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United States Department of Agriculture

Agricultural Research Service

Research Project: Analysis of Clinal Variation in Maize: Implementation of An Experimental Framework for Studying Crop Adaptation

Location: Corn Insects and Crop Genetics Research

2013 Annual Report


1a.Objectives (from AD-416):
The proposed project has two general goals: first, to increase knowledge about the genetic architecture of response to artificial selection for adaptation; second, to characterize geoclimatic influences on tropical maize phenotypes, haplotypes, and ecology. The specific scientific aims of this project are.
1)Evaluate Association-Selection Mapping as an experimental approach for characterizing the genetic architecture of adaptation, and.
2)Identify geoclimatic responsive haplotypes limiting temperate adaptation and maize improvement.


1b.Approach (from AD-416):
Increasing the resiliency and sustainability of crop production requires approaches that harness genetic diversity to adapt plants to existing and future environmental challenges. Tropical maize possesses significantly greater genetic variation than U.S. maize and harbors favorable alleles for numerous traits that are absent from U.S. maize that will be important for adapting to climate change. The search for favorable alleles for maize productivity under abiotic stress and emerging pathogens will require meaningful phenotypic evaluation of tropical diversity in the temperate target environments where maize is produced.

This proposal leverages contemporary conventional breeding techniques combined with technologies that utilize recent advances in genomic sequence information to develop new plant varieties. It addresses core issues related to access and use of novel genetic diversity and will directly facilitate crop improvement by increasing knowledge of adaptation and response to selection.

The interdisciplinary team will conduct Association-Selection Mapping studies across 10 environments in North America, test ecogeographic consequences of photoperiod and temperature during artificial selection, and identify alleles that can mitigate the photoperiod-response problem faced by corn breeders.


3.Progress Report:

In the second year of this project, we have remained focused on developing the experimental germplasm and theoretical frameworks to address our overarching objectives. For the development of the Nearly Isogenic Line Allelic Series (NILAS) resources, we performed the third and fourth rounds of molecular marker assisted backcrossing on four genomic locations known to affect photoperiod responsiveness. All four of these genetic loci are breeding targets because photoperiod sensitivity is a major barrier to leveraging valuable tropical alleles in modern breeding schemes. The alleles from seven diverse tropical lines are being introgressed into each of two elite temperate maize lines. Our work in year two included DNA isolations for ~32,000 plants and collection of 1,100,000 genotypic data points to obtain genetic fingerprints. We used the data to choose which genetic stocks should be advanced and delivered these results to our nursery team. The NILAS resources (56 projects = seven tropical donors x two temperate recurrent parents x four genetic targets) are on track for completion by the end of project year three and will provide a unique resource for dissecting photoperiodism genetics and addressing the consequences of artificial selection. NILAS is the first resource of its kind to be developed, in part because the technologies required for molecular marker assisted breeding at this scale have only recently become cost effective for such an effort. Despite the advances in molecular marker technologies, NILAS development remains an intense effort for a small team to execute. To optimize our efforts, we performed simulation studies prior to the first marker-assisted breeding steps with the aim of determining if any points in the breeding scheme should be handled differently than originally proposed. In accord with our simulation study findings, we increased the scale of our efforts in the generations three and four by 25 percent, and did so while staying on budget. This will ensure the highest possible quality for the 56 NILAS collections we are developing. As part of the effort to perform artificial selections across an extreme latitudinal cline on the same base germplasm, we advanced the selection of the Tropic Synthetic population by one full cycle in Ames, Iowa. This is being performed at ten latitudes ranging from Puerto Rico to Wisconsin, and will allow the team to study how the environment in which the selection is imposed affects the outcome of the process. To coordinate our efforts, we held bi-monthly conference calls and convened in St. Charles, IL in March 2013 for a one-day project team meeting. To further build connectivity across the research groups, work trips to our breeding nurseries at Third Millennium Genetics in Puerto Rico were coordinated among teams so that interdisciplinary training could occur. Three members of the Ames team also worked alongside the University of Delaware team in June, 2013 to accomplish sample collection from 16,000 plants. At the Maize Genetics Conference held in St. Charles, IL in March 2013, our research group presented four posters and gave one invited talk as part of this research project.


Last Modified: 7/23/2014
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