Asian-Australasian Journal of Animal Sciences

  • 제28권9호
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  • Pages.1235-1243
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  • 2015
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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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SNP Discovery from Transcriptome of Cashmere Goat Skin

  • Wang, Lele (College of Animal Science, Inner Mongolia Agricultural University) ;
  • Zhang, Yanjun (College of Animal Science, Inner Mongolia Agricultural University) ;
  • Zhao, Meng (College of Animal Science, Inner Mongolia Agricultural University) ;
  • Wang, Ruijun (College of Animal Science, Inner Mongolia Agricultural University) ;
  • Su, Rui (College of Animal Science, Inner Mongolia Agricultural University) ;
  • Li, Jinquan (College of Animal Science, Inner Mongolia Agricultural University)
  • 투고 : 2015.02.27
  • 심사 : 2015.06.13
  • 발행 : 2015.09.01
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초록

The goat Capra hircus is one of several economically important livestock in China. Advances in molecular genetics have led to the identification of several single nucleotide variation markers associated with genes affecting economic traits. Validation of single nucleotide variations in a whole-transcriptome sequencing is critical for understanding the information of molecular genetics. In this paper, we aim to develop a large amount of convinced single nucleotide polymorphisms (SNPs) for Cashmere goat through transcriptome sequencing. In this study, the transcriptomes of Cashmere goat skin at four stages were measured using RNA-sequencing and 90% to 92% unique-mapped-reads were obtained from total-mapped-reads. A total of 56,231 putative SNPs distributed among 10,057 genes were identified. The average minor allele frequency of total SNPs was 18%. GO and KEGG pathway analysis were conducted to analyze the genes containing SNPs. Our follow up biological validation revealed that 64% of SNPs were true SNPs. Our results show that RNA-sequencing is a fast and efficient method for identification of a large number of SNPs. This work provides significant genetic resources for further research on Cashmere goats, especially for the high density linkage map construction and genome-wide association studies.

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참고문헌

  1. Barbazuk, W. B., S. J. Emrich, H. D. Chen, L. Li, and P. S. Schnable. 2007. Snp discovery via 454 transcriptome sequencing. Plant J. 51:910-918. https://doi.org/10.1111/j.1365-313X.2007.03193.x
  2. Cai, H. F., Z. Chen, and W. X. Luo. 2014. Associations between polymorphisms of the gfi1b gene and growth traits of indigenous chinese goats. Genet. Mol. Res. 13:872-880. https://doi.org/10.4238/2014.February.13.5
  3. Chu, M. X., L. Lu, T. Feng, R. Di, G. L. Cao, P. Q. Wang, L. Fang, Y. H. Ma, and K. Li. 2011. Polymorphism of bone morphogenetic protein 4 gene and its relationship with litter size of jining grey goats. Mol. Biol. Rep. 38:4315-4320. https://doi.org/10.1007/s11033-010-0556-6
  4. Cingolani, P., A. Platts, L. Wang le, M. Coon, T. Nguyen, L. Wang, S. J. Land, X. Lu, and D. M. Ruden. 2012. A program for annotating and predicting the effects of single nucleotide polymorphisms, snpeff: Snps in the genome of drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6:80-92. https://doi.org/10.4161/fly.19695
  5. Cloonan, N., A. R. Forrest, G. Kolle, B. B. Gardiner, G. J. Faulkner, M. K. Brown, D. F. Taylor, A. L. Steptoe, S. Wani, G. Bethel, A. J. Robertson, A. C. Perkins, S. J. Bruce, C. C. Lee, S. S. Ranade, H. E. Peckham, J. M. Manning, K. J. McKernan, and S. M. Grimmond. 2008. Stem cell transcriptome profiling via massive-scale mrna sequencing. Nat. Methods 5:613-619. https://doi.org/10.1038/nmeth.1223
  6. Garvin, M. R., K. Saitoh, and A. J. Gharrett. 2010. Application of single nucleotide polymorphisms to non-model species: A technical review. Mol. Ecol. Resour. 10:915-934. https://doi.org/10.1111/j.1755-0998.2010.02891.x
  7. Gotz, S., J. M. Garcia-Gomez, J. Terol, T. D. Williams, S. H. Nagaraj, M. J. Nueda, M. Robles, M. Talon, J. Dopazo, and A. Conesa. 2008. High-throughput functional annotation and data mining with the blast2go suite. Nucleic Acids Res. 36:3420-3435. https://doi.org/10.1093/nar/gkn176
  8. Helyar, S. J., M. T. Limborg, D. Bekkevold, M. Babbucci, J. van Houdt, G. E. Maes, L. Bargelloni, R. O. Nielsen, M. I. Taylor, R. Ogden, A. Cariani, G. R. Carvalho, F. Consortium, and F. Panitz. 2012. Snp discovery using next generation transcriptomic sequencing in atlantic herring (clupea harengus). PLoS One 7:e42089. https://doi.org/10.1371/journal.pone.0042089
  9. Hou, J. X., X. P. An, Y. X. Song, J. G. Wang, T. Ma, P. Han, F. Fang, and B. Y. Cao. 2013. Combined effects of four snps within goat prlr gene on milk production traits. Gene 529:276-281. https://doi.org/10.1016/j.gene.2013.07.057
  10. Hou, J. X., F. Fang, X. P. An, Y. Yan, T. Ma, P. Han, F. X. Meng, Y. X. Song, J. G. Wang, and B. Y. Cao. 2014. Polymorphisms of prlr and folr1 genes and association with milk production traits in goats. Genet. Mol. Res. 13:2555-2562. https://doi.org/10.4238/2014.January.24.1
  11. Jiang, D. I., X. M. Xu, L. Ainiwaer, Y. H. Zhang, K. C. Tian, L. J. Yu, W. W. Wu, H. Tulafu, X. F. Fu, and M. Yasen. 2014. Genome array on differentially expressed genes of skin tissue in cashmere goat at early anagen of cashmere growth cycle using DNA microarray. J. Integr. Agric. 13:2243-2252. https://doi.org/10.1016/S2095-3119(13)60606-1
  12. Krause, K. and K. Foitzik. 2006. Biology of the hair follicle: The basics. Semin. Cutan. Med. Surg. 25:2-10. https://doi.org/10.1016/j.sder.2006.01.002
  13. Lan, X. Y., Y. Pan Ch, H. Chen, Z. Lei Ch, F. Y. Li, H. Y. Zhang, and Y. S. Ni. 2009. Novel snp of the goat prolactin gene (prl) associated with cashmere traits. J. Appl. Genet. 50:51-54. https://doi.org/10.1007/BF03195652
  14. Li, S., X. Zhang, Z. Sun, F. Li, and J. Xiang. 2013. Transcriptome analysis on chinese shrimp fenneropenaeus chinensis during wssv acute infection. PLoS One 8:e58627. https://doi.org/10.1371/journal.pone.0058627
  15. Li, Z., Z. Chen, X. Lan, L. Ma, Y. Qu, Y. Liu, M. Li, P. Wang, F. Li, and H. Chen. 2010. Two novel csnps of weaver gene in chinese indigenous goat and their associations with milk yield. Mol. Biol. Rep. 37:563-569. https://doi.org/10.1007/s11033-009-9810-1
  16. Liao, P. Y. and K. H. Lee. 2010. From SNPs to functional polymorphism: The insight into biotechnology applications. Biochem. Eng. J. 49:149-158. https://doi.org/10.1016/j.bej.2009.12.021
  17. Monreal, A. W., B. M. Ferguson, D. J. Headon, S. L. Street, P. A. Overbeek, and J. Zonana. 1999. Mutations in the human homologue of mouse dl cause autosomal recessive and dominant hypohidrotic ectodermal dysplasia. Nat. Genet. 22:366-369. https://doi.org/10.1038/11937
  18. Ouji, Y., M. Yoshikawa, A. Shiroi, and S. Ishizaka. 2006. Promotion of hair follicle development and trichogenesis by wnt-10b in cultured embryonic skin and in reconstituted skin. Biochem. Biophys. Res. Commun. 345:581-587. https://doi.org/10.1016/j.bbrc.2006.04.142
  19. Plasari, G., S. Edelmann, F. Hogger, Y. Dusserre, N. Mermod, and A. Calabrese. 2010. Nuclear factor i-c regulates tgf-{beta}-dependent hair follicle cycling. J. Biol. Chem. 285:34115-34125. https://doi.org/10.1074/jbc.M110.120659
  20. Saitoh, A., L. A. Hansen, J. C. Vogel, and M. C. Udey. 1998. Characterization of wnt gene expression in murine skin: Possible involvement of epidermis-derived wnt-4 in cutaneous epithelial-mesenchymal interactions. Exp. Cell Res. 243:150-160. https://doi.org/10.1006/excr.1998.4152
  21. Schmidt-Ullrich, R. and R. Paus. 2005. Molecular principles of hair follicle induction and morphogenesis. Bioessays 27:247-261. https://doi.org/10.1002/bies.20184
  22. Shu, Y., Y. Li, Z. Zhu, X. Bai, H. Cai, W. Ji, D. Guo, and Y. Zhu. 2011. Snps discovery and caps marker conversion in soybean. Mol. Biol. Rep. 38:1841-1846. https://doi.org/10.1007/s11033-010-0300-2
  23. Stenn, K. S. and R. Paus. 2001. Controls of hair follicle cycling. Physiol. Rev. 81:449-494.
  24. Sultan, M., M. H. Schulz, H. Richard, A. Magen, A. Klingenhoff, M. Scherf, M. Seifert, T. Borodina, A. Soldatov, D. Parkhomchuk, D. Schmidt, S. O'Keeffe, S. Haas, M. Vingron, H. Lehrach, and M. L. Yaspo. 2008. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321:956-960. https://doi.org/10.1126/science.1160342
  25. Van Tassell, C. P., T. P. Smith, L. K. Matukumalli, J. F. Taylor, R. D. Schnabel, C. T. Lawley, C. D. Haudenschild, S. S. Moore, W. C. Warren, and T. S. Sonstegard. 2008. Snp discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat. Methods 5:247-252. https://doi.org/10.1038/nmeth.1185
  26. Wang, X., Z. D. Zhao, H. R. Xu, L. Qu, H. B. Zhao, T. Li, and Z. Y. Zhang. 2012. Variation and expression of kap9.2 gene affecting cashmere trait in goats. Mol. Biol. Rep. 39:10525-10529. https://doi.org/10.1007/s11033-012-1937-9
  27. Yeo, G. W., N. G. Coufal, T. Y. Liang, G. E. Peng, X. D. Fu, and F. H. Gage. 2009. An rna code for the fox2 splicing regulator revealed by mapping rna-protein interactions in stem cells. Nat. Struct. Mol. Biol. 16:130-137. https://doi.org/10.1038/nsmb.1545
  28. Yu, Y., J. Wei, X. Zhang, J. Liu, C. Liu, F. Li, and J. Xiang. 2014. Snp discovery in the transcriptome of white pacific shrimp litopenaeus vannamei by next generation sequencing. PLoS One 9:e87218. https://doi.org/10.1371/journal.pone.0087218
  29. Zhao, H., X. Wu, H. Cai, C. Pan, C. Lei, H. Chen, and X. Lan. 2013. Genetic variants and effects on milk traits of the caprine paired-like homeodomain transcription factor 2 (pitx2) gene in dairy goats. Gene 532:203-210. https://doi.org/10.1016/j.gene.2013.09.062
  30. Zhou, J. P., X. P. Zhu, W. Zhang, F. Qin, S. W. Zhang, and Z. H. Jia. 2011. A novel single-nucleotide polymorphism in the 5' upstream region of the prolactin receptor gene is associated with fiber traits in liaoning cashmere goats. Genet. Mol. Res. 10:2511-2516. https://doi.org/10.4238/2011.October.13.8

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