2007 Annual Report 1a.Objectives (from AD-416) 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. 1b.Approach (from AD-416) Linkage mapping and candidate association approaches will be used to dissect these traits. Diverse profiling and high throughpout phenotyping approaches will be used to characterize these populations and relate molecular aspects with agronomic phenotypes. Key to this process will be the development of bioinformatic solutions to relate these genomic and agronomic datasets. 3.Progress Report This report documents research conducted under a specific cooperative agreement between ARS and Cornell University. Additional details of research can be found in the report for the in-house associated project 1907-21000-021-00D, “Dissecting complex traits in maize by applying genomics, bioinformatics, and genetic resources”. Researchers at Cornell have identified the molecular basis of genes controlling carotenoid content. They have also continued a survey of genes involved in nitrogen transport. Cornell provided bioinformatic support and extensive phenotyping efforts to start characterizing kernel quality in 5000 diverse maize lines. Additionally, they have collaborated extensively in the integration of the mixed model, the creation of TASSEL into a pipeline, and increased its ability to deal with pedigrees in the TASSEL software package. This project is monitored through weekly meetings.