Assessment of the Insular Organization of the Wheat D Genome by Physical Mapping

University Of California-Davis, Davis CA

Investigators

Abstract

Common wheat, Triticum aestivum, originated by interspecific hybridization of three diploid species, Triticum urartu, Aegilops speltoides and Ae. tauschii. The wheat nucleus therefore contains three pairs of genomes, designated AA, BB, and DD, respectively. One of the attributes of wheat genomes is that they are large compared to the genomes of the model plants Arabidopsis thaliana and rice. In small genomes, genes are separated by intergenic DNA of a uniform length. This has been shown directly by sequencing the genome of Arabidopsis thaliana. In large genomes, stretches of noncoding DNA separating the genes are likely to vary. Indirect evidence suggests that in wheat, there may be gene-rich islands (gene insulae) in which genes are separated by short stretches of intergenic DNA. These gene insulae are speculated to be separated by gene-poor or gene-empty space. To obtain a detailed picture of gene distribution in the wheat D genome, DNA fragments isolated from Ae. tauschii (the genome of Ae. tauschii is completely equivalent to the D genome of wheat) will be cloned in bacterial artificial chromosomes (BACs) and ordered as they are in wheat chromosomes. These groups of ordered DNA fragments are called contigs. A total of 300,000 BAC clones will be characterized by the global fingerprinting method and assembled into contigs on the basis of fingerprint sharing among the clones. Fingerprinting of this large number of BAC clones and their assembly into contigs will be accomplished by automation of the fingerprinting process and computer-based contig assembly. The position of each contig on the chromosome will be determined and neighboring contigs identified and joined to generate the physical map of each of the seven D-genome chromosomes. Thousands of cDNA clones of wheat genes will be placed on the D-genome physical map to integrate the existing D-genome linkage and deletion maps with its physical map and to chart a detailed picture of gene distribution across each D-genome chromosome. The nucleotide sequences of these cDNA clones are being determined in another project funded by the NSF Plant Genome Program. Comparisons of the positions of corresponding genes on the physical maps of the wheat D-genome (large genome), the maize genome (medium-size genome) and the genome sequence of the rice genome (small genome) will provide information on changes in genome structure as a function of genome size increase in the grass family. The identification of gene insulae in the wheat D genome and their mapping will have great practical significance since it will facilitate gene discovery and isolation and, ultimately, the sequencing of the most relevant regions of wheat genomes.