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Title: EFFECT OF POPULATION SIZE ON THE ESTIMATION OF BARLEY STRIPE RUST QTL

Author
item VALES, M - OREGON STATE UNIV
item SCHON, C - PLT BREED INST, GERMANY
item CAPETTINI, F - ICARDA/CIMMYT MEXICO
item Chen, Xianming
item COREY, A - OREGON STATE UNIV
item MATHER, D - UNIVERSITY OF ADELAIDE
item MUNDT, C - OREGON STATE UNIV
item RICHARDSON, K - OREGON STATE UNIV
item SANDOVAL-ISLAS, J - MEXIC0
item UTZ, H - PLT BREED INST, GERMANY
item HAYES, P - OREGON STATE UNIV

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/27/2005
Publication Date: 11/1/2005
Citation: Vales, M.I., Schon, C.C., Capettini, F., Chen, X., Corey, A.E., Mather, D.E., Mundt, C.C., Richardson, K.L., Sandoval-Islas, J.S., Utz, H.F., Hayes, P.M. 2005. Effect of population size on the estimation of barley stripe rust qtl. Theor. Appl. Genet. 111:1260-1270.

Interpretive Summary: 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 with a large (409 lines) doubled haploid population. 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 stripe rust resistance QTL genes, but the susceptible parent also contributed some resistance genes. 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. The information is useful in selecting population size and methods to study QTL and also useful in breeding barley cultivars for resistance to stripe rust.

Technical 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 vs. phenotyping.