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

massive amounts of information for plant breeding (Stuber et al., 1999; Miflin, 2000), an option of improving Crop modelers and geneticists have developed a vision of their roles breeding efficiency is to develop and utilize a thorough in plant breeding from their own perspective. However, to improve breeding efficiency, interdisciplinary collaboration becomes increasunderstanding of morphophysiological factors that deingly important. The objective of this paper is to explore opportunities termine yield (Bindraban, 1997). However, only in a for collaboration between modelers and geneticists in ideotype breedlimited number of instances has plant physiology led to ing for high crop yield. The advent of molecular markers enables varicrop improvement; rather, its role in breeding so far ation of a complex trait to be dissected into the effects of quantitative has been to provide possible explanations for the imtrait loci (QTL) and assists the transfer of these QTL into desired provements that have been achieved. Miflin (2000) sugcultivars or lines. A recent study in which QTL information was linked gested that this situation may change in the future if to crop modeling has shown that QTL analysis removes part of random the links between physiology and genetics are established. errors of measured model input parameters and that QTL information This suggestion agrees with a main conclusion from an can successfully be coupled with crop models to replace measured extensive survey (Jackson et al., 1996) that there is a parameters. The QTL-based modeling overcomes the limitations in designing ideotypes by using models that ignore the inheritance of model general agreement among plant breeders and physioloinput traits. On the other hand, crop modeling can potentially be a gists that physiological knowledge can be applied to powerful tool to resolve genotype environment interactions and to improve breeding efficiency in the future. dissect yield into characters that might be under simpler genetic conAs early as in the 1960s, Donald (1968) proposed an trol. Based on the complementary aspects of crop modeling and QTL approach based much more explicitly on the design of mapping, we propose an approach that integrates marker-assisted plants or ideotypes for target environment, using known selection into model-based ideotype framework to support breeding principles of physiology and agronomy. Rasmusson for high crop yield. For this approach to be effective, there is a need (1987) suggested improvements to Donald’s approach, to develop crop models that are capable of predicting yield differences considering correlations between traits, and designed a among genotypes in a population under various environmental conbarley (Hordeum vulgare L.) ideotype for the Midwest ditions. USA with desired changes in culm, leaf, and head characteristics. Rasmusson (1991) reported that while some characteristics appeared to afford little opportunities B for high-yielding crop cultivars for spefor obtaining gains, others did show more promise. Based cific environments is a major challenge to feed growon the concept of ideotype approach, International Rice ing world populations. Through extensive selection, based Research Institute (IRRI) launched a program in 1989 largely on empirical field observations, breeders have to develop a “new plant type” rice that combines multibeen successful in creating high-yielding cultivars. In ple innovations (Peng et al., 1999). While so far these many instances, progress has been attained from changes new lines have not broken the yield barrier as hoped for, in a relatively few genes, e.g., those involved in plant progress is being made at IRRI with refined ideotype height and photoperiodism (Miflin, 2000). However, designs (S. Peng, personal communication, 2002). A further improvement has been increasingly complex and convincing example of ideotype approach is the breeddifficult (Bindraban, 1997), and in some crops such as ing for the superhybrid rice by Professor Yuan Longrice (Oryza sativa L.), no progress in increasing yield ping’s group in China. Rather than count on heterosis potential has been achieved in the past decades (Peng alone to raise yields, he also incorporated morphophysiet al., 1999). Difficulties in manipulating yield are reological characters such as long, narrow and erect top lated to its genetic complexity: polygenic nature, interleaves and large panicles that hang close to ground, the actions between genes (epistasis), and environmentcharacteristics that physiologists have expected to endependent expression of genes (Ribaut and Hoisington, hance efficiency of crop light capture (Setter et al., 1995). 1998). For more efficient crop improvement, joint interField trials at four separate locations showed potential disciplinary ventures to develop new knowledge and tools yields of the superhybrid were 15 to 20% higher than are increasingly becoming important (Shorter et al., 1991). 10.5 t ha 1 for existing hybrids (Normile, 1999). Besides recent developments in genomics (such as Using crop physiology in ideotype breeding can be genome sequencing) that will provide useful tools and more feasible than ever because of the development of dynamic process-based crop growth simulation models X. Yin and M.J. Kropff, Crop and Weed Ecol. Group, Wageningen (crop models hereafter). These models quantify causalUniv., P.O. Box 430, 6700 AK Wageningen, the Netherlands; P. Stam, Lab. of Plant Breeding, Wageningen Univ., P.O. Box 386, 6700 AJ Wageningen, the Netherlands; and A.H.C.M. Schapendonk, Plant Abbreviations: AFLP, amplification fragment length polymorphism; Dynamics, Englaan 8, 6703 EW Wageningen, the Netherlands. Joint G E, genotype environment interaction; h2, heritability; MAB, contrib. from Plant Res. Int. and the C.T. de Wit Graduate School for marker-assisted breeding; QTL, quantitative trait locus or loci; QTL Prod. Ecol. and Resour. Conserv. Received 1 May 2001. *CorrespondE, quantitative trait loci environment interaction; RFLP, restriction ing author ([email protected]). fragment length polymorphism; RIL, recombinant inbred line; SLA, specific leaf area. Published in Agron. J. 95:90–98 (2003).