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The causal molecular variants that affect QTL are called quantitative trait nucleotides (QTNs). The distribution of QTN allele frequencies can indicate the nature of the selective forces operating on the trait. Inference of QTN allele frequencies is limited to association mapping (see Chapter 20) designs in which all the variants in a candidate gene or gene region have been identified. QTNs allow researchers to map phenotype to genotype in the absence of biological context. QTNs consist of two components: eQTL(expression quantitative trait loci) and QTT(quantitative trait transcripts) (Figure 4.8).

Figure 4.8 Systems genetics of complex traits: An integrative framework showing the relationship between DNA sequence variation and quantitative variation for gene expression and an organismal phenotype. QTNs allow researchers to map phenotype to genotype in the absence of biological context. In order to gain this context, they need to describe the flow of information from DNA to the organismal phenotype through RNA intermediates, proteins and other molecular endophenotypes.

The eQTL is a region of the genome containing one or more genes that affect variation in gene expression, which is identified by linkage to polymorphic marker loci. It is technically a marriage of high‐throughput expression profiling technology and QTL analysis. QTT is a transcript for which variation in its expression is correlated with variation in an organismal level quantitative trait phenotype. Numerous (even several hundreds) of QTT are believed to be associated with any single quantitative trait phenotype. Further, these QTT are genetically correlated.