1. The Potato Genome Sequencing Consortium: An Update
Christian Bachem (coordiaor)
Richard Visser (director)
PLANT BTREEDING, DEPT OF PLANT SCIENCES, WUR, WAGENINGEN

2. AIMS
The PGSC comprises a group of 14 Laboratories from around the world who have the aim of sequencing the complete genome of potato by 2010
In addition to the benefits accruing from the sequencing the worlds fourth most important food crop the PGSC aims to actively build capacity in countries lacking a plant genomics infrastructure
The PGSC aims to form the basis of a research network for the scientific exploitation of the sequence data in the post-genomics era.
PGSC

3. Sequencing strategy: PGSC
The 840 Mbp of the potato genome will be sequenced on a BAC by BAC and Chromosome by chromosome basis
A diploid genotype is being used (RH ) for which a 78K clone BAC library is available giving a 10x genome coverage
The average BAC length is 130kb
A Physical map is being constructed based on a 10K marker AFLP genetic map from the SH x RH population
PGSC

4. Features of the genetic map:
Offspring size = 250 plants
384 AFLP primer combinations used for mapping
Markers:
4200 maternal,
3200 paternal, and
2700 bridge markers
Map is divided in bin segments
Each bin represents a single cross-over event (0.8 cM)
Published: Genetics 173: (June 2006)
PGSC

5. gray scale = marker density
Paternal genetic map: used for contig anchoring
gray scale = marker density
~50% empty bins (white)
PGSC

6. Construction of a physical map
BAC clones are fingerprinted using AFLP (+0)
Fingerprints aligned by FPC to produce Contigs
Contigs screened for presence of genomic AFLP markers for anchoring
AFLP markers anchor contigs to genetic map
PGSC

7. Status potato physical map, December 2006
76000 BACs fingerprinted (94%)
First build FPC fingerprint map => 7000 contigs
Further reductions with contig merging (15%)
25% contigs with 2 or more markers
Paired markers confirm map locations
Around 40 anchored contigs/chromosome
PGSC

8. Status potato physical map, November 200610 20 30 40 50 60 70 1 2 3 4 5 6 7 8 9 11 12
Chromosome number
Anchored contigs
PGSC

9. Status potato physical map, November 2006
PGSC

10. Status potato physical map, November 2006
PGSC

11. Actual sequence overlaps v. consensus band map overlaps
T7 RH066F01
SP6 T7
RH121C15 SP6
6.7kb
(2 bands)
3.6kb
(3 bands) T7
Ctg 309, Chr 1
T RH051I SP6
T7 RH095I08
SP6
10.8kb
(5 bands)
Ctg 656, Chr 5
SP RH071N T7
T7 RH185H09
SP6
35.1kb
(6 bands)
(6 bands)
Ctg 903, Chr 5
SP RH052M T7
PGSC

12. PGSC Status: Jan 2007 PGSC Netherlands have now sequenced ~100 BACs
~ 60 more are in the pipeline
USA, Netherlands and Ireland have started sequencing work
BAC library is being sent out to all partners
A physical map browser is available to the partners
BAC registry database and genome browser will be set up in the next weeks
PGSC

13. PGSC FISH with BACs from Chromosome 1 RH083J12 4.6cM RH092C10 14.6cM
RH158N cM
RH083J cM
RH092C cM
RH096H cM
FISH with BACs from Chromosome 1
PGSC

14. RH089H04 9.2cM need Cot 100 blocking

15. RH044A cM
RH081B cM
Chromosome 5 of Potato

16. RH095I cM
Chromosome 5 of Potato

17. PGSC 1 2 3 4 5 6 7 8 9 10 11 12 Not decided yet UK US KR CN NL JP INES FR IT
Not decided
yet
PGSC