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United States Department of Agriculture

Agricultural Research Service

Research Project: DISSECTING COMPLEX TRAITS IN MAIZE AND BIOFUEL GRASSES BY APPLYING GENOMICS, BIOINFORMATICS, AND GENETIC RESOURCES

Location: Plant, Soil and Nutrition Research

2008 Annual Report


1a.Objectives (from AD-416)
This project will develop a genetic platform to identify useful variation in a high throughput fashion, and then use this platform to identify those genes and alleles that control kernel quality and tolerance to abiotic stresses. Bioinformatic tools will be developed in conjunction with the above to allow for the rapid analysis of plant germplasm diversity. Although the direct application of these approaches will be in maize and biofuel grasses, many of these genetic, statistical, and bioinformatic approaches could have broad implications for both the plant and animal genetics community at large. Objective 1: Develop statistical, genetic, and genomic approaches for dissecting complex traits in crop plants. Objective 2: Identify key genes and natural allelic variation for improving abiotic stress tolerance, nitrogen use efficiency, nutritional quality, and biofuel potential for maize and related grasses. Objective 3: Development of bioinformatic tools to mine and present functional allelic variation.


1b.Approach (from AD-416)
This project will use the natural variation inherent in the maize and biofuel grass genomes for the dissection of complex traits and for the identification of superior alleles. Such discovery is important to the development of improved breeding strategies for maize, the number one production crop in the world. First, this project will develop genetic resources that allow for the rapid dissection of any complex trait to the gene level. These resources will involve the creation of germplasm, the genotyping of this germplasm, and the development of statistical analyses. Using this platform, the project will then dissect the quantitative traits of nutritional quality, nitrogen use, biofuel productivity, and aluminum tolerance. The identification of advantageous alleles could allow for marker-assisted improvement of maize’s nutrition profile for humans and animals, increased processing efficiency, lower fertilizer requirements, and better adaptation to acidic soils. Finally, this project will improve access to diversity data and analysis tools for plant breeders and geneticists. We will facilitate the use of these materials by creating analysis tools, user friendly websites, and breeder decision making tools.


3.Progress Report
In collaboration with ARS researchers at Raleigh, NC and Columbia, MO, we have released the largest set of mapping lines for complex trait dissection in any species. 5000 diverse maize inbred lines have been produced. Seed for the vast majority of lines were deposited in the ARS Maize Stock Center. This genetic resource will also provide the anchor for future molecular diversity characterization in maize.

Initiated analysis of flowering time and a series of developmental traits. These initial analysis are some of the most powerful and detailed analysis of complex traits ever. They are suggesting the basis of complex traits are likely a moderate number of genes (50-100) with numerous rare alleles at each gene.

This work fits into the action plan for NP301 Plant, Microbial, and Insect Genetic Resources, Genomics and Genetic Improvement. Specifically, this project contributes to Component 1 (Genetic Resource Management) by characterizing phenotypic variation in diverse maize germplasm. The main focus of this research corresponds with Component 2 (Crop Informatics, Genomics, and Genetic Analyses), where resources to dissect complex traits are developed and applied. The bioinformatic tools for the facilitation of breeding decisions also support Component 3 (Genetic Improvement of Crops).


4.Accomplishments
1. Released Genetic Resources for Mining Maize Diversity. Maize is the most diverse crop in the world, but much of that useful genetic variation is found in maize unadapted to US agriculture. This project is working to unlock the molecular basis of this genetic variation and make it more accessible to agriculture. In collaboration with ARS researchers at Raleigh, NC and Columbia, MO, we have released the largest set of mapping lines for complex trait dissection in any species. 5000 diverse maize inbred lines have been produced. Seed for the vast majority of lines were deposited to the ARS Maize Stock Center. This genetic resource will also provide the anchor for future molecular diversity characterization in maize. This accomplishment addresses NP301 Program, Component 3 (Genetic Improvement of Crops). Problem Statements 3A & B.


5.Significant Activities that Support Special Target Populations
None.


6.Technology Transfer

None

Last Modified: 10/1/2014
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