Linking ecophysiological modelling with quantitative genetics to support marker-assisted crop design for improved yields of rice (Oryza sativa) under drought stress

Background and Aims Genetic markers can be used in combination with ecophysiological crop models to predict the performance of genotypes. Crop models can estimate the contribution of individual markers to crop performance in given environments. The objectives of this study were to explore the use of crop models to design markers and virtual ideotypes for improving yields of rice (Oryza sativa) under drought stress. Methods Using the model GECROS, crop yield was dissected into seven easily measured parameters. Loci for these parameters were identified for a rice population of 94 introgression lines (ILs) derived from two parents differing in drought tolerance. Marker-based values of ILs for each of these parameters were estimated from additive allele effects of the loci, and were fed to the model in order to simulate yields of the ILs grown under well-watered and drought conditions and in order to design virtual ideotypes for those conditions. Key Results To account for genotypic yield differences, it was necessary to parameterize the model for differences in an additional trait 'total crop nitrogen uptake' (N-max) among the ILs. Genetic variation in N-max had the most significant effect on yield; five other parameters also significantly influenced yield, but seed weight and leaf photosynthesis did not. Using the marker-based parameter values, GECROS also simulated yield variation among 251 recombinant inbred lines of the same parents. The model-based dissection approach detected more markers than the analysis using only yield per se. Model-based sensitivity analysis ranked all markers for their importance in determining yield differences among the ILs. Virtual ideotypes based on markers identified by modelling had 10-36% more yield than those based on markers for yield per se. Conclusions This study outlines a genotype-to-phenotype approach that exploits the potential value of marker-based crop modelling in developing new plant types with high yields. The approach can provide more markers for selection programmes for specific environments whilst also allowing for prioritization. Crop modelling is thus a powerful tool for marker design for improved rice yields and for ideotyping under contrasting conditions.