines of broiler chickens. Anim Genet 2015;46:37-49. https://doi.org/10.1111/age.12252
  8. Wilkinson S, Lu ZH, Megens HJ, et al. Signatures of diversifying selection in European pig breeds. Plos Genet 2013;9: e1003453. https://doi.org/10.1371/journal.pgen.1003453
  9. Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population structure. Evolution 1984;38:1358-70. https://doi.org/10.2307/2408641
  10. Heyer E, Segurel L. Looking for signatures of sex-specific demography and local adaptation on the X chromosome. Genome Biol 2010;11:203. https://doi.org/10.1186/gb-2010-11-1-203
  11. Ma Y, Zhang H, Zhang Q, Ding X. Identification of selection footprints on the X chromosome in pig. PloS one 2014;9: e94911. https://doi.org/10.1371/journal.pone.0094911
  12. Zhu C, Fan H, Yuan Z, et al. Detection of selection signatures on the X chromosome in three sheep breeds. Int J Mol Sci 2015;16:20360-74. https://doi.org/10.3390/ijms160920360
  13. Rubin CJ, Megens HJ, Martinez Barrio A, et al. Strong signatures of selection in the domestic pig genome. Proc Natl Acad Sci USA 2012;109;19529-36. https://doi.org/10.1073/pnas.1217149109
  14. Browning BL, Browning SR. A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet 2009;84: 210-23. https://doi.org/10.1016/j.ajhg.2009.01.005
  15. Wang K, Li M, Hadley D, et al. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res 2007;17:1665-74. https://doi.org/10.1101/gr.6861907
  16. Jakobsson M, Scholz SW, Scheet P, et al. Genotype, haplotype and copy-number variation in worldwide human populations. Nature 2008;451:998-1003. https://doi.org/10.1038/nature06742
  17. Glessner JT, Reilly MP, Kim CE, et al. Strong synaptic transmission impact by copy number variations in schizophrenia. Proc Natl Acad Sci USA 2010;107:10584-9. https://doi.org/10.1073/pnas.1000274107
  18. Redon R, Ishikawa S, Fitch KR, et al. Global variation in copy number in the human genome. Nature 2006;444:444-54. https://doi.org/10.1038/nature05329
  19. Maceachern S, Hayes B, Mcewan J, Goddard M. An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic cattle. BMC Genomics 2009;10:181. https://doi.org/10.1186/1471-2164-10-181
  20. Ashburner M, Ball CA, Blake JA, B et al. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 2000;25:25-9. https://doi.org/10.1038/75556
  21. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 2010;38 (Database issue):D355-60. https://doi.org/10.1093/nar/gkp896
  22. Zeng Tao ZF, Wang Guangkai, WU Mingming, et al. Genomewide detection of signatures in sheep populations with use of population differentiation index Fst. Acta Vet Zootec Sin 2013;44:1891-9. https://doi.org/10.11843/j.issn.0366-6964.2013.12.005
  23. Clop A, Vidal O, Amills M. Copy number variation in the genomes of domestic animals. Anim Genet 2012;43:503-17. https://doi.org/10.1111/j.1365-2052.2012.02317.x
  24. Marenne G, Rodriguez-Santiago B, Closas MG, et al. Assessment of copy number variation using the Illumina Infinium 1M SNP-array: a comparison of methodological approaches in the Spanish Bladder Cancer/EPICURO study. Hum Mutat 2011;32:240-8. https://doi.org/10.1002/humu.21398
  25. Jiang L, Jiang J, Yang J, et al. Genome-wide detection of copy number variations using high-density SNP genotyping platforms in Holsteins. BMC Genomics 2013;14:131. https://doi.org/10.1186/1471-2164-14-131
  26. Moradi MH, Nejati-Javaremi A, Moradi-Shahrbabak M, Dodds KG, McEwan JC. Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition. BMC Genet 2012;13:10. https://doi.org/10.1186/1471-2156-13-10
  27. Zhu C, Fan H, Yuan Z, et al. Detection of selection signatures on the X chromosome in three sheep breeds. Int J Mol Sci 2015;16:20360-74. https://doi.org/10.3390/ijms160920360
  28. Qiu J, Cheng R, Zhou X, et al. Gene expression profiles of adipose tissue of high-fat diet-induced obese rats by cDNA microarrays. Mol Biol Rep 2010;37:3691-5. https://doi.org/10.1007/s11033-010-0021-6
  29. Xu Y, Yu W, Xiong Y, et al. Molecular characterization and expression patterns of serine/arginine-rich specific kinase 3 (SPRK3) in porcine skeletal muscle. Mol Biol Rep 2011;38:2903-9. https://doi.org/10.1007/s11033-010-9952-1
  30. Xiong X, Tao R, DePinho RA, Dong XC. Deletion of hepatic FoxO1/3/4 genes in mice significantly impacts on glucose metabolism through downregulation of gluconeogenesis and upregulation of glycolysis. PLoS One 2013;8:e74340. https://doi.org/10.1371/journal.pone.0074340

피인용 문헌

  1. Genomic Scan for Selection Signature Reveals Fat Deposition in Chinese Indigenous Sheep with Extreme Tail Types vol.10, pp.5, 2020, https://doi.org/10.3390/ani10050773
  2. Trends towards revealing the genetic architecture of sheep tail patterning: Promising genes and investigatory pathways vol.52, pp.6, 2020, https://doi.org/10.1111/age.13133