Mapping QTL with Molecular Markers

Application of Molecular Markers to Selection

What Is A Quantitative Trait Locus?

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What Is A Quantitative Trait Locus?

Traditional quantitative genetic research defined a quantitative trait in terms of variances. The total phenotypic was first partitioned into genetic and environmental variances. The genetic variance could then be further divided into additive, dominance and epistatic effects. From this information it was then possible to estimate the heritability of the trait and predict the response of the trait to selection. It was also possible to estimate the minimum number of genes which controlled the trait.

Mapping markers linked to QTLs identifies regions of the genome that may contain genes involved in the expression of the quantitative trait. But what functions could these genes be encoding. To answer this question we should consider a trait such as yield. What types of qualitative genes (genes inherited as simple genetic factors) could be involved in the expression of yield? The first event required for yield is meiosis. Therefore any gene that is involved in gamete formation could potentially be considered a QTL. Any of the genes involved in the protein and carbohydrate biosynthetic pathways could also affect the final yield of a plant and could also be considered to be QTLs. As we saw above, the markers associated with a QTL each account for only a portion of the genetic variance. Likewise each of these genes of known function may only account for a portion of the final yield. An important question that can now be posed is whether any known genes map as QTLs.

Beavis et al. (1991, TAG 83:141-145) analyzed four populations of maize and found molecular markers linked to plant height. No marker was consistently associated as a QTL with plant height in all four populations. Each of the ten maize chromosomes contained a marker linked to a QTL for at least one of the four populations. The authors further were able to demonstrate that a number of the QTLs identified by the molecular markers mapped to regions containing genes known to have a qualitative effect on plant height. For example, on chromosome 9 the gene d3 resides within 10 cM of a plant height QTL. This gene is involved in gibberellic acid sensitivity. Mutants do not respond to the hormone and do not undergo the normal cell elongation. These mutants are phenotypically shorter than normal maize plants. The question that needs to be raised is if the QTL that was being identified by the molecular marker is actually the d3 gene. It could be possible that what is actually being measured by the marker is the linkage of the marker with the gene.

The statistical analysis of quantitative traits provided valuable information for the plant breeder. Molecular analysis of quantitative traits now provides new tools, not only as selection tools for plant breeding, but as starting points for the cloning of these genes. These objectives could not have been realized without molecular markers.

Copyright © 1998. Phillip McClean