From Pankaj:

-   All the QTLs for trait-A mapped to linkage group-X 
 
-   All the QTLs for trait-A&B mapped to linkage group-X 
 
-   All the QTLs for trait-A mapped to linkage group-X and Y 
 
-   All the QTLs for trait-A&B mapped to linkage group-X and Y 
 
-   All the QTLs for trait-A&B BUT_NOT mapped to linkage group-X AND/OR Y 
 
-   All the QTL's for tait-A from species_1 and 2 
 
-   All the QTL's for tait-A&B from species_1 
 
-   All the QTL's for tait-A&B from species_1 and 2 
 
-   All the QTL's for tait-A&B from species_1 and 2 mapped to linkage 
    group -X and/or Y 
 
-   All the QTLs for trait-X mapped on a population where the cross had 
    Germplasm-Y Only. 
 
-   All the QTLs for trait-X mapped on a populations where the cross had 
    EITHER-BOTH/ANY-ONE of Germplasm-a & b. 
 
-   All the QTLs for trait-X mapped on a population where the cross had 
    Germplasm-a & b. 
 
-   All the QTLs on trait-x that were reported in the literature from 
    year-xxxx 

From Jeff Glaubitz (Panzea):

1)   Markers of a given type in a chromosomal region (near gene of
     interest).
a.   If you don't know the Panzea name of your gene of interest, use
     the Panzea BLAST utility.
b.   Use Gene/Locus search on the Panzea name to find chromosome
     and position.
c.   Choose the marker type of interest (scoring_tech_group = `SNP')
     in the Gene/Locus search, and restrict to loci in a specific
     region (in cM) encompassing your gene of interest.
d.   Show the initial gene/locus of interest in the table along with
     the flanking markers, sorted by map position.
e.   Allow download of this table in tab-delimited format.
f.   Should display marker names rather than gene/locus names.

2)   Markers of a given type polymorphic between two accessions.
a.   Choose the marker type of interest (SNPs or SSRs).
b.   Allow the user to select two accessions from a list of
     accessions for which we have extensive genotype data for that
     marker type (e.g., for SNPs, the set of 25 inbred lines crossed
     to B73 = 26 RIL parents;  later, the 281 plants in the maize
     association mapping population).  Limit to inbred lines?
c.   Determine the number and identity of markers in common and
     polymorphic between the two accessions (div_stock_id must be
     consistent for each accession?).
d.   Display the genotypes at the set of common loci for the two
     accessions (table with:  Accession, Marker, Chromosome, Map
     position (ibm2n2004), Accession 1 genotype, Accession 2
     genotype).
e.   Allow download of this table in tab-delimited format.
f.   Complications arise when duplicate genotypes exist for the same
     div_stock, div_obs_unit &/or div_obs_unit_sample (particularly
     if the replicate genotypes do not agree!).

3)   All markers of a given type on a particular chromosome.
a.   Choose the chromosome.
b.   Choose the marker type of interest (SNP, SSR, sequence - use
     scoring_tech_group).
c.   Generate table (or CMap view) displaying the mapped markers of
     that type on that chromosome, sorted by their map position.
d.   Should display marker names rather than gene/locus names.

4)   All candidate (or "random") genes on a chromosome or in
     chromosomal region.
a.   We will need a new field (in cdv_map_details and/or
     cdv_map_feature) to distinguish these in the database.
b.   Would be nice to see these two sets in a whole genome context
     (all 10 chromosomes), but a chromosome by chromosome view in the
     CMap viewer would be fine.  Probably too many loci for whole
     genome view.
c.   For table output, need to be able to limit to a particular
     map region.

5)   Highlight domestication loci in a map view (graphical).
a.   Will need a new field (in cdv_map_details and/or
     cdv_map_feature) to distinguish these in the database.
b.   Again, would be nice to see this in a genome wide format (all 10
     chromosomes), with the 638 mapped genes shown (from the full set
     of 774 genes investigated), and the 30 genes suspected to have
     been under selection during the domestication bottleneck
     highlighted.
c.   A chromosome by chromosome view in the CMap viewer will be
     fine, though.
d.   The quickest (and perhaps best?) way would be to show Fig 3 from
     the Wright et al. paper (copyright issues???).  This further
     highlights selected loci involved in growth or amino acid
     biosythesis.

6)   Find allelic diversity in the maize/teosinte homolog of my
     favorite rice or arabidopsis gene (e.g. lfy = GenBank
     NM_125579).
a.   Since the names of the genes/loci often differ, should start
     with BLAST search of Panzea.
b.   Use the Panzea gene/locus name of the highest scoring hit(s) and
     do a Gene/Locus search.
c.   Click on the sequence alignment link to see the "big picture"
     alignment (would be nice if the alignment viewer could show
     which SNPs we have actually developed into markers - these could
     link either to local alignment, details about the SNP marker
     [see 7.c] or genotypes).
d.   Click on particular SNPs to see their local alignment.
e.   Download the sequences to align with user's own sequence (with
     user's own alignment software).
f.   Display some summary statistics of the observed genetic
     diversity at that locus in maize/teosinte (pi, theta, Tajuma's
     D, number of haplotypes, gene diversity).  This requires new
     code, or output of the sequences in arlequin format or that of
     some other popgen analysis program (tassel?).

7)   Find the available SNPs in a gene of interest so that you can
     assay them in you own maize or teosinte germplasm.
a.   Start with BLAST search of Panzea using sequence from your gene
     of interest.
b.   Polymorphism Experiment search on name from highest
     scoring hit(s).
c.   Link to each SNP under "Assay Name" (or under "Assays" in
     results from a Gene/Locus search) could lead to summary page of
     information for that particular SNP assay, including the
     context sequence, the SNP position, the Genaissance id, primer
     pair for the amplicon (might be useful to design your own SNP
     assay) and a link to the compiled set of genotypes (compiled
     across separate allele_assays for the same cdv_marker_id).
     Currently the link leads to a table of genotypes, but you have
     no idea where in the alignment the SNP comes from - in theory
     you could retrieve the context sequence from the Excel download
     file, but in practice the gene/locus names do not always match
     the marker names.  For example, marker zen1.1 has a gene/locus
     name of CF649098.
d.   Either contact Genaissance to have them assay the set of chosen
     SNPs for you (large scale), or design your own SNP assay based
     upon the context sequence (and primer pair for amplicon).

8)   Develop additional SNPs in your gene of interest based upon the
     available seq alignment(s).
a.   The user may want to develop SNPs in a gene (or some genes) that
     we have an alignment for but no SNPs as yet.
b.   Find the alignment as in (6) or (7) and then download sequences
     in Fasta format - use your own SNP development program or
     perhaps John's Python scripts.

9)   Develop CAPs/PCR indel assays for your gene of interest based
     upon our alignments.

10)  Develop overgo probe for your gene of interest based upon our
     alignments.

11)  Find overgo's in MaizeGDB corresponding to our loci.

12)  How much genetic diversity is in teosinte vs. landraces vs.
     diverse inbred lines vs. elite inbred lines vs. commercially
     planted U.S maize hybrids vs. typical cornfield?
a.   The idea would be to show the domestication bottleneck as well
     as those due to modern crop improvement and commercial
     deployment.
b.   Could simulate the approximate representation of the commercial
     inbred lines in the U.S. corn crop.
c.   Could draw equal samples from the simulated U.S. corn crop and
     the other germplasm categories and compare the diversity using
     allelic richness and gene diversity (using SNP markers for which
     we have a lot of data).
d.   This could all be pre-computed, or could perhaps enable the user
     to customize things.
e.   Could categorize results by locus type (candidate vs. random,
     domestication vs. other, etc.)

13)  Diversity that is unique to U.S. maize inbreds (or teosinte, or
     landraces and tropical lines).  Alleles "private" to
     particular groups of germplasm.
a.   Are there alleles that seem to be unique to modern corn
     (presumably from post-domestication mutations)?
b.   Though the sample is limited, this might work best with the
     sequence alignments, since the SNPs may be ruined (for this
     question) by ascertainment bias.  On the other hand, SNPs that
     were monomorphic in the 16 teosinte in the panel may be
     polymorphic in a larger teosinte sample.

14)  Obtain the seeds and genotypes of the 7000 RILs in the permanent
     mapping population so that you can perform a QTL study for your
     own traits of interest.
a.   Download sufficient information to acquire these from NCRPIS
     (but not deposited yet).
b.   Download the genotypes in a useful format.

15)  Obtain the seed and genotypes (or DNA) to undertake your own
     association analysis with our maize (or teosinte) association
     analysis population.
a.   Assuming that you will score a new phenotype related to one of
     our candidate genes; or could find some random genes matching
     your set of seq motifs.
b.   Download sufficient information to acquire the seed from NCRPIS.
c.   Download the genotypes.

16)  Find the candidate genes from the various categories.
a.   Need to keep track of this info in Aztec.
b.   Categories of candidate genes include flowering time,
     inflorescence architecture (tassel, ear), kernel quality
     (endosperm), meristem, leaf development, other
     plant/development/architecture, MADS box.

17)  Obtain specific sets of germplasm.
a.   These sets include the 7000 RILs, 1000 maize-teosinte RILs,
     maize assoc. mapping pop, teosinte assoc. mapping pop, set
     of exotic maize landrace inbred lines, set of teosinte
     inbred lines.
b.   Download sufficient information to acquire these from NCRPIS
     (not deposited yet).

18)  Use GDPC to interact with panzea database and tassel for
     analysis.
a.   But neither of these softwares are web-based.
