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Effect of population size on the estimation of QTL: a test using resistance to barley stripe rust
Authors:M. I. Vales  C. C. Schön  F. Capettini  X. M. Chen  A. E. Corey  D. E. Mather  C. C. Mundt  K. L. Richardson  J. S. Sandoval-Islas  H. F. Utz  P. M. Hayes
Affiliation:(1) Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331-3002, USA;(2) State Plant Breeding Institute, University of Hohenheim, 70593 Stuttgart, Germany;(3) ICARDA/CIMMYT Barley Program, Apdo. Postal 6-641, 06600 Mexico, Mexico;(4) U.S. Department of Agriculture, Agricultural Research Service, Washington State University, Pullman, WA 99164-6430, USA;(5) School of Agriculture and Wine, University of Adelaide / Molecular Plant Breeding Cooperative Research Centre, PMB 1, Glen Osmond, SA, 5064, Australia;(6) Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331-2902, USA;(7) Instituto de Fitosanidad, Colegio de Postgraduados, Montecillo, 56230 Mexico, Mexico;(8) Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany
Abstract:The limited population sizes used in many quantitative trait locus (QTL) detection experiments can lead to underestimation of QTL number, overestimation of QTL effects, and failure to quantify QTL interactions. We used the barley/barley stripe rust pathosystem to evaluate the effect of population size on the estimation of QTL parameters. We generated a large (n=409) population of doubled haploid lines derived from the cross of two inbred lines, BCD47 and Baronesse. This population was evaluated for barley stripe rust severity in the Toluca Valley, Mexico, and in Washington State, USA, under field conditions. BCD47 was the principal donor of resistance QTL alleles, but the susceptible parent also contributed some resistance alleles. The major QTL, located on the long arm of chromosome 4H, close to the Mlo gene, accounted for up to 34% of the phenotypic variance. Subpopulations of different sizes were generated using three methods—resampling, selective genotyping, and selective phenotyping—to evaluate the effect of population size on the estimation of QTL parameters. In all cases, the number of QTL detected increased with population size. QTL with large effects were detected even in small populations, but QTL with small effects were detected only by increasing population size. Selective genotyping and/or selective phenotyping approaches could be effective strategies for reducing the costs associated with conducting QTL analysis in large populations. The method of choice will depend on the relative costs of genotyping versus phenotyping. Electronic Supplementary Material Supplementary material is available for this article at
Keywords:Hordeum vulgare    Puccinia striiformis f. sp. hordei   Quantitative trait loci  Selective genotyping  Selective phenotyping  Random sampling
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