Construction of BAC library and physical mapping of the wheat chromosome 3D
Project goals
The large size and polyploid nature of the nuclear genome of bread wheat pose a great challenge for the understanding of complete genome information, genome sequencing and gene discovery. This task could be simplified by fractionating the genome into small and defined parts. Here we propose to create two subgenomic BAC libraries specific for short and long arm of wheat chromosome 3D. Their creation will mark the completion of BAC resources for homeologous group 3, which has been selected for the pilot phase of the wheat genome sequencing project. 3D-specifc BAC resources developed in this project will be used to develop a molecular cytogenetic map and, in collaboration with Prof. J. Dvořák (UC, Davis), a physical contig map of 3D. They will alsobe usedfor targeted isolation of low-copy (potentially coding) DNA sequences, discovery of gene-rich regions on 3D, and for high-throughput mapping of expressed sequences to chromosome 3D using wheat GeneChip (collaboration with Prof. T. Close, UC,
Keywords
Public support
Provider
Czech Science Foundation
Programme
Standard projects
Call for proposals
Standardní projekty 9 (SGA02006GA-ST)
Main participants
—
Contest type
VS - Public tender
Contract ID
521/06/1723
Alternative language
Project name in Czech
Konstrukce BAC knihovny a fyzické mapování chromozómu 3D pšenice
Annotation in Czech
Značná velikost a polyploidní původ jaderného genomu pšenice seté komplikují jeho sekvenování, analýzu a klonování genů. Tyto postupy mohou být zjednodušeny rozdělením genomu na malé definované části. Navrhujeme připravit dvě subgenomové knihovny DNA klonované ve vektoru BAC, specifické pro krátké a dlouhé rameno chromozómu 3D. Jejich konstrukcí bude dokončena příprava genomových zdrojů pro homeologní skupinu 3, která byla mezinárodním konsorciem zvolena pro pilotní fázi sekvenování genomu pšenice. BACknihovny specifické pro chromozóm 3D použijeme pro odvození cytogenetické mapy a ve spolupráci s J. Dvořákem (UC, Davis) pro přípravu fyzické mapy chromozómu. Použijeme je rovněž pro izolaci potenciálně kódujících sekvencí DNA, identifikaci genově bohatých oblastí a pro hromadné mapování exprimovaných sekvencí DNA na chromozómu 3D pomocí DNA čipu (ve spolupráci s T. Close, UC, Davis). Řešení projektu otevře nové možnosti pro komparativní analýzu evoluce genomu pšenice a studium interakce jejích
Scientific branches
R&D category
ZV - Basic research
CEP classification - main branch
GE - Plant cultivation
CEP - secondary branch
EB - Genetics and molecular biology
CEP - another secondary branch
EI - Biotechnology and bionics
10603 - Genetics and heredity (medical genetics to be 3)
10604 - Reproductive biology (medical aspects to be 3)
10605 - Developmental biology
10608 - Biochemistry and molecular biology
10609 - Biochemical research methods
20801 - Environmental biotechnology
20802 - Bioremediation, diagnostic biotechnologies (DNA chips and biosensing devices) in environmental management
20803 - Environmental biotechnology related ethics
20901 - Industrial biotechnology
20902 - Bioprocessing technologies (industrial processes relying on biological agents to drive the process) biocatalysis, fermentation
20903 - Bioproducts (products that are manufactured using biological material as feedstock) biomaterials, bioplastics, biofuels, bioderived bulk and fine chemicals, bio-derived novel materials
30101 - Human genetics
30401 - Health-related biotechnology
30402 - Technologies involving the manipulation of cells, tissues, organs or the whole organism (assisted reproduction)
30403 - Technologies involving identifying the functioning of DNA, proteins and enzymes and how they influence the onset of disease and maintenance of well-being (gene-based diagnostics and therapeutic interventions [pharmacogenomics, gene-based therapeutics])
30404 - Biomaterials (as related to medical implants, devices, sensors)
30405 - Medical biotechnology related ethics
40105 - Horticulture, viticulture
40106 - Agronomy, plant breeding and plant protection; (Agricultural biotechnology to be 4.4)
40401 - Agricultural biotechnology and food biotechnology
40402 - GM technology (crops and livestock), livestock cloning, marker assisted selection, diagnostics (DNA chips and biosensing devices for the early/accurate detection of diseases) biomass feedstock production technologies, biopharming
40403 - Agricultural biotechnology related ethics
Completed project evaluation
Provider evaluation
U - Uspěl podle zadání (s publikovanými či patentovanými výsledky atd.)
Project results evaluation
Two BAC (Bacterial Artificial Chromosome) libraries specific for the short and long arms of wheat chromosome 3D were constructed. The libraries represent 11x and 12x equivalents of 3DS and 3DL, respectively, and are the first of this type for the D genom
Solution timeline
Realization period - beginning
Jan 1, 2006
Realization period - end
Dec 31, 2008
Project status
U - Finished project
Latest support payment
Apr 25, 2008
Data delivery to CEP
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data delivery code
CEP09-GA0-GA-U/02:2
Data delivery date
Oct 22, 2009
Finance
Total approved costs
3,431 thou. CZK
Public financial support
3,431 thou. CZK
Other public sources
0 thou. CZK
Non public and foreign sources
0 thou. CZK
Basic information
Recognised costs
3 431 CZK thou.
Public support
3 431 CZK thou.
100%
Provider
Czech Science Foundation
CEP
GE - Plant cultivation
Solution period
01. 01. 2006 - 31. 12. 2008