Many traits important to crop production, such as yield potential, end-use quality characteristics, and stress tolerance, are quantitatively inherited, i.e., they are controlled by many genes acting together to produce the desired plant type. These quantitative traits are characterized by continuous variation, in contrast to qualitative traits, which show discrete variation and are controlled by one or two major genes (Fig. 1). Because of the often subtle differences among individuals for quantitative traits, they are evaluated by precise measurement rather than by classification.
Until recently, it has been difficult to focus on the individual genes (known as polygenes or QTLs) that contribute to quantitative traits. However, the advent of molecular markers and the chromosome maps derived from them has enabled the genetic control of quantitative traits to be dissected into its component parts. By applying the methodology known as QTL analysis in an appropriate population, a researcher can locate the genes of interest in specific chromosome regions, estimate the size of their effects, and determine whether their gene action is additive or dominant. These are initial steps in manipulating the genes in breeding programs to produce superior varieties.
QTL analysis is a multi-step process outlined in Fig. 2. Each of the major components, indicated by the numbers 1 to 4, will be described in the sections that follow. Careful implementation of each component is critical to success in accurately identifying QTLs.