Topic 23.20

Genetic Mapping Of Dormancy: Quantitative Trait Locus (QTL) Scoring of Vegetative Dormancy Combined with a Candidate Gene Approach

Complex traits, e.g. dormancy, are affected by many different, often unlinked genes. Consequently, attempts to map them result in continuous, or quantitative, variation within a mapping population. Quantitative trait locus (QTL) mapping is used in these instances to map individual genes affecting the trait. In QTL mapping, inbred lines that differ in the trait of interest are crossed and an F₂ population is produced. The F₂ population has continuous variation for the trait of interest, and the goal of the analysis is to determine which chromosomal segments contain genes affecting the trait. Using marker loci along each chromosome (loci that have different alleles between the parental inbred lines), the genotypes of entire chromosomal segments in each F₂ individual can be inferred as being homozygous for one or the other parental lines or heterozygous (Web Figure 23.20.A). If the inheritance of a chromosomal segment is correlated with the trait of interest, then a gene affecting the trait is likely to be between the two marker loci. By analyzing chromosomal segments along each of the chromosomes, the number and locations of genes affecting the quantitative trait can be determined.

Web Figure 23.20.A Two parental (P) inbred lines, A & B, which differ for a trait of interest (e.g. dormancy) are crossed to produce heterozygote F₁ progeny which have an intermediate degree of dormancy. Only one chromosome pair is depicted for simplicity. The F₁ progeny are crossed to produce a large segregating F₂ population (usually 100-500 individuals are analyzed, here only five individuals, I-V, are depicted). Because of recombination during F₁ meiosis, the F₂ individuals have varying genetic combinations of the original inbred lines (depicted by shading of chromosomes) and have continuous variation, from high to low, in degree of dormancy. In order to estimate whether segments of the chromosome are homozygous for one of the parental-lines or heterozygote, the F₂ individuals are scored for marker loci (1-6) along the chromosome. For example, loci 1 & 2 are identified as homozygous for A-line alleles in individual III, as heterozygous in individuals I & V and as homozygous for B-line alleles in individuals II & IV. The F₂ individuals are also scored for their dormancy. After scoring many F₂ individuals a correlation between the genotypes at locus 1 & 2 and phenotype is determined and therefore this segment likely contains at least one gene affecting dormancy (bar graph). The analysis is repeated for each chromosomal segment to identify which ones are likely to contain genes affecting dormancy. (Click image to enlarge.)

Candidate genes are specific loci, identified by predicted biochemical function or homology to regulatory genes from other species, that are suspected of affecting the trait of interest. Molecular differences between the parental alleles at these loci can be used to determine whether they map to the same region as any of the QTLs, thereby supporting the hypothesis that a given gene contributes to regulation of the trait.