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Funding Update for Mar 24, 2009

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Comparative Genomics of Phenotypic Variation in the Compositae

Start Date: March 15, 2009
Expires: February 28, 2010
Awarded Amount to Date: $2,263,021
Principal Investigator: Loren Rieseberg
Sponsor: Indiana University

The primary goal of this project is to develop genomic resources for the continued study of the plant family of Composiate, also known as Asteraceae. This work will include sequencing the gene-rich regions of the lettuce, sunflower, and safflower genomes; generation of "gene catalogs" for 25 additional taxa, including six crops, three weeds, the wild progenitors of 10 crops and weeds, representatives of five taxonomically important subfamilies within the family, and an outgroup; analyses of the prevalence of variation in gene copy number versus nucleotide variation; analyses of the effects of whole-genome duplications on diversification rates within the family; identification of parallel genetic changes across crop/weed lineages; construction of ultra-high density genetic maps of lettuce, sunflower, and chicory; development of permanent populations for genetic mapping in key Compositae species; and the identification and validation of candidates for genes underlying important crop- and weed-related traits.


Improving the Sequence of the Maize Genome

Start Date: March 1, 2009
Expires: February 28, 2010
Awarded Amount to Date: $1,538,919
Principal Investigator: Richard Wilson
Sponsor: Washington University School of Medicine

A draft sequence of the maize genome was generated, funded as part of the Maize Genome Sequencing Project: An NSF/DOE/USDA Joint Program, and released in February 2008. This project seeks to provide additional analysis and annotation information and provide the research community with a continuous, annotated reference genome sequence for maize. The specific aims of the project are to sequence and finish 500 fosmid clones; produce an eight-fold whole genome shotgun sequence using a 454 platform; and increase the scope of the genome assembly, analysis, and annotation.
Project information and data will be available through a website accessible through the Washington University Genome Sequencing Center. Maize sequence assemblies and maize genetic resources will be incorporated into Gramene and MaizeGDB.


Construction of High Resolution Physical Maps for Large Plant Genomes

Start Date: March 1, 2009
Expires: February 28, 2010
Awarded Amount to Date: $952,211
Principal Investigator: Shahryar Kianian
Sponsor: North Dakota State University Fargo

The success of radiation hybrid mapping in humans has inspired its use in the construction of complete physical maps for the majority of animal genomes prior to complete sequencing. This project will develop high-resolution RH physical maps that will be used to anchor existing bacterial artificial chromosome contigs and clones for the 4.2 Gb D-genome of hexaploid wheat. This anchoring and alignment will complement a larger effort by the international wheat genomics community to develop a global physical map and whole-genome sequence of this genome.

The tools, methods, and knowledge developed in this project can be applied to other crop species and will facilitate the construction of physical maps at a fraction of the cost of current methods, according to the grant abstract. The maps generated will provide easy access to genes of biological and agricultural importance and will enable the development of new strategies to manipulate wheat to better serve the needs of a growing world population. In addition, the information developed in this project will allow for comparative analysis of wheat with rice, maize and other grass genomes to address important biological questions regarding gene organization and chromosome evolution, the abstract states.


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Generation and Analysis of a Reference Sequence for the West African Cultivated Rice - Oryza Glaberrima (CG14)

Start Date: March 1, 2009
Expires: February 28, 2011
Awarded Amount to Date: $1,477,785
Principal Investigator: Rod Wing
Sponsor: University of Arizona

The objective of this project is to generate and analyze a reference genome sequence of the West African cultivated rice Oryza glaberrima (CG14). The reference sequence will be generated using a minimum tiling path of bacterial artificial chromosome clones selected from an existing NSF-funded O. glaberrima physical map, which encompasses the entire genome. DNA from these clones will be purified, pooled, and sequenced using 454/Roche GS FLX Titanium and paired-end pyrosequencing technologies. A standardized annotation process will be applied across the whole genome taking advantage of the well-curated annotation for the Asian cultivated rice species — Oryza sativa. In addition, customized analyses targeted at specific biological questions will be performed. The genome sequence and its annotation will be accessible via public databases, such as GenBank and Gramene.


A Medicago Truncatula HapMap as a Platform for Exploring the Genetics of Legume Symbioses

Start Date: March 1, 2009
Expires: February 28, 2010
Awarded Amount to Date: $2,186,028
Principal Investigator: Nevin Young
Sponsor: University of Minnesota-Twin Cities

Medicago truncatula is a widely studied model species for legume genomics, and one important question focuses on the identity of naturally occurring genes that control variation in symbiosis in legumes. This project will use association mapping techniques to create a Medicago "HapMap." In brief, 384 diverse genetic lines obtained from collaborators at INRA-Montpellier, Ecole National Superieur Agronomique de Toulouse, and the Noble Foundation will be resequenced using next-generation sequencing technology for SNPs between the different Medicago lines. SNP discovery through genome resequencing is possible because a reference sequence for the gene-rich euchromatin of Medicago has already been created through previous NSF funding. The massive database of SNPs between Medicago lines enables the prediction of genome segments with shared ancestry, or haplotypes, which can then be associated statistically with trait variation in symbiosis. Because of the exceedingly high level of SNP density, association mapping can approach the resolution of a single gene.


Computational Methods for High-Throughput Sequencing and Population Genomics Analysis

Start Date: March 1, 2009
Expires: February 28, 2010
Awarded Amount to Date: $116,107
Principal Investigator: Yun Song
Sponsor: University of California-Berkeley

In an effort to understand the biological mechanisms through which genetic polymorphisms affect phenotypes, the principal investigator is developing tools to improve all aspects of data acquisition, error rate reduction, and reduction of the cost of high-throughput sequencing by increasing the throughput per run. He has been working closely with Solexa/Illumina high-throughput sequencing data and the source code for this project. The research "aims to set a high standard for the commercial sector to meet in the future," according to the grant abstract. Further, this project is developing computational methods to annotate genomic variation, including structural variation, and applying them in a large-scale Drosophila resequencing project. Finally, scalable informatics tools for population genomics analysis are being developed. This work is also enabling accurate inference of selection and demography on the whole-genome scale in multiple populations and is being applied in a novel approach to the study of human migration patterns.


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Leveraging Untapped Genetic Diversity in Soybean

Start Date: March 1, 2009
Expires: February 28, 2010
Awarded Amount to Date: $2,977,012
Principal Investigator: Scott Jackson
Sponsor: Purdue University

This project will develop a set of tools that will allow investigators to leverage the recently released draft soybean genome sequence to exploit genetic diversity in the genus Glycine and to begin to understand the nature of species/genome diversification in the genus, according to the grant abstract. Important in this process is an understanding of the cycle of polyploidization followed by diploidization found in this set of species. The specific objectives are to overlay diversity maps onto the soybean genome sequence using genomic clones from a set of phylogenetically informative Glycine species; explore genome evolution in the genus Glycine at the chromosomal/sequence level to understand the polyploidy/diploidization cycle; sequence targeted orthologous regions across the Glycine species in order to understand levels of linkage disequilibrium and genetic diversity that can be exploited for genetics and breeding; and integrate data with other legumes which is necessary to extend its usefulness to other so-called "orphan" legumes such as common bean.


Complete Genome Sequencing of the Chromatically Adapting Cyanobacterium Fremyella diplosiphon

Start Date: September 1, 2008
Expires: August 31, 2009
Awarded Amount to Date: $165,722
Principal Investigator: George Weinstock
Sponsor: Washington University School of Medicine

This project will produce a genome sequence of the fresh-water filamentous cyanobacterium Fremyella diplosiphon UTEX 481. Pyrosequencing will be used to sequence the 12 million base pairs of this genome, one of the largest known in bacteria. These data will be used to compile a complete description of the genes contained in this bacterium, to reveal important physiological and regulatory mechanisms involved in prokaryotic responses to changes in ambient light color. The genetic content will also be compared to other sequenced cyanobacteria and photosynthetic bacteria, to provide a broad picture of the evolution of photosynthesis and the cyanobacteria. F. diplosiphon is a well-developed model organism that for some forty years has been used to advance understanding of how microorganisms sense and respond to their environment.

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