Modeling QTL effects and MAS in plant breeding

The empirical evidence accumulated to date indicates that the genetic architecture of the different traits of organisms, emphasizing here those relevant to plant breeding, should be viewed as a genetic complexity continuum. This concept is not new to plant breeders. What is new is that geneticists and plant breeders can now apply high throughput molecular technologies to identify and study the genes and alleles responsible for the standing genetic and phenotypic variation for traits in elite breeding populations. Plant breeders undertake research to develop robust breeding strategies that take advantage of this growing body of trait genetics knowledge and seek breeding methods that can be practically applied to improve multiple traits to achieve defined breeding objectives. While experimental and quantitative methods are developed to detect quantitative trait loci (QTL) and to implement marker-assisted selection (MAS) for the detected trait QTL as components of a comprehensive plant breeding strategy, simulation modeling methods can be applied to quantify the robustness of the chosen QTL analysis and MAS methods for the trait genetics complexity continuum. We review methods that can be applied to model the effects of QTL and outcomes from MAS in plant breeding as our view of the trait genetic complexity continuum unfolds. Some key lessons from this body of research are discussed