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United States Department of Agriculture

Agricultural Research Service

Research Project: Genomic Analysis of Plant Genetic Load and Development

Location: Plant, Soil and Nutrition Research

Project Number: 1907-21000-039-02
Project Type: Specific Cooperative Agreement

Start Date: Sep 18, 2013
End Date: Sep 17, 2015

Objective:
The proposed work is a joint effort to develop genomic and bioinformatic approaches to dissect maize, maize’s wild relatives, and other crops' agronomic traits. The goal is to identify specific nucleotide variants that could be used in crop improvement with a special emphasis on those that are the source of genetic load. 1. Genomically characterize germplasm for rare nucleotide variants. 2. Characterize germplasm for hybrid vigor, developmental traits, and cold tolerance. 3. Develop statistical analysis approaches for relating genotype and phenotype and to identify mutations contributing to genetic load. Deploy these analysis approaches in easy to use software for the entire community.

Approach:
1. Inbred lines and testcross germplasm will be created that will be efficient for detecting genetic load. Parts of USDA germplasm collection will be genotyped with high throughput next generation sequencing technologies to identify rare alleles. 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.

Last Modified: 8/21/2014
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