proposal for a evidence code

[Pankaj Jaiswal]

Dear GO Friends,


In Gramene (www.gramene.org), we are presently curating rice mutants/phenotypes
that have been characterized using
one or more of the techniques outlined in the list of Evidence codes.  We are
proposing the
introduction of a new line of evidence called, "IAGP: Inferred from Association
between Genotype
and Phenotype".

We could have used the GO code, IGI (inferred from genetic interaction). However
after looking
carefully at the description of IGI, we felt that by using it we might not
justify the evidence type. The
reason we are proposing this new code of evidence is because many of the
phenotypes in crop plants
(in general from cereal crops ) are characterized using genetic markers and
populations or genetic
stocks that are well known to plant geneticists and breeders, and we felt that
listing them
specifically will help us clarify the nature of evidence used to define the
relationships between
the phenotypes and the genotypes, as defined by markers on the genetic and
physical maps.

  This is going to be very important while curating information related to
functional and comparative
  genomics. Entries in the rice Mutant database will use primarily the GO terms
and Trait terms (TO) for
  defining both the morphological and physiological (Biochemical)
mutants/phenotypes, and the
  Evidence code would include the following in addition to the presently defined
ones:


  PROPOSED NEW EVIDENCE CODE :

  IAGP  (inferred from association between genotype and phenotype)

  #       Based on detection of polymorphism or segregation of genetic markers
e.g.. isozymes, RFLPs
  (Random Fragment Length Polymorphism), RAPDs (Random amplified polymorphic
DNA), AFLPs
  (Amplified Fragment Length Polymorphism), SNPs (Single Nucleotide
Polymorphisms), Microsatellite markers or SSR (Simple Sequence Repeats), TD
  (Transposon Display).

  #       Based on detection of polymorphism or segregation of physical markers
e.g.. FISH,
  centromeric,heterochromatic regions, chromosomal banding patterns.

  #       Based on detection of polymorphisms in segregating plant material
derived from bi-parental
  crosses e.g.. F2 lines, F3 families, Back cross populations, viz., BC1, BC2
etc.; Doubled Haploid lines
  (DH), Recombinant Inbred Lines (RIL).

  #       Based on detection of polymorphisms in genetic stocks, e.g., Near
Isogenic Lines (NIL),
  Introgression Lines (IL), Radiation Hybrids (RH), Cytogenetic Stocks (CG),
i.e., trisomics, aneuploids,
  etc.


  We look forward to getting your feedback on this proposal.

Sincerely

Pankaj


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Pankaj Jaiswal, Ph.D.                                   
Postdoctoral Associate
Dept. of plant Breeding                             
Cornell University                                   
Ithaca, NY-14853, USA   

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org   http://ars-genome.cornell.edu/rice
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