Maps and Markers

Gramene SAB ReportJan 2006

CMap Improvements

• Expanded, reorganized and hidden menus• New map glyphs

– Number of features– Crop map– Magnify map

• Improved comparative map selection• Filtering of features• Collapse overlapping features• Correspondence aggregation

CMap: Reorganized menus

CMap: Collapse Features

CMap: Collapse Features

CMap: Filter Features

CMap: Crop/Zoom map

New & Updated Maps

• New maps– Rice – Gramene IRGSP

Assm 2005– Maize – Bins– Wheat – Composite 2004– Wheat – Consensus SSR

2004– 7 OMAP physical maps– 3 Rice Class I SSR maps– 15 QTL maps

• Updated TIGR assembly– Gene models– BAC end sequence from

wild relatives of rice– Additional markers and

ESTs

Marker Database

Marker Type Markers

AFLP 950

BAC end sequence 676,959

Clone 602,304

EST 2,530,661

EST Cluster 601,935

Gene Primer 19

mRNA 91,074

Primer 34

RAPD 135

RFLP 7,791

SSR 16,835

STS 65

Tos17 18,023

Undefined 823

4,547,608 total

Species Markers

Barley (Hordeum spp.) 535,720

Maize (Zea spp.) 1,089,433

Oat (Avena spp.) 8,215

Rice (Oryza spp.) 1,475,049

Rye (Secale spp.) 13,260

Sorghum (Sorghum spp.) 260,634

Sugarcane (Saccharum spp.) 339,657

Wheat (Triticum spp. + Aegilops spp.)

787,493

Other 38,147

Marker Search (Users)

Marker Admin Tool (Curators)

Dataflow Through MarkersDB (I)

• Gramene-created maps (Genome browser)– Create or update markers in database– Extract marker data– Run through genome pipeline– Update positions in markersDB, Ensembl,

CMap

Dataflow Through MarkersDB (II)

• Existing maps (non-Gramene generated)– Enter map positions into database– Reconcile features with markers

• Marker name, species, type

– Create markers if necessary– Output to CMap

MarkersDB Issues

• Improved searches– Marker details– Maps

• Improved data downloads– Include marker details

• Marker accession IDs• Batch loading of marker data• Map load and output scripts• Ensure all mapped features (except QTL and genes)

have a corresponding marker• Reconciliation of new markers with existing ones• Continued curation of undefined markers