The Potato Genome Sequencing Consortium: An Update

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Presentation transcript:

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

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

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 (RH89-039-16) 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

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 173:1075-1087 (June 2006) PGSC

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

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

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

Status potato physical map, November 2006 10 20 30 40 50 60 70 1 2 3 4 5 6 7 8 9 11 12 Chromosome number Anchored contigs PGSC

Status potato physical map, November 2006 PGSC

Status potato physical map, November 2006 PGSC

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 T7 RH051I12 SP6 T7 RH095I08 SP6 10.8kb (5 bands) Ctg 656, Chr 5 SP6 RH071N17 T7 T7 RH185H09 SP6 35.1kb (6 bands) (6 bands) Ctg 903, Chr 5 SP6 RH052M07 T7 PGSC

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

PGSC FISH with BACs from Chromosome 1 RH083J12 4.6cM RH092C10 14.6cM RH158N18 36.4cM RH083J12 4.6cM RH092C10 14.6cM RH096H03 80.2cM FISH with BACs from Chromosome 1 PGSC

RH089H04 9.2cM need Cot 100 blocking

RH044A21 47.3cM RH081B09 2.3cM Chromosome 5 of Potato

RH095I08 16.2cM Chromosome 5 of Potato

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