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Crop Modeling, QTL Mapping, and Their Complementary Role in Plant Breeding

^a Crop and Weed Ecol. Group, Wageningen Univ., P.O. Box 430, 6700 AK Wageningen, the Netherlands
^b Lab. of Plant Breeding, Wageningen Univ., P.O. Box 386, 6700 AJ Wageningen, the Netherlands
^c Plant Dynamics, Englaan 8, 6703 EW Wageningen, the Netherlands

View larger version (31K): [in a new window]   Fig. 1. Seed weight of three F2 seed-color genotypes of a cross between two lines of bean (data of Sax, 1923).

View larger version (46K): [in a new window]   Fig. 2. Amplification fragment length polymorphism (AFLP) marker map for chromosome 3, established by the use of software JoinMap (Stam, 1993), for Apex x Prisma recombinant inbred line population of barley (redrawn from Yin et al., 1999b). The AFLP markers are labeled E45M55-408, E44M58-196, etc., and their map positions are counted in genetic map units, cM (1 cM corresponds to 1% recombination per meiosis), from the top terminal marker. The position of the denso dwarfing gene is highlighted.

View larger version (20K): [in a new window]   Fig. 3. The QTL mapping of six traits in barley (data of the 1997 field experiment reported by Yin et al., 1999b). The interval mapping method (Lander and Botstein, 1989) was used. By moving the position of the putative QTL along the genetic map (horizontal axis), a profile of the test statistics, QTL likelihood (LOD), was produced for each chromosome, and results are given here for chromosome 3. The peak of the LOD profile indicates the most likely position of a QTL affecting the trait under study. Results indicate a major QTL at 126.4 cM on chromosome 3 (note that this is also the position of the denso gene as shown in Fig. 2). A in each figure refers to the additive effect of this QTL on the trait, defined as (mean of dwarf genotypes - mean of nondwarf genotypes)/2. DS, developmental stage.

View larger version (23K): [in a new window]   Fig. 4. Plot of QTL likelihood (LOD) over chromosome 3 for specific leaf area (SLA) in barley measured at 27 d after emergence (DAE) and for SLA corrected at the same developmental stage (DS) of 0.35, roughly equivalent to the time of 27 DAE (redrawn from Yin et al., 1999a). The horizontal line at a height of 2.5 indicates the threshold for the presence of a QTL. The dotted curve is from the use of the interval mapping method (Lander and Botstein, 1989), and the thin continuous one is from the use of the multiple-QTL mapping method (Jansen, 1995).

View larger version (27K): [in a new window]   Fig. 5. Comparisons between observed grain yields in barley and those predicted by the two models, QTL-BL and SYP-BL (redrawn from Yin et al., 2000a). Because the denso gene affected most model input traits, QTL-BL predicted two clusters in yields that match the segregation of the gene (the dwarf recombinant inbred lines had higher yields than the tall lines).

View larger version (38K): [in a new window]   Fig. 6. Proposed framework of combining crop modeling and QTL mapping for an integrated approach to select crop ideotype for a specific environment. The dotted part in the figure is optional for this framework because development of crop models that are capable of resolving epistasis may take a long-term effort. G x E, genotype x environment interaction; AFLP, amplification fragment length polymorphism.