Genetics, Vol. 168, 435-446, September 2004, Copyright © 2004
doi:10.1534/genetics.104.026831

Linkage Disequilibrium Mapping of Yield and Yield Stability in Modern Spring Barley Cultivars

Arnold T. W. Kraakman, Rients E. Niks, Petra M. M. M. Van den Berg, Piet Stam and Fred A. Van Eeuwijk¹

Wageningen University and Research Center, Laboratory of Plant Breeding, 6700 AJ Wageningen, The Netherlands

¹ Corresponding author: Wageningen University and Research Center, Laboratory of Plant Breeding, P.O. Box 386, 6700 AJ Wageningen, Binnenhaven 5, 6709 PD Wageningen, The Netherlands.
E-mail: fred.vaneeuwijk{at}wur.nl

Associations between markers and complex quantitative traits were investigated in a collection of 146 modern two-row spring barley cultivars, representing the current commercial germ plasm in Europe. Using 236 AFLP markers, associations between markers were found for markers as far apart as 10 cM. Subsequently, for the 146 cultivars the complex traits mean yield, adaptability (Finlay-Wilkinson slope), and stability (deviations from regression) were estimated from the analysis of variety trial data. Regression of those traits on individual marker data disclosed marker-trait associations for mean yield and yield stability. Support for identified associations was obtained from association profiles, i.e., from plots of P-values against chromosome positions. In addition, many of the associated markers were located in regions where earlier QTL were found for yield and yield components. To study the oligogenic genetic base of the traits in more detail, multiple linear regression of the traits on markers was carried out, using stepwise selection. By this procedure, 18–20 markers that accounted for 40–58% of the variation were selected. Our results indicate that association mapping approaches can be a viable alternative to classical QTL approaches based on crosses between inbred lines, especially for complex traits with costly measurements.

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