Project: Objectives
Project Summary
The primary goal of the project is to discover and map single nucleotide polymorphisms in tetraploid and
hexaploid wheat and develop appropriate bioinformatic tools for public access to this resource. The
secondary goal is to employ this resource in preliminary characterization of genetics structure of the
genepools of tetraploid and hexaploid wheat and wheat diploid ancestors. To accomplish the two goals, the
following objectives are targeted.

(1) SNP discovery. Select approximately 6,000 EST unigenes detecting single or at most two genes per
wheat genome from the database of mapped ESTs and other EST databases, and design conserved PCR
primers for the development of STSs spanning one or more introns. Use STS polymorphism among the
three wheat diploid ancestors to develop A-, B-, and D-genome specific primers. Amplify STSs from the
wheat A, B and D genomes in a sample of wild emmer and bread wheat lines, sequence the amplicons
and assess haplotype polymorphism in wild and cultivated wheats. Integrate these new SNPs into wheat
genetic maps.

(2) Bioinformatics. In collaboration with Gramene, create public databases of conserved and
genome-specific PCR primers for amplification of STSs from genomic DNA of wheat and its immediate
relatives, conserved and genome-specific sequencing primers for sequencing STSs from wheat and its
immediate diploid ancestors, DNA sequences, electropherograms, haplotypes, SNPs, and positions of
SNP markers on wheat linkage maps. Create links from the databases to GrainGenes databases, EST
database, the database of Aegilops tauschii BAC contigs, and other cereal databases.

(3) Preliminary characterization of genetic structure of wheat genepools. Produce 20 sets of orthologous
STSs from the genomes of representative samples of Triticum urartu, Ae. speltoides, Ae. tauschii, wild and
cultivated tetraploid wheat, and cultivated hexaploid wheat. Obtain preliminary data on the contribution of
gene flow from diploid ancestors to the polyploid taxa. Estimate nucleotide polymorphism at the
replacement and silent codon positions and introns, and analyze the data in relation to recombination rates
in the vicinity of each locus and mating system.

(4) Broader social impact (Education and Outreach). (a) Develop and implement a coherent plan for
undergraduate student summer internships in the area of marker development or evolutionary genomics.
(b) Organize summer training courses for graduate students and postdoctoral trainees in SNP detection. (c)
Develop a program for lectures in institution with large undergraduate student body social groups
traditionally underrepresented in science. (d) In collaboration with the Partnership for Plant Genomics
Education Program at UC Davis, develop an educational video on wheat evolution and the origin of
agriculture in the Southwestern Asia.