Validation of a major QTL for scab resistance with SSR markers and use of marker-assisted selection in wheat W-C. Z HOU 1 , F. L. K OLB 1,4 , G-H. B AI 2 , L. L. D OMIER 3 , L. K. B OZE 1 and N. J. S MITH 1 1 Department of Crop Science, University of Illinois, 1102 South Goodwin Avenue, Urbana, IL 61801; 2 Department of Plant & Soil Sciences, Oklahoma State University, Stillwater, OK 74078; 3 Department of Crop Sciences, USDA-ARS-MWA, 1102 South Goodwin Avenue, Urbana, IL 61801, USA; 4 Corresponding author, E-mail: f-kolb@uiuc.edu With 6 figures and 5 tables Received June 6, 2002/Accepted October 17, 2002 Communicated by P. Wehling Abstract The objectives of this study were to validate the major quantitative trait locus (QTL) for scab resistance on the short arm of chromosome 3B in bread wheat and to isolate near-isogenic lines for this QTL using marker-assisted selection (MAS). Two resistant by susceptible popu- lations, both using ‘Ning7840’ as the source of resistance, were developed to examine the effect of the 3BS QTL in different genetic backgrounds. Data for scab resistance and simple sequence repeat (SSR) markers linked to the resistance QTL were analyzed in the F 2:3 lines of one population and in the F 3:4 lines of the other. Markers linked to the major QTL on chromosome 3BS in the original mapping population (‘Ning7840’/‘Clark’) were closely associated with scab resistance in both validation populations. Marker-assisted selection for the QTL with the SSR markers combined with phenotypic selection was more effective than selection based solely on phenotypic evalua- tion in early generations. Marker-assisted selection of the major QTL during the seedling stage plus phenotypic selection after flowering effectively identified scab resistant lines in this experiment. Near- isogenic lines for this 3BS QTL were isolated from the F 6 generation of the cross ‘Ning7840’/‘IL89–7978’ based on two flanking SSR markers, Xgwm389 and Xbarc147. Based on these results, MAS for the major scab resistance QTL can improve selection efficiency and may facilitate stacking of scab resistance genes from different sources. Key words: Triticumaestivum –– Fusarium head blight –– SSR markers –– near-isogenic lines Wheat head scab, also called Fusarium head blight, is a serious disease of wheat (Triticumaestivum L.) in humid and semihumid areas of the world (Schroeder and Christensen 1963). Scab epidemics cause significant losses in grain yield and quality (McMullen et al. 1997). Scab infection in susceptible varieties results in altered protein content, reduced test weight, and mycotoxin contamination (Wong et al. 1995, Wu et al. 1996, Wu et al. 1997). Growing resistant varieties is an effective way of reducing losses from scab infection. (Bai and Shaner 1994, Bai 1995, Mesterhazy 1995, Parry et al. 1995, McMullen et al. 1997). Scab resistance is quantitatively inherited and involves several loci on different chromosomes (Yao et al. 1997, Buerstmayr et al. 1999, Waldron et al. 1999, Bai et al. 2000, Anderson et al. 2001, Zhou et al. 2002a,b). Evaluation of scab resistance is time consuming, laborious and costly because the inheritance of resistance is complex and phenotypic expression is significantly affected by environmental factors (Bai 1995). Molecular mapping has been successfully used to elucidate the scab resistance quantitative trait locus (QTL). Restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers linked to scab resistance QTLs have been reported (Bai et al. 1999, Waldron et al. 1999, Zhou et al. 2000, Anderson et al. 2001, Buerstmayr et al. 2002). Simple sequence repeat markers linked to major scab resistance QTLs provide a new approach for selection of resistant plants from segregating populations and provide a fast, cheap, accurate and efficient method for tagging QTLs with agronomic importance in breeding programmes. Marker-assisted selection can facilitate the rapid introgression and combination of different scab resistance QTLs. The codominant nature of SSR markers facilitates differentiation of homozygotes and hetero- zygotes in early generations of segregating populations. The target homozygotes can be accurately selected in early gener- ations, but this is not as effective with phenotypic selection because many plants selected according to phenotypic selec- tion in early generations will be heterozygous. This feature can significantly speed up the breeding process and improve selection efficiency. Recently, a major QTL for scab resistance was identified on chromosome 3BS by a number of research groups using various types of markers (Bai et al. 1999, Anderson et al. 1999, Waldron et al. 1999, Zhou et al. 2000, Chen et al. 2000, Gupta et al. 2000, Gupta et al. 2001, Anderson et al. 2001, Buerstm- ayr et al. 2002, Zhou et al. 2002a,b). Some of the markers closely linked to the QTL explained approximately 50% of the phenotypic variation in the recombinant inbred line popula- tion derived from ‘Ning7840’/‘Clark’ (Bai et al. 1999), while smaller percentages of the phenotypic variation were explained in other populations (Waldron et al. 1999). In addition, a recessive epistatic effect of 3BS QTL on a 2BL QTL has been reported, and it has been suggested that selection for the 3BS QTL should be a high priority in breeding for scab resistance (Zhou et al. 2002a,b). The genetic effect of the 3BS QTL and the linkage between markers and this QTL were evaluated using either recombinant inbred lines (RIL) or doubled haploid populations. For molecular markers to be useful in plant breeding, the markers must be validated by examining the segregation of markers with QTLs for the trait of interest in different genetic backgrounds (Langridge and Chambers 1998). Validation of the mapped 3BS major scab resistance QTL in additional wheat breeding populations is important because many loci have been identified from similar sources of resistance, but some of these loci have not had consistent effects across environments (Kolb et al. 2001). Validation of U. S. Copyright Clearance Center Code Statement: 0179–9541/2003/2201–0040 $ 15.00/0 www.blackwell.de/synergy Plant Breeding 122, 40—46 (2003) Ó 2003 Blackwell Verlag, Berlin ISSN 0179-9541