NSF Award Abstract - #0321756

AWSFL008-DS3

Coupling Expressed Sequences and Bacterial Artificial Chromosome Resources to
Access the Barley Genome

Abstract

Several cereal crops of major economic and social importance, including barley, wheat, rye and triticale, are members of the tribe Triticeae. These crops account for over 30% of the world's grain production, with more than 35% of the human population using them as a staple food. In the United States, Triticeae crops are sown on approximately 81 million acres each year with an average value over 9 billion dollars. Although products derived from the Triticeae crops are diverse (bread, pastries, pasta, beer, malt whiskey, soup ingredients, animal feed), the species are genetically closely related. The Triticeae genomes, each with a size of about 5 x 109 base pairs per haploid genome, are too large to seriously consider whole-genome sequencing at present. This is about 12 times the size of rice. Yet, reliable methods can be immediately employed to gain access to the majority of expressed genes in Triticeae genomes. During the past several years, considerable progress has been made in the establishment of core public resources in barley genomics. These core resources include genomic "bacterial artificial chromosome" (BAC) libraries and cDNA libraries, several widely used mapping populations, more than 360,000 partial cDNA sequences ("Expressed Sequence Tags; ESTs) representing about 75% of all genes in the barley genome, and a microarray that makes it possible to simultaneously monitor the expression of more than 21,000 barley genes. The purpose of this project is to couple these resources to facilitate access of US and worldwide researchers to the barley genome, thereby building a fuller understanding of cereal plant traits that are pertinent to agriculture and biology. The unifying objective is to accelerate a transition to comprehensive physical mapping and the sequencing of all gene-containing regions of the barley genome. The project is structured into six progressive objectives, each oriented toward gradual extraction of the essence of the barley genome. The first objective will utilize knowledge of unigene sequences to identify the majority of BAC clones that carry expressed genes, expected to be about 20% of all BAC clones. The second objective will use a genetic fingerprinting technique to create many thousands of contiguous alignments ("contigs") of these BAC clones, and from them define a minimal set representing all. The third and fourth objectives place special emphasis on 1000 genes that are related to abiotic stress, including drought, low temperature, heat, and salinity by adding these contigs and genes to the barley genetic linkage map. The fifth and sixth objectives will create easy access to this information through a database browser that will offer users a choice of purely web-based functionality or, for those who prefer more speed, hybrid software that operates principally on personal computers and relies on the web only for supplemental information.

Deliverables Information on gene-specific and popular overgo probes will be available during year #1. Sub-arrays of the entire BAC library enriched for the gene-rich portion of the genome will be available beginning at the end of year #2. Physical maps of BAC contigs related to this portion of the genome will be available starting year #1, with additions through year #2. BAC contigs and ESTs related to 1000 genes pertinent to abiotic stress will be anchored to the genetic linkage through year #4. The total compilation of progress will be freely available through the project web site (http://harvest.ucr.edu) throughout and after the end of the project.