Functional mapping of genotype-environment interactions for soybean growth by a semiparametric approach

Abstract Background Functional mapping is a powerful approach for mapping quantitative trait loci (QTLs) that control biological processes. Functional mapping incorporates mathematical aspects of growth and development into a general QTL mapping framework and has been recently integrated with composite interval mapping to build up a so-called composite functional mapping model, aimed to separate multiple linked QTLs on the same chromosomal region. Results This article reports the principle of using composite functional mapping to estimate the effects of QTL-environment interactions on growth trajectories by parametrically modeling the tested QTL in a marker interval and nonparametrically modeling the markers outside the interval as co-factors. With this new model, we can characterize the dynamic patterns of the genetic effects of QTLs governing growth trajectories, estimate the global effects of the underlying QTLs during the course of growth and development, and test the differentiation in the shapes of QTL genotype-specific growth curves between different environments. By analyzing a real example from a soybean genome project, our model detects several QTLs that cause significant genotype-environment interactions for plant height growth processes. Conclusions The model provides a basis for deciphering the genetic architecture of trait expression adjusted to different biotic and abiotic environments for any organism.