Accuracy and Training Population Design for Genomic Selection on Quantitative Traits in Elite North American Oats

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 fi ve traits on 446 oat (Avena sativa L.) lines genotyped with 1005 Diversity Array Technology (DArT) markers and two GS methods (ridge regression–best linear unbiased prediction [RR-BLUP] and BayesCπ) under various training designs. Our objectives were to (i) determine accuracy under increasing marker density and training population size, (ii) assess accuracies when data is divided over time, and (iii) 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 linkage disequilibrium (LD) relationships changed across subpopulations. Across many scenarios involving large training populations, the accuracy of BayesCπ 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. THE DECREASING COST of high-density molecular markers allows saturation of crop genomes with genetic markers and off ers an approach to predict genetic merit. Th ese markers can help capture the eff ects of many quantitative trait loci (QTL) controlling polygenic traits regardless of location of the QTL in the genome by using linkage disequilibrium (LD), the nonrandom association of alleles at diff erent loci (Falconer and Mackay, 1996). Meuwissen et al. (2001) proposed genomic selection (GS) based on prediction of the genetic value of individuals or the genomic estimated breeding values (GEBV) from high-density markers positioned throughout the genome. Because GS includes all markers, major and polygenic eff ects can be captured, potentially explaining more genetic variance (Solberg et al., 2008). Th erefore, the objective of GS is to predict the breeding value of each individual instead of identifying QTL for use in a traditional marker-assisted selection (MAS) program. Selection methods can be evaluated by measuring accuracy, a major component of the response to selection equation, R = irσA, in which R is the response, i is the selection intensity, r is the accuracy, and σA is the additive genetic standard deviation (Falconer and Mackay, 1996). As a general term in statistics, accuracy is the degree of similarity Published in The Plant Genome 4:132–144. Published 21 June 2011. doi: 10.3835/plantgenome2011.02.0007 © Crop Science Society of America 5585 Guilford Rd., Madison, WI 53711 USA An open-access publication All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. F.G. Asoro, M.A. Newell, and W.D. Beavis, Dep. of Agronomy, Iowa State Univ., Ames, IA 50011; M.P. Scott, USDA-ARS, Corn Insects and Crop Genetics Research Unit, Dep. of Agronomy, Ames, IA 50011; J.-L. Jannink, USDA-ARS, R.W. Holley Center for Agriculture and Health, Dep. of Plant Breeding and Genetics, Cornell Univ., Ithaca, NY 14853. Received 25 Feb. 2011. *Corresponding author (jeanluc.jannink@ars.usda.gov). Abbreviations: ARS, Agricultural Research Service; BLUP, best linear unbiased prediction; C, cluster; GBLUP, genomic relationship BLUP; GEBV, genomic estimated breeding values; GS, genomic selection; GWAS, genome-wide association studies; LD, linkage disequilibrium; PC, principal component; QTL, quantitative trait loci; QUON, Quaker Uniform Oat Nursery; RR-BLUP, ridge regression–best linear unbiased prediction; TBV, true breeding value; UOPN, Uniform Oat Performance Nursery. Published July, 2011