Home / Projects / IWGSC Bread Wheat Projects / Physical mapping / 3B physical map

3B physical map

Targeted chromosomes

3B
3B
Click on a chromosome to access associated data (when available) at URGI Sequences Repository.

Project team

First nameLast nameEmailInstitutionCountry
Etienne PAUX etienne.pauxSPAMFILTER@clermont.inra.fr INRA France
Pierre SOURDILLE pierre.sourdilleSPAMFILTER@clermont.inra.fr INRA France
Frederic CHOULET fchouletSPAMFILTER@clermont.inra.fr INRA France
Philippe LEROY philippe.leroySPAMFILTER@clermont.inra.fr INRA France
Georges GAY GgaySPAMFILTER@clermont.inra.fr INRA France
Camille RUSTENHOLZ crustenSPAMFILTER@clermont.inra.fr INRA France

Project collaborators

First nameLast nameEmailInstitutionCountry
Jaroslav DOLEZEL dolezelSPAMFILTER@ueb.cas.cz IEB Czech Republic
Abraham KOROL korolSPAMFILTER@research.haifa.ac.il University of Haifa Israel
Rudi APPELS rapp1495SPAMFILTER@bigpond.net.au Murdoch University Australia
Hélène BERGES hbergesSPAMFILTER@toulouse.inra.fr INRA CNRGV France
Michael ALAUX michael.alauxSPAMFILTER@versailles.inra.fr INRA URGI France
Hadi QUESNEVILLE Hadi.QuesnevilleSPAMFILTER@versailles.inra.fr INRA URGI France
Wolfgang SPIELMEYER Wolfgang.SpielmeyerSPAMFILTER@csiro.au CSIRO Australia
Shahryar KIANIAN s.kianianSPAMFILTER@ndsu.edu North Dakota State University USA

Project funding

The physical map of chromosome 3B has been funded by grants from the ANR (ANR-05-BLANC-0258-01), the TriticeaeGenome project within the European Community's 7th Framework Programme (FP7/ 2007-2013) under the grant agreement n°FP7-212019” and the INRA.

Abstract

The 3B physical map has been constructed in two steps:

The first map was obtained after fingerprinting about 68'000 clones and assembling 56,952 high quality BAC fingerprints into contigs using the FPC software (Paux et al., Science, 2008). The final build of the physical map v1 (1 e-25) covered 811 Mb, and, with an estimated size of 995 Mb (18) for chromosome 3B, represented 82% of the chromosome. This 9.6X physical map was integrated with 1443 markers (SSRs, ESTs, ISBPs...) onto genetic maps following two strategies: meiotic mapping and deletion mapping. The 680 contigs harbouring a marker were assigned to one of 16 deletion bins using Chinese Spring cytogenetic stocks. In total, 599 were unambiguously assigned to one of the 16 physical intervals delimited by the deletions bins with 256 contigs (240 Mb) distributed in 9 bins on the short arm and 343 contigs (316 Mb) in 7 bins on the long arm of chromosome 3B.

Further integration of the 3B physical map was performed by meiotic mapping on two linkage maps: a single reference genetic map developed from a F2 population (CsRe) derived from the cross between Chinese Spring (Cs) and Renan (Re) and a “3B neighbour map” combining the position of loci from 13 different genetic maps including the CsRe map. In total, 636 SSR, RFLP, STS, DArT and ISBP markers were mapped to these genetic maps and led to the anchoring of 213 contigs (225 Mb).

A second version of the physical map has been obtained in the framework of the TriticeaeGenome project using a new BAC library of (80,464 clones that were fingerprinted together with the 7440 BAC clones from the first minimal tiling path (MTP) of the 3B physical map. The first assembly of the chromosome 3B physical map was used as a backbone to integrate the new fingerprints and a second version of the physical map was built with a total of 131 792 high quality fingerprints. The final assembly (1e-45) contains 1283 contigs rerpesenting 961 Mb (97% of the chromosome) with a 19.6 x coverage.The minimal tiling path which is comprised of 8448 clones is being used to sequence the chromosome within the framework of the ANR flagship project 3BSEQ

The physical map is available at the URGI website at : http://urgi.versailles.inra.fr/cgi-bin/gbrowse/wheat_FPC_pub/

Publications

  • Paux E, Sourdille P, Salse J, Saintenac C, Choulet F, Leroy P, Korol A, Michalak M, Kianian S, Spielmeyer W, Lagudah E, Somers D, Kilian A, Alaux M, Vautrin S, Bergès H, Eversole K, Appels R, Safar J, Simkova H, Dolezel J, Bernard M, Feuillet C (2008). A physical map of the 1-gigabase bread wheat chromosome 3B. Science, 322, 101-104