Quantitative Trait Locus (QTL) Analysis 2 Glossary


One of the different forms of a gene (or marker) that can exist at a single locus. A single allele for each locus is inherited separately from each parent.


A genetic structure in a cell composed of condensed DNA, which contains the genetic code for an organism.

gene action

The phenotypic response observed when the dosage of an allele changes. For example, in the allelic series AA, AB, and BB, the dosage of the B allele changes from 0 to 1 to 2. Gene action may be additive (if AA<AB<BB), dominant (if AB=BB), or overdominant (if AB>BB).


The inherited association of alleles at loci due to their proximity on a chromosome. The degree of linkage is estimated as the percentage of recombination between loci. Linkage maps are thus based on mathematical distances among loci rather than actual physical distances. However, the order of loci along a chromosome in a linkage map should represent the actual order.

linkage disequilibrium

The condition whereby alleles at two loci occur together in a population at a greater frequency than that predicted by the product of the individual allele frequencies.


The site on a chromosome where a particular gene (or other sequence) is located (plural=loci).


Abbreviation for logarithm of odds, a significance measure used in maximum likelihood statistics. In interval mapping, the LOD score is log10 of the ratio of the probability that a QTL is present to the probability that a QTL is absent. For example, if the presence of a QTL is 1000 times more probable than its absence, then the LOD score = 3, because log10 of 1000 = 3.


An easy to detect trait controlled by a known gene. Markers, such as antibiotic or herbicide resistance, are often used to determine if an organism is transgenic.

molecular marker

An identifiable DNA sequence on a chromosome. A marker can be a gene, part of a gene, or a sequence in a non-gene region. SSR, RFLP, RAPD, and AFLP are acronyms for commonly used marker techniques.

phenotypic trait

An observable physical characteristic of an organism. See Phenotype.


The control of more than one trait by a single gene.


Existing in multiple forms. When a marker locus is polymorphic, there are detectable differences in DNA sequence at that locus.


Quantitative trait locus. (1) a locus that influences the expression of a quantitative trait. (2) a chromosome region detected by statistical analysis that is significantly associated with variation for a quantitative trait.


The characteristic that results from an expressing gene(s). Ex. Upright leaves, drought tolerance, Bt resistance. A trait can be influenced by the environment.