Question

You conduct a QTL mapping experiment to find the genes that contribute to variation in flower color in a plant species. You find that for genetic marker A, the mean flower color is significantly darker in individuals with the A1 allele than for individuals with the A2 allele. What do you conclude? Only one sentence needed for this answer.

Answer 1

Answer:

The pale pink color of M. lewisii flowers results from a low concentration of anthocyanins and the absence of carotenoids (except in the nectar guides). The red color of M. cardinalis flowers is produced by a combination of high concentrations of both pigments. Both anthocyanin and carotenoid concentrations contribute to pollinator discrimination between the two species in their natural habitat.

A major quantitative trait locus (QTL) underlying floral anthocyanin concentration was identified as a dominant repressor in M. lewisii in a previous QTL mapping experiment. The recessive allele in M. cardinalis leads to higher anthocyanin concentration in homozygotes. Here we generate genome sequences of these two species to facilitate fine-scale genetic dissection of this major anthocyanin QTL and to establish an efficient in planta transformation system for M. lewisii to perform functional characterization of target genes by transgenic experiments.

QTL mapping will identify a genomic region containing one or more candidate genes affecting the trait. Determining which one(s) are causal is the next step. The most straightforward method is highresolution recombination mapping. However, this method is limited to QTL alleles with large effects and to organisms amenable to the experimental generation of tens of thousands of recombinants.

Otherwise, we need to seek corroborating evidence, such as DNA polymorphisms between alternative alleles of one of the candidate genes that could change the protein, a difference in mRNA expression levels between genotypes, or expression of RNA or protein in tissues thought to be relevant to the trait. Associations of markers in candidate genes with the trait that are replicated in independent studies also constitute strong evidence that the gene affects variation in the trait. In model organisms, it is possible to test whether a mutation in one of the candidate genes affects the trait, or whether the mutant gene fails to complement QTL alleles.

Formal proof that a specific allelic substitution affects the trait comes from replacing the allele of a candidate gene in one strain with that of the other, without introducing any other changes in the genetic background, but this is not possible in very many organisms.