2011 Annual Report
1a.Objectives (from AD-416)
The proposed work is a joint effort to develop genomic and bioinformatic approaches to dissect maize, grape and other crops' agronomic traits. The goal is to identify specific genes and alleles that could be used in crop improvement.
1. Develop and molecularly characterize germplasm that capture high levels of genetic diversity.
2. Characterize germplasm for a wide range of agronomic and developmental traits.
3. Develop statistical analysis approaches for relating genotype and phenotype. Deploy these analysis approaches in easy to use software for the entire community.
1b.Approach (from AD-416)
1. Inbred lines and testcross germplasm will be created that will be efficient for trait dissection. The USDA maize and grape germplasm will be genotyped with high throughput next generation sequencing technologies.
2. Germplasm will be evaluated in replicated field trials for agronomic and developmental traits in both temperate and tropical environments.
3. Statistical approaches will be developed to deal with complex haplotypes, rare alleles, quantitative trait model building approaches, and breeding prediction. The software will be deployed in open source statistical scripts and in the TASSEL software package.
During 2011, researchers at Cornell have identified the molecular basis of genes controlling complex traits. Cornell provided bioinformatic support and extensive phenotyping efforts for characterizing diverse maize lines for multiple traits. A Cornell developer is switching our field-based phenotyping tools over to Android devices that can directly send real time field data directly to our servers. Additionally, he created the bioinformatics necessary to track 10,000s of samples using genotyping-by-sequencing technologies. A Cornell statistical geneticist has developed, led, and supported five large-scale genome wide association studies this year. He has also developed innovative approaches for combining linkage and association mapping populations in a single study. This researcher is also helping to coordinate collaboration between our USDA group and Chinese CAAS scientist to understand drought tolerance in diverse maize.
In the grape project, researchers in collaboration with another USDA-ARS scientist and the curators of the USDA grape collection, genotyped over 2,000 samples with 9,000 SNPs. They determined relatedness among this set of germplasm and surprisingly were able to show that nearly every Vitis vinifera (wine and table grapes) variety is related to one another by first degree relationships. This study was published in PNAS and highlighted in The New York Times. A study focusing on the wild species of Vitis is in preparation for later this year. Additionally, they have collaborated extensively in the integration of the advanced statistics into TASSEL.
This project is monitored through weekly meetings.