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United States Department of Agriculture

Agricultural Research Service

Research Project: BIOINFORMATIC METHODS AND TOOLS TO PREDICT SMALL GRAIN FIELD PERFORMANCE Title: Comparison of genomic, marker-assisted, and pedigree-BLUP selection methods to increase beta-glucan concentration in elite oat germplasm

Authors
item Asoro, Franco -
item Newell, Mark -
item Beavis, William -
item Scott, Marvin
item Tinker, Nicholas -
item Jannink, Jean-Luc

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 13, 2013
Publication Date: July 1, 2013
Citation: Asoro, F., Newell, M., Beavis, W., Scott, M.P., Tinker, N., Jannink, J. 2013. Comparison of genomic, marker-assisted, and pedigree-BLUP selection methods to increase beta-glucan concentration in elite oat germplasm. Crop Science. 53(5):1894-1906.

Interpretive Summary: Beta-glucan, a soluble fiber found in oat grain, is good for human health, and selection for higher levels of this compound is regarded as an important breeding objective. Recent advances in oat DNA markers allow high-density markers to be scored for a reasonable cost (about $50 per line) and present an opportunity to investigate new selection methods for polygenic traits such as beta-glucan concentration. Marker-assisted selection involves identifying a relatively small number (less than ten) markers that are significantly associated with a trait and using those markers for selection. Genomic selection involves using all markers as predictors of a trait, whether they are significantly associated with it or not. Our objectives in this study were to compare marker-assisted, genomic, and phenotypic selection for short-term response and ability to maintain genetic variance for beta-glucan concentration. Starting with a collection of 446 elite oat lines from North America, each selection method was conducted for two cycles of selection. The averages of marker-based selection methods after Cycle 2 were greater than those of phenotypic selection. We also found that marker-based selection methods maintained greater genetic variance than did phenotypic selection, potentially enabling greater future selection gains. Overall, the results of these experiments suggest that genomic selection is a superior method for selecting a polygenic complex trait like beta-glucan concentration.

Technical Abstract: Beta-glucan, a soluble fiber found in oat grain, is good for human health, and selection for higher levels of this compound is regarded as an important breeding objective. Recent advances in oat DNA markers present an opportunity to investigate new selection methods for polygenic traits such as beta-glucan concentration. Our objectives in this study were to compare genomic, marker-assisted, and BLUP-based phenotypic selection for short-term response to selection and ability to maintain genetic variance for beta-glucan concentration. Starting with a collection of 446 elite oat lines from North America, each selection method was conducted for two cycles of selection. The average beta-glucan concentration increased by 2.09 to 2.31% over two cycles of selection from an average of 4.57% in Cycle 0. The averages of marker-based selection methods after Cycle 2 were greater than those of phenotypic selection. Moreover, the highest beta-glucan progenies came from the marker-based selection methods, demonstrating the effectiveness of molecular markers in developing superior progenies. However, MAS for higher beta-glucan concentration resulted in a later heading date. We also found that marker-based selection methods maintained greater genetic variance than did BLUP phenotypic selection, potentially enabling greater future selection gains. Overall, the results of these experiments suggest that genomic selection is a superior method for selecting a polygenic complex trait like beta-glucan concentration.

Last Modified: 10/23/2014
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