WP 1 - Establishment of genomic resources for physical mapping of wheat
WP Leader: Dr. Catherine Feuillet (INRA, E-mail: catherine.feuillet@clermont.inra.fr)
The overall objective of WP1 is to establish the genomic resources needed to construct physical maps of 6 chromosomes from group 1 and 3 (WP2) for wheat and barley, isolate genes of interest (WP3) such as disease resistance, yield and quality traits, and develop markers for breeding (WP4) in the most cost effective manner.
In plants, most of measurable characters are not defined by the expression of one gene but controlled by several chromosomal areas containing one or several genes. These areas are called QTL (Quantitative Trait Loci).
Researchers will construct banks of DNA fragments (BAC libraries), fingerprint the BACs and assemble them with the help of bioinformatics and molecular tools in physical maps representing the chromosomes.
WP1 aims to:
- construct BAC libraries from flow-sorted wheat chromosome arms,
- fingerprint all the BAC clones,
- assemble the BACs into contigs (assembling overlapping sequenced fragments) using existing software (FPC) and/or new programs (WP5),
- create pools of the libraries based on the minimal tiling path as well as pool plates for efficient anchoring by PCR screening with markers (WP2) and
- perform BAC end sequencing to provide about 6 Mb of sequence per chromosome arm in wheat for marker development (for use in WP2 and WP4).
At the end of the 3rd project year, WP1 is completely achieved with the following significant results:
- BAC libraries produced for all chromosomes (3B, 3DS, 3DL, 1BS, 1BL, 1AS and 1AL). These are stored at INRA-CNRGV and are available upon request and under MTA for the international community. A publication by Safar et al. (2010, Cytogenetic and Genome Research, 129:1-13) has been achieved.
- Physical maps assemblies for all chromosomes of the project using the same procedure. These assemblies are currently anchored in WP2.
- A guideline for physical map assembly produced and adopted by the IWGSC community.
- Validation of the new assembly software developed by HU partner in WP5 on data from WP1 on 3B and 1BS (Frenkel et al. (2010), BMC bioinformatics, 11:584). The demonstration that LTC provides more robust assemblies and can help to correct the FPC assemblies before sequencing a full MTP.
- BAC end sequences (>64Mb in total) produced for all MTPs from the target chromosomes (see Deliverable 1.7).
- Two results obtained in addition to the original plan: IEB produced DNA amplified using phi29 polymerase from wheat chromosome 3B and chromosome arms 1AS, 1AL, 1BS, 1BL, , 3DS, 3DL as well as from barley chromosome arms 3HS and 3HL for NGS sequencing to identify genic sequences, facilitate comparative genome analysis and develop DNA markers in WP2. A publication on the group 1 data has been achieved (Wicker et al, 2011; Plant Cell 3:1706-1718). INRA has performed a pilot project with Keygene to assess the feasibility of using their new physical mapping technique called Whole Genome profiling. A publication is underway.
Deliverables:
D1.1: Construction of BAC libraries 3Bv2/3DS/3DL/1BS/1BL/1AS/1AL (Month 18) available
D1.2: Contig assembly of 3B and 3DL (Month 12)
D1.3: Contig assembly of 3DS (Month 18)
D1.4: Contig assembly of 1BS and 1BL (Month 24)
D1.5: Contig Assembly of 1AS and 1AL
D1.6: Rearranging DNA according to the MTP for BAC end sequencing and 3D-pooling, Plate-pooling for each wheat BAC libraries; 3D-pools from the MTP of the barley BAC library (Month 30) available
D1.7: BAC end sequencing (Month 42) available
Other WPs:
- WP2 - Construction of anchored chromosome- and genomic physical maps of wheat and barley
- WP3 - Gene isolation and new allele discovery
- WP4 - Markers for molecular breeding
- WP5 - Bioinformatics
- WP6 - Dissemination, Technology Transfer and training
- WP7 - Management
This project is supported by the European Commission under the 7th Framework Programme
for Research and Technological Development