quantitative trait locus quantitative trait locus a quantitative trait locus (qtl) is a locus (section of dna) that correlates with variation of a quantitative trait in the phenotype of a population of organisms. qtls are mapped by identifying which molecular markers (such as snps or aflps) correlate with an observed trait. this is often an early step in identifying the actual genes that cause the trait variation. definition a quantitative trait locus (qtl) is a region of dna which is associated with a particular phenotypic trait, which varies in degree and which can be attributed to polygenic effects, i.e., the product of two or more genes, and their environment. these qtls are often found on different chromosomes. the number of qtls which explain variation in the phenotypic trait indicates the genetic architecture of a trait. it may indicate that plant height is controlled by many genes of small effect, or by a few genes of large effect. typically, qtls underlie continuous traits (those traits which vary continuously, e.g. height) as opposed to discrete traits (traits that have two or several character values, e.g. red hair in humans, a recessive trait, or smooth vs. wrinkled peas used by mendel in his experiments). moreover, a single phenotypic trait is usually determined by many genes. consequently, many qtls are associated with a single trait. another use of qtls is to identify candidate genes underlying a trait. the dna sequence of any genes in this region can then be compared to a database of dna for genes whose function is already known, this task being fundamental for marker-assisted crop improvement. history mendelian inheritance was rediscovered at the beginning of the 20th century. as mendel's ideas spread, geneticists began to connect mendel's rules of inheritance of single factors to darwinian evolution. for early geneticists, it was not immediately clear that the smooth variation in traits like body size (i.e., incomplete dominance) was caused by the inheritance of single genetic factors. although darwin himself observed that inbred features of fancy pigeons were inherited in accordance with mendel's laws (although darwin didn't actually know about mendel's ideas when he made the observation), it was not obvious that these features selected by fancy pigeon breeders can similarly explain quantitative variation in nature. an early attempt by william ernest castle to unify the laws of mendelian inheritance with darwin's theory of speciation invoked the idea that species become distinct from one another as one species or the other acquires a novel mendelian factor. castle's conclusion was based on the observation that novel traits that could be studied in the lab and that show mendelian inheritance patterns reflect a large deviation from the wild type, and castle believed that acquisition of such features is the basis of "discontinuous variation" that characterizes speciation. darwin discussed the inheritance of similar mutant features but did not invoke them as a requirement of speciation. instead darwin used the emergence of such features in breeding populations as evidence that mutation can occur at random within breeding populations, which is a central premise of his model of selection in nature. later in his career, castle would refine his model for speciation to allow for small variation to contribute to speciation over time. he also was able to demonstrate this point by selectively breeding laboratory populations of rats to obtain a hooded phenotype over several generations. castle's was perhaps the first attempt made in the scientific literature to direct evolution by artificial selection of a trait with continuous underlying variation, however the practice had previously been widely employed in the development of agriculture to obtain livestock or plants with favorable features from populations that show quantitative variation in traits like body size or grain yield. castle's work was among the first to attempt to unify the recently rediscovered laws of mendelian inheritance with darwin's theory of evolution. still, it would be almost thirty years until the theoretical framework for evolution of complex traits would be widely formalized. in an early summary of the theory of evolution of continuous variation, sewall wright, a graduate student who trained under castle, summarized contemporary thinking about the genetic basis of quantitative natural variation: "as genetic studies continued, ever smaller differences were found to mendelize, and any character, sufficiently investigated, turned out to be affected by many factors." wright and others formalized population genetics theory that had been worked out over the preceding 30 years explaining how such traits can be inherited and create stably breeding populations with unique characteristics. quantitative trait genetics today leverages wright's observations about the statistical relationship between genotype and phenotype in families and populations to understand how certain genetic features can affect variation in natural and derived populations. quantitative traits