Display options
Cite
Bovo S, Bertolini F, Schiavo G, et al. Reduced Representation Libraries from DNA Pools Analysed with Next Generation Semiconductor Based-Sequencing to Identify SNPs in Extreme and Divergent Pigs for Back Fat Thickness. Int J Genomics. 2015;2015:950737doi: 10.1155/2015/950737.
Bovo, S., Bertolini, F., Schiavo, G., Mazzoni, G., Dall'Olio, S., & Fontanesi, L. (2015). Reduced Representation Libraries from DNA Pools Analysed with Next Generation Semiconductor Based-Sequencing to Identify SNPs in Extreme and Divergent Pigs for Back Fat Thickness. International journal of genomics, 2015950737. https://doi.org/10.1155/2015/950737
Bovo, Samuele, et al. "Reduced Representation Libraries from DNA Pools Analysed with Next Generation Semiconductor Based-Sequencing to Identify SNPs in Extreme and Divergent Pigs for Back Fat Thickness." International journal of genomics vol. 2015 (2015): 950737. doi: https://doi.org/10.1155/2015/950737
Bovo S, Bertolini F, Schiavo G, Mazzoni G, Dall'Olio S, Fontanesi L. Reduced Representation Libraries from DNA Pools Analysed with Next Generation Semiconductor Based-Sequencing to Identify SNPs in Extreme and Divergent Pigs for Back Fat Thickness. Int J Genomics. 2015;2015:950737. doi: 10.1155/2015/950737. Epub 2015 Mar 04. PMID: 25821781; PMCID: PMC4364060.
Copy Download .nbib Format: NLM
Share it on

Int J Genomics. 2015;2015:950737. doi: 10.1155/2015/950737. Epub 2015 Mar 04.

Reduced Representation Libraries from DNA Pools Analysed with Next Generation Semiconductor Based-Sequencing to Identify SNPs in Extreme and Divergent Pigs for Back Fat Thickness.

International journal of genomics

Samuele Bovo, Francesca Bertolini, Giuseppina Schiavo, Gianluca Mazzoni, Stefania Dall'Olio, Luca Fontanesi

Affiliations

  1. Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy.

PMID: 25821781 PMCID: PMC4364060 DOI: 10.1155/2015/950737

Abstract

The aim of this study was to identify single nucleotide polymorphisms (SNPs) that could be associated with back fat thickness (BFT) in pigs. To achieve this goal, we evaluated the potential and limits of an experimental design that combined several methodologies. DNA samples from two groups of Italian Large White pigs with divergent estimating breeding value (EBV) for BFT were separately pooled and sequenced, after preparation of reduced representation libraries (RRLs), on the Ion Torrent technology. Taking advantage from SNAPE for SNPs calling in sequenced DNA pools, 39,165 SNPs were identified; 1/4 of them were novel variants not reported in dbSNP. Combining sequencing data with Illumina PorcineSNP60 BeadChip genotyping results on the same animals, 661 genomic positions overlapped with a good approximation of minor allele frequency estimation. A total of 54 SNPs showing enriched alleles in one or in the other RRLs might be potential markers associated with BFT. Some of these SNPs were close to genes involved in obesity related phenotypes.

References

  1. Nature. 2012 Nov 15;491(7424):393-8 - PubMed
  2. Sci Rep. 2014 Apr 14;4:4678 - PubMed
  3. BMC Genomics. 2012 Nov 15;13:583 - PubMed
  4. PLoS Comput Biol. 2013 Apr;9(4):e1003031 - PubMed
  5. Anim Genet. 2014 Apr;45(2):304-7 - PubMed
  6. BMC Genomics. 2012 Jul 24;13:341 - PubMed
  7. BMC Bioinformatics. 2012 Sep 20;13:239 - PubMed
  8. J Appl Genet. 2010;51(2):153-68 - PubMed
  9. Bioinformatics. 2009 Aug 15;25(16):2078-9 - PubMed
  10. BMC Genomics. 2012 Aug 14;13:391 - PubMed
  11. J Anim Sci. 2010 Jul;88(7):2235-45 - PubMed
  12. Front Genet. 2014 Jul 09;5:214 - PubMed
  13. BMC Genomics. 2013 Mar 05;14:148 - PubMed
  14. Nature. 2011 Jul 20;475(7356):348-52 - PubMed
  15. Mol Biol Rep. 2010 Jan;37(1):461-6 - PubMed
  16. J Anim Sci. 2012 Aug;90(8):2450-64 - PubMed
  17. Nat Genet. 2011 May;43(5):491-8 - PubMed
  18. Database (Oxford). 2011 Jul 23;2011:bar030 - PubMed
  19. Nat Commun. 2014 Jul 15;5:4392 - PubMed
  20. Bioinformatics. 2011 Mar 15;27(6):863-4 - PubMed
  21. Nat Biotechnol. 2011 Jan;29(1):24-6 - PubMed
  22. PLoS One. 2009 Aug 05;4(8):e6524 - PubMed
  23. Protein Pept Lett. 2014;21(8):840-6 - PubMed
  24. Genome Res. 2001 May;11(5):863-74 - PubMed
  25. Nature. 2000 Sep 28;407(6803):513-6 - PubMed
  26. Bioinformatics. 2009 Jul 15;25(14):1754-60 - PubMed
  27. Bioinformatics. 2010 Aug 15;26(16):2069-70 - PubMed
  28. BMC Genet. 2008 Dec 04;9:81 - PubMed
  29. Nat Methods. 2008 Mar;5(3):247-52 - PubMed
  30. BMC Med Genomics. 2014 Sep 30;7:57 - PubMed
  31. PLoS One. 2013 May 17;8(5):e62137 - PubMed

Publication Types