QTL mapping and association mapping.pptx

QTL mapping

1. QTLs Mapping

2. What is QTL? Quantitative Trait Locus

3. Goal of QTL mapping to identify the chromosomal regions within which one or more genes reside that effect the quantitative trait In practice, chromosomal regions identified in QTL mapping experiments rarely include just a single gene but many other genes not related to the trait

4. F our basic components to all QTL mapping experiment (1) Segregating or mapping population(s); ( 2) Phenotypic measurements of the quantitative trait(s) for all members of the mapping population; e.g plant height ( 3) Genetic marker data; ( 4) Statistical analysis for mapping QTLs and estimating the magnitude of their influence on phenotype

5. Steps for QTL mapping Step 1. Mate two parent trees at the extremes of the phenotypic distribution of the trait (e.g. a large tree and a small tree) that are also different for a large number of genetic markers (e.g. AA versus aa ). Mate an F1 progeny that is intermediate for the phenotype and heterozygous at marker loci with a similar F1 ( F1'). This can be either a full-sib mating or more often a cross between two unrelated F1 's. The progeny resulting from the F1 x F1' mating segregate for both the phenotype and the genetic markers . Step 2. Each of the progeny is genotyped at all marker loci. In the example the B locus marker is codominant so both homozygotes (BB andbb ) and the heterozygote (Bb) can be scored .

6. Step 3 . A statistical test is then performed to test for differences in mean phenotypic values among genotypic classes. In this example, BB genotypes are associated with large trees, Bb heterozygotes with intermediate size trees and bb homozygotes with small trees. The inference that can be drawn is that a QTL for tree size resides on the chromosome somewhere near the B genetic marker. This analysis is performed for all markers on all chromosomes to discover QTLs controlling the phenotype

7. C onclusion the B locus appears to be associated with tree size because BB homozygotes are large trees, Bb heterozygotes are intermediate size trees and bb homozygotes are small trees. It is easy to see how the effects of alternate alleles at the B locus on tree size phenotype can be estimated.