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United States Department of Agriculture

Agricultural Research Service


Location: Plant, Soil and Nutrition Research

2012 Annual Report

1a. Objectives (from AD-416):
Objective 1. Association mapping of b-glucan content and structure in elite oat germplasm and replicated comparison of phenotypic with marker-assisted selection. Objective 2. Association mapping of b-glucan content from the National Plant Germplasm System: complementation of elite oat. Objective 3. Educational initiatives to pipeline students into plant breeding and to educate professionals.

1b. Approach (from AD-416):
Objective 1. We will apply association analysis to a population of elite oat lines tested in the USDA UOPN since 1996. The b-glucan content of lines is known. We will genotype lines using DArT markers. We will apply both mixed-model association analysis controlling for kinship using pedigree information and whole genome analysis. Results will feed into two cycles of MAS using both analyses. Conversion of UOPN data files on GrainGenes to a relational database that will also hold genotypic data will provide informatic support and a future resource for the oat community. Objective 2. The GRIN system contains b-glucan content observations on 5382 oat accessions. We will pick 250 lines from each tail of the distribution to genotype. Objective 2 will either confirm loci identified in Objective 1, or to identify new loci. For loci mapped in Objectives 2 but not 1, we will determine whether the elite population carries the allele conferring higher b-glucan content as shown by analysis of the NPGS population. Objective 3. We will develop an interactive distance short course entitled “Association analysis and its application to plant breeding.” The course syllabus and content will emerge from the research proposed here and from the Barley CAP. The target audience will be plant breeding professionals and upper-level graduate students in plant breeding nationwide. Two educational activities will help draw new students to plant breeding. First, a one-hour presentation oriented toward high-school students will be used at recruitment venues organized by ISU. Second, a week-long teaching module on biotechnology and computational biology in plant breeding will be introduced into two lower-level Agronomy courses and one upper-level Food Science course.

3. Progress Report:
Two cycles of selection using each of three methods (phenotypic, marker-assisted, and genomic selection) were completed. Each method was also replicated twice such that six breeding programs were in fact implemented. We found that all replicates of selection that used markers generated greater gain than either of the two replicates of phenotypic selection. Furthermore, greater genetic variance was maintained in programs that use markers than in the phenotypic selection programs. A manuscript will be submitted shortly on these results. Association mapping of beta-glucan concentration has now been completed in a global oat collection and in an elite North-American collection. In both cases sequence similarity of associated markers to rice sequence was used to target plausible candidate genes. Map position of associated markers was also related to positions of QTL identified in bi-parental mapping. These efforts generated two publications. Iowa State University Department of Agronomy Distance Education Program will be using an outline for a course on association methods in plant breeding developed by this project.

4. Accomplishments

Last Modified: 10/19/2017
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