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United States Department of Agriculture

Agricultural Research Service

Research Project: BIOINFORMATIC METHODS AND TOOLS TO PREDICT SMALL GRAIN FIELD PERFORMANCE

Location: Plant, Soil and Nutrition Research

Title: Accuracy and training population design for genomic selection in elite north american oats

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

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 10, 2011
Publication Date: June 21, 2011
Citation: Asoro, F.G., Newell, M.A., Beavis, W.D., Jannink, J., Scott, M.P. 2011. Accuracy and training population design for genomic selection in elite north american oats. The Plant Genome. 4:132-144.

Interpretive Summary: Genomic selection (GS) is a method to predict the performance of new breeding lines by using markers throughout the genome. The method estimates parameters for a prediction model using a “training population” that has both marker and trait information. Predictions are then calculated on a separate validation population. We evaluated the accuracy of GS using data from five traits on 446 oat lines each genotyped with 1005 markers. Our objectives were to: 1) determine the effects of marker density and training population size on prediction accuracy; 2) evaluate accuracy when the training population is composed of older breeding lines; and 3) examine accuracy when the training and validation population are not closely related. Accuracy increased as the number of markers and training size become larger. Including older lines in the training population increased or maintained accuracy, indicating that older generations retained information useful for prediction. When training and validation subpopulations were closely related accuracy was greater than when they were distantly related. Across many scenarios involving large training populations, the accuracy of the two GS methods we tested did not differ. This empirical study provided guides for oat and other small grains breeders to improve their implementation of GS to hasten the delivery of improved cultivars.

Technical Abstract: Genomic selection (GS) is a method to estimate the breeding values of individuals by using markers throughout the genome. We evaluated the accuracies of GS using data from five traits on 446 oat lines genotyped with 1005 Diversity Array Technology (DArT) markers and two GS methods (RR-BLUP and BayesC') under various training designs. Our objectives were to: 1) determine accuracy under increasing marker density and training population size; 2) assess accuracies when data is divided over time; and 3) examine accuracy in the presence of population structure. Accuracy increased as the number of markers and training size become larger. Including older lines in the training population increased or maintained accuracy, indicating that older generations retained information useful for predicting validation populations. The presence of population structure affected accuracy: when training and validation subpopulations were closely related accuracy was greater than when they were distantly related, implying that LD relationships changed across subpopulations. Across many scenarios involving large training populations, the accuracy of BayesC' and RR-BLUP did not differ. This empirical study provided evidence regarding the application of GS to hasten the delivery of cultivars through the use of inexpensive and abundant molecular markers available to the public sector.

Last Modified: 7/24/2014
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