Understanding the genetic control of quantitatively inherited traits is fundamental to agricultural, evolutionary and biomedical genetic research. A detailed picture of the genetic architecture of quantitative traits can be elucidated with a well-saturated genetic map of molecular markers. The parameters that quantify the genetic architecture of a trait include the number of individual quantitative trait loci (QTL), their genomic positions, their genetic actions and interactions, and their responsiveness to biotic or abiotic factors. A variety of genetic designs and statistical models have been developed to estimate and test these architecture-modeling parameters. With the availability of very highly abundant single nucleotide polymorphism markers, DNA sequence variants, i.e., quantitative trait nucleotides (QTNs), which contribute to quantitative variation can be identified. A newly emerging active area - functional mapping, has shown its value to unravel the genetic machinery of dynamic traits at the QTL or QTN level that change their phenotypes with time or other variables. Functional mapping provides a quantitative framework for testing the interplay between genetic effects and trait formation and development and, thus, appeals to push statistical genetic analysis and modeling into the context of developmental biology. Some of the statistical methods for genetic mapping have been patented.