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United States Department of Agriculture

Agricultural Research Service

Research Project: ASSOCIATION MAPPING IN CROP PLANTS

Location: Plant, Soil and Nutrition Research

2013 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.


3.Progress Report:

The molecular basis of genes controlling complex traits was identified. Extensive phenotyping efforts were conducted to characterize diverse maize lines for multiple traits from the US and with numerous global collaborators. Additionally, bioinformatics was used to track 10,000s of samples using genotyping-by-sequencing technologies and to update these datasets daily. Multiple large-scale genetic mapping studies were carried out this year across genetic and breeding germplasm. Innovative approaches were developed for evaluating the effects of heterosis (hybrid vigor) at the DNA nucleotide level. Collaboration between our USDA group and scientists from the Chinese Academy of Agricultural Sciences and Cornell Univeristy helped us understand yield and drought tolerance in diverse maize. The genetic relationships between all the USDA-ARS maize inbred lines were carried out and provided a detailed and comprehensive understanding of all lines in the germplasm collection for the first time. These results were made available through a publication, online dataset, and queryable tool through MaizeGDB.

Additionally, we have integrated advanced statistics and bioinformatics into TASSEL.


Last Modified: 10/21/2014
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