Project Number: 1907-21000-029-01
Project Type: Specific Cooperative Agreement

Start Date: Sep 15, 2003
End Date: Sep 14, 2008

Objective:
This research will evaluate natural allelic variation in maize and rice for kernel quality, nitrogen use efficiency, and aluminum tolerance. The molecular basis for key genes controlling these pathways will be identified along with useful alleles for plant breeding. In addition, a pilot scale demonstration of the capability of the new generation of sequence technologies to identify genetic variation in a non-model species, namely grape, will be initiated. Our labs are currently implementing these emerging DNA sequencing technologies for SNP genotyping in maize; the objective here is to demonstrate the feasibility and value of this approach in the most valuable horticultural crop in the world, capitalizing on the fact that the grape genome has recently been sequenced.

Approach:
With respect to trait dissection, linkage mapping and candidate association approaches will be used. Diverse profiling and high throughput phenotyping approaches will be used to characterize these populations, and relate molecular aspects with agronomic phenotypes. Additionally, bioinformatic solutions will be developed to relate these genomic and agronomic datasets. The grape genotyping project will use the following approaches: 1. Bioinformatically identify 5000 SNPs for Vitis, using publically available sequence; 2. Validate a subset of these SNPs; 3. Design SNP arrays to genotype 2500 samples; 4. Run the samples on an Illumina Beadstation; 5. Estimate diversity, population structure, breeding values, and associate genetic variation with agronomic traits.