Welcome to

Wheat SNP Development!

2008

Mark Sorrells, Organizer
• International Wheat SNP Working Group: A Prospectus
  The primary goal of this working group is to facilitate the development of advanced open-access marker technologies based on SNPs by providing an organizational structure for communication and for making the results, both materials and information, available to broad wheat community.
• Minutes of the SNP Workshop, 11th International Wheat Genetics Symposium, 2008

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  2002

  Peter Isaac, Organizer
  Last update 1 December 2003

  Proposition

  The wheat breeding and research community would benefit from coordinating its efforts to develop SNPs in wheat, to ensure that the alignments of ESTs are exploited to the full with minimum duplication of effort between laboratories.

  The Wheat SNP Development project aims to facilitate this coordination. This is a public project, and all work done will be accessible and in the public domain. The effort is open to all groups to participate.

  There is an email discussion group for participants. To be included, contact matthews@greengenes.cit.cornell.edu.

  • General modus operandi
  • Assemblies
    • 12 December 2002 (Build 3) -- includes the Dupont ESTs. 410,000 ESTs total. Statistics.
      • Sugar Plums -- A bumper crop! 9346 contigs with eight or more ESTs
        • Allocation of the sugar plums -- Both the Build 1 and Build 3 contigs, correlated with each other.
      • BLAST against the contig consensus sequences.
      • Nomenclature -- cultivar codes used to name the ESTs
      • AssembliesDB -- now contains all three WheatSNP assemblies plus CerealsDB's plus the US NSF project's.
      • The Whole Thing: wheatESTs_121102R3.tar.gz. Includes contigs and singletons.
      • Browse the whole directory -- 40,000 contig files, all alike (slow)
    • 28 October 2002 (Build 2) -- More overassembled, 90% identity instead of 95%.
      • Plums+ -- the 5605 contigs that contain eight or more ESTs
      • Nomenclature -- the coding system used to name the ESTs and contigs
      • The Whole Thing
        • Contigs, 0.WheatAssembly.28oct2002.clusters.tar.gz
        • Singletons, 0.WheatAssembly.28oct2002.singlets.gz
      • Browse the whole directory -- 22,000 contig files, all alike (slow)
    • 20 June 2002 (Build 1)
      • Super Plums, 20 Jan 03 -- the 1168 biggest contigs are now being allocated!
        Groups now participating: Azanza, Balyan, Berry, Blake, Buerstmayr, Henry, Isaac, Korzun, Laforest, See, Somers, Stephenson.
      • Plums -- the 5343 contigs that contain seven or more ESTs
      • Apples -> Oranges -- Translation of the EST names to their corresponding GenBank accessions.
      • The Whole Thing -- including singletons. File "0.WheatAssembly.20jun2002.tar.gz", 15MB. 200MB uncompressed.
      • CONTIG Database -- includes results of BLAST against GenBank. Example.
      • Browse the whole directory -- 23,000 contig files, all alike (slow)
      • Nomenclature -- the (old) coding system used to name the ESTs and contigs
  • Software Updated, 1 Dec
  • Genotypes and seed stocks
  • Validation methods
  • Reports -- Example
  • SNP nomenclature proposal
  • Mapping

  Resources for SNP discovery

  • New! 1 Dec SNPF, Single Nucleotide Polymorphism Finder
    From Daniel Nwankwo, John Innes Centre.
  • AutoSNP [ Top page | Example SNP report ]
    More than 3300 SNP-containing clusters from an assembly of 132,000 wheat ESTs.
    From cerealsDB at IACR-LARS.
  • Jalview [ Server ]
    A tool for viewing and manipulating contig alignments to extract SNPs by eye.
    From Michele Clamp, EBI.
    
  • ace2fasta
    A Perl script to convert CAP3's ".cap.ace" output to padded-FASTA format. (Only one contig at a time.)
    • ace2fasta_multi
      Does a whole directory of contig files at once.
  • Other wheat EST assemblies
    • CerealsDB, UK
    • US NSF project
    • HarvEST
    • PlantGDB
    • TaGI, TIGR's T. aestivum Gene Index
    • NCBI's UniGene set
  • AssembliesDB
    A database to compare assemblies vs. each other.

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