physical maps of mouse, medaka, sugar beet …. and ... · pooled 35mer oligo probes on...

Heinz HimmelbauerMax-Planck-Institute of

Molecular GeneticsBerlin, Germany

Physical maps of mouse, medaka, sugar beet …. and Physcomitrella

Construction of a physical YAC/BAC map

of the mouse genome

IRS-PCR principle and application

Probe A Probe B

Strain X

Strain Y

IRS-products fromYAC pool DNA

IRS-products fromRH line DNA

IRS-products fromgenetic cross DNA

YAC clones Position onRH map

Position ongenetic map

YAC pool filter hybridisation

Scoring tool for data entry

Advanced mouse YAC map including BAC frameworkdata access at www.molgen.mpg.de/~rodent

- Browse the map- Identify map intervals and clones- Obtain clones and markers- Query database- Download data

Phylogenetic position of the medaka

Probe poolplate1/A5-H5

Probe poolplate1/B1-B6

Pooled 35mer oligo probes on 36,864-clone medaka BAC array

Total number of medaka BAC map segments (mapped, ambiguous, unmapped)1st generation map (January 2004)

464 4299

758

88

1878

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M A Un

ProbesMap segments

Sugar beet (Beta vulgaris) BAC mapProject launched Sept 1st, 2004

Goal:

Phase-1 map:

* 10,000 probes (ESTs, BAC ends, genetically mapped markers) as 35-mer oligos* mapped onto 37,000 BACs (120 kb avg. insert size / 5 x coverage)* 1000 contigs, 800 kb avg. length

Phase-2 map* Further 2000 probes from contig ends* additional Bac resources (avg. insert size 160 kb)* final product: 500 contigs, 1.6 Mb avg. length

Proposal for a Physcomitrella BAC map

Assumption: BAC library (36,000 clones avg. insert size 120 kb, 8.4 x coverage) available

Phase-1 map:

* 6000 BAC end probes (3000 BAC clones) as 35-mer oligos* 1000 ESTs* ~ 700 contigs, ~700 kb avg. length* ~ ~1500 genetically mapped markers are needed

Phase-2 map* Further 1400 probes from contig ends* final product: ~350 contigs, ~1.4 Mb avg. length