User requirements for molecular breeding informatics

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Contents

Marker Assisted Selection (MAS) Programs

CIMMYT Rainfed Wheat Breeding Program

Storage needs:
  • gene or introgression
  • trait associated
  • trait source (line/s where the gene was/is found)
  • marker name
  • allele designation & other alternate allele names
  • marker type
  • marker mode of inheritance
  • marker chromosome & linkage
  • marker source
  • references for marker / gene
  • primer names & sequences
  • expected product size of marker
  • genotyping scores = allele frequencies and allele incidence
  • comment field for describing marker "behavior", i.e. false heterozygotes
Query needs:
  • query for a specific name, pedigree, or GID which gives you all markers that have been run for that name across the different years
  • query for populations that have been associated with a certain genotype, and giving the segregation ratios for the markers in the population
  • query for markers and alleles across populations

ACIAR Molecular marker technologies for faster wheat breeding in India

  • Given a parental line with known genes from one list (Australian list), shows complementing lines from another list (Indian list) to cross with it
  • Extend the previous for crossing blocks and giving automatic options on which lines to cross best
  • Create automatic input files for Q-sim

Marker Assisted Recurrent Selection (MARS) Breeding Programs

CIMMYT Maize MARS Pilot Projects

Storage needs:

for SNP data...

  • marker name
  • Illumina chip ID for marker
  • oligo sequences
  • Illumicode sequence
  • TopGenomic sequence
  • assay format
  • allele variants
  • Allele1-Top & Allele2-Top scores
  • GC Score (or other quality indicator)
  • in silico mapping results - linked to genetic maps

Agriculture and Agri-Food Canada storage and query requirements

Storage needs:
  • Marker detector type (SSR, DArT, AFLP, etc) (already in GEMS 5.1)
  • Marker synonyms (already in GEMS 5.1)
  • Multiple marker references
  • Min/Max/Expected molecular variants for markers (from literature)
  • Chromosomal locations of molecular variants (already in GEMS, but need tool to enter this)
  • Associated genes or traits
  • Protocols (annealing temperature, primer sequences, marker repeats or motif, other PCR information such as cocktail components) - (already in GEMS, but need better tools to load this information)
  • Maps (who did it, type of map, population, etc)
  • Work order information (project purpose, communication, notes) - memo fields?
  • Have both central (public) and local (private) DMS and GEMS databases for storing molecular data and establish protocols/tools for updating the Central GEMS.
Query needs:
  • Output list of synonyms for markers
  • Get protocols being used for each marker (dyes, annealing temperatures, etc)
  • Search to see which markers associated with traits have been run on potential parents.
  • Combine the phenotypic data for a trait with the genotypic data for associated markers.
  • Have a "Work Order" output that states the purpose of the project/task
  • Have a "Communications" output which shows all emails and notes that have gone back and forth between involved parties regarding the project.
  • Various choices of output formats (tab delimited text files, input files, Excel spreadsheets, etc) to work with molecular software (i.e. MapMaker, MapQTL, etc)
  • Link to GrainGenes
  • Output list of markers by chromosomal location
  • Output list of markers by annealing temperature
  • Tools to export data from existing GEMS to GEMS 6.0.
  • A new GEMSCat tool to load marker information manually and by batch load (an expansion of the current GEMCat that will handle all marker information).

Other Problems Observed with the Old Schema

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