Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Chromosome Based Strategies To Decipher The Hexaploid Wheat Genome: Chromosome 3B, A Case Study

Etienne Paux¹ , Pierre Sourdille¹ , Jérôme Salse¹ , Philippe Leroy¹ , Jan Bartos³ , Imen Mestiri² , Boulos Chalhoub³ , Francis Quetier⁴ , Michel Bernard¹ , Jaroslav Dolezel³ , Catherine Feuillet¹

¹  Genetics and Plant Breeding, UMR INRA-UBP, Domaine de Crouelle, 234 Ave du Brezet, 63100 Clermont-Ferrand, France

²  Organization and Evolution of plant genomes, (INRA-URGV), 2 rue Gaston Crémieux, CP 5708, F-91057 Évry Cedex, France

³  Laboratory of Molecular Cytogenetics and Cytometry, IEB, Sokolovska 6, CZ-77200 Olomouc, Czech Republic

⁴  Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP 5706, F-91057 Évry Cedex, France

With 17% of all crop area, wheat is the staple food for 40% of the world’s population. Improvement of bread wheat quality and yield in the context of sustainable agriculture is needed in the next decades to meet human needs by 2050. To accelerate gene discovery and marker development in wheat, significant advances must be achieved in the understanding of the structure and function of the wheat genome. Currently, whole genome analyses are hampered by its size (16,000 Mb), allohexaploid nature and high repetitive DNA content (~80%). Using laser flow cytometry and aneuploid lines, individual chromosomes or chromosome arms can be sorted at high speed providing an alternative approach for dissecting nuclear genomes into small and defined parts. To date, three BAC libraries were created from sorted chromosomes (1BS, 3B, 1D-4D-6D) in wheat (1,2). To test the feasibility of the chromosome specific strategy for the construction of a physical map and the ultimate sequencing of the hexaploid wheat genome, we have recently initiated the construction of a physical map of chromosome 3B. The ~68,000 BAC clones of the 3B chromosome-specific BAC library (2) were fingerprinted leading to about 3,000 contigs in a first phase of BAC assembly and contig construction. The finishing of contig assembly and the anchoring of the physical contigs to the genetic map with about 2,000 markers (SSR, EST, RFLP) are currently underway. In parallel, 20,000 BAC-ends sequences were obtained providing 10 Mb of novel sequence for genome analysis and marker development. Finally, to get a better insight into the wheat gene space, we are analysing the location, distribution and density of genes along chromosome 3B by screening the BAC library with ~1,500 EST derived from wheat and from orthologous region of rice chromosome 1. The availability of the 3B physical map and the definition of gene islands will allow a better understanding of the structure, composition and evolution of the wheat genome as well as to accelerate map-based cloning of genes of interest from 3B and homoeologous chromosomes.
(1) Janda et al., Theor. Appl. Genet. 109:1337, 2004; (2) Šafár et al., Plant J. 39:960, 2004.