Marker Genotype Imputation in a Low- Marker-Density Panel with a High-Marker- Density Reference Panel: Accuracy Evaluation in Barley Breeding Lines

We evaluated a strategy in which the scores of markers untyped in a low-density experimental panel were imputed on the basis of data from a high-density reference panel, in its application to whole-genome genotyping of barley (Hordeum vulgare L.) breeding lines. Using a barley core set consisting of 98 lines genotyped with 3205 markers (high-density reference panel), we imputed marker scores untyped in 863 barley breeding lines genotyped with 1330 common markers (low-density experimental panel). In repeated analyses, the scores of one common marker were masked in the experimental panel, and then imputed as an untyped marker. Imputation accuracy was evaluated by comparing imputed scores with true ones. The correct imputation rate was >0.9 in 92% of markers. The square of correlation coeffi cient between true genotypes and mean imputed genotypes was >0.6 in 90% of the markers. Factors affecting imputation accuracy were minor allele frequency, linkage disequilibrium with neighbor common markers, minimum distance to the closest common marker, and degree of differentiation among subpopulations. Actual quantitative trait loci (QTL) would be unobserved in both reference and experimental panels. Markers masked in both panels to mimic this situation sometimes showed larger correlation to imputed markers than to typed common markers, indicating that imputation can sometimes capture the variation of unknown QTL better than the genotypes of common markers. H. Iwata, National Agriculture and Food Research Organization, National Agricultural Research Center, Tsukuba, Ibaraki 305-8666, Japan; J.-L. Jannink, USDA-ARS, R.W. Holley Center for Agriculture and Health, Cornell Univ., Ithaca, NY 14853. H. Iwata, current address: Univ. of Tokyo, Graduate School of Agricultural and Life Sciences, Bunkyo, Tokyo 113-8657, Japan. Received 9 Aug. 2009. *Corresponding author ([email protected]). Abbreviations: BOPA, barley oligonucleotide pool assay; CAP, Coordinated Agricultural Project; DArT, diversity arrays technology; LD, linkage disequilibrium; MAF, minor allele frequency; POPA, pilot oligonucleotide pool assay; QTL, quantitative trait loci; SNP, single nucleotide polymorphism. Published in Crop Sci. 50:1269–1278 (2010). doi: 10.2135/cropsci2009.08.0434 Published online 20 Apr. 2010. © Crop Science Society of America | 5585 Guilford Rd., Madison, WI 53711 USA 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.