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Doddamani D, Khan AW, Katta MA, et al. CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea. Database (Oxford). 2015;2015doi: 10.1093/database/bav078.
Doddamani, D., Khan, A. W., Katta, M. A., Agarwal, G., Thudi, M., Ruperao, P., Edwards, D., & Varshney, R. K. (2015). CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea. Database : the journal of biological databases and curation, 2015. https://doi.org/10.1093/database/bav078
Doddamani, Dadakhalandar, et al. "CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea." Database : the journal of biological databases and curation vol. 2015 (2015). doi: https://doi.org/10.1093/database/bav078
Doddamani D, Khan AW, Katta MA, Agarwal G, Thudi M, Ruperao P, Edwards D, Varshney RK. CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea. Database (Oxford). 2015 Aug 19;2015. doi: 10.1093/database/bav078. Print 2015. PMID: 26289427; PMCID: PMC4541373.
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Database (Oxford). 2015 Aug 19;2015. doi: 10.1093/database/bav078. Print 2015.

CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea.

Database : the journal of biological databases and curation

Dadakhalandar Doddamani, Aamir W Khan, Mohan A V S K Katta, Gaurav Agarwal, Mahendar Thudi, Pradeep Ruperao, David Edwards, Rajeev K Varshney

Affiliations

  1. Research Program Grain Legumes, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502 324, Telangana State, India.
  2. School of Agriculture and Food Sciences, University of Queensland, St Lucia, Queensland, Australia 4072, School of Plant Biology, The University of Western Australia, Perth, Western Australia, Australia 6009 and.
  3. School of Plant Biology, The University of Western Australia, Perth, Western Australia, Australia 6009 and Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia 6009.
  4. Research Program Grain Legumes, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502 324, Telangana State, India, School of Plant Biology, The University of Western Australia, Perth, Western Australia, Australia 6009 and [email protected].

PMID: 26289427 PMCID: PMC4541373 DOI: 10.1093/database/bav078

Abstract

Molecular markers are valuable tools for breeders to help accelerate crop improvement. High throughput sequencing technologies facilitate the discovery of large-scale variations such as single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs). Sequencing of chickpea genome along with re-sequencing of several chickpea lines has enabled the discovery of 4.4 million variations including SNPs and InDels. Here we report a repository of 1.9 million variations (SNPs and InDels) anchored on eight pseudomolecules in a custom database, referred as CicArVarDB that can be accessed at http://cicarvardb.icrisat.org/. It includes an easy interface for users to select variations around specific regions associated with quantitative trait loci, with embedded webBLAST search and JBrowse visualisation. We hope that this database will be immensely useful for the chickpea research community for both advancing genetics research as well as breeding applications for crop improvement. Database URL: http://cicarvardb.icrisat.org.

© The Author(s) 2015. Published by Oxford University Press.

References

  1. Nucleic Acids Res. 2009 Jan;37(Database issue):D951-3 - PubMed
  2. J Biosci. 2012 Nov;37(5):811-20 - PubMed
  3. Database (Oxford). 2011;2011:bar009 - PubMed
  4. Nat Biotechnol. 2013 Mar;31(3):240-6 - PubMed
  5. Plant Biotechnol J. 2011 Oct;9(8):922-31 - PubMed
  6. Biology (Basel). 2013 Nov 25;2(4):1357-77 - PubMed
  7. BMC Genomics. 2012;13 Suppl 1:S15 - PubMed
  8. Plant Biotechnol J. 2012 Aug;10(6):716-32 - PubMed
  9. Curr Opin Plant Biol. 2002 Apr;5(2):94-100 - PubMed
  10. Bioinformatics. 2014 May 1;30(9):1236-40 - PubMed
  11. Plant Biotechnol J. 2009 May;7(4):326-33 - PubMed
  12. BMC Bioinformatics. 2014;15:212 - PubMed
  13. Plant Biotechnol J. 2012 Aug;10(6):743-9 - PubMed
  14. Nucleic Acids Res. 2014 Jan;42(Database issue):D1245-52 - PubMed
  15. Brief Bioinform. 2013 Mar;14(2):172-7 - PubMed
  16. Genetics. 2006 Jan;172(1):569-77 - PubMed
  17. J Mol Biol. 1990 Oct 5;215(3):403-10 - PubMed
  18. Genome Res. 2004 Sep;14(9):1812-9 - PubMed
  19. Biology (Basel). 2012 Aug 27;1(2):370-82 - PubMed
  20. BMC Bioinformatics. 2012;13:219 - PubMed
  21. Am J Bot. 2012 Feb;99(2):186-92 - PubMed
  22. PLoS One. 2012;7(12):e52443 - PubMed
  23. BMC Genomics. 2009;10:523 - PubMed
  24. Fly (Austin). 2012 Apr-Jun;6(2):80-92 - PubMed
  25. Theor Appl Genet. 2013 Jan;126(1):1-11 - PubMed
  26. Trends Biotechnol. 2009 Sep;27(9):522-30 - PubMed
  27. Plant Physiol. 2003 May;132(1):84-91 - PubMed
  28. DNA Res. 2012 Oct;19(5):357-73 - PubMed
  29. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D752-7 - PubMed
  30. Plant Biotechnol J. 2015 Jan;13(1):97-104 - PubMed
  31. Theor Appl Genet. 2010 May;120(7):1415-41 - PubMed

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