Quantitative trait loci and global expression patterns offer insight into phenotypic plasticity
Abstract
Phenotypic plasticity, i.e. changes in phenotype with environment, may allow organisms
to produce optimal phenotypes in all environments (adaptive plasticity). There is
considerable discussion about the genetic mechanisms for phenotypic plasticity.
However, there is some agreement that changes in gene expression must be involved. In
order to examine how natural selection has acted on phenotypic plasticity on the trait
bolting time trait (transition to reproduction) and gene expression patterns in past
populations, a set of Recombinant Inbred Lines (RILs) of Arabidopsis thaliana were
used. We tested the effect of cold-treating seeds (stratification) on bolting time in
Arabidopsis thaliana. Cold stratification of seeds may be one environmental factor
contributing to variation in spring versus fall germination in A. thaliana populations.
Variation in both the direction and degree of plasticity was observed in a set of 120 RILs
screened; genotypic selection analysis showed that past selection had favored bolting
earlier in both environments. Three RILs that displayed extreme plasticities for bolting
time in opposing directions across cold treatments were identified and global gene
expression patterns were measured in a microarray experiment. A total of 294 genes were
identified as being differentially expressed across cold treatments for the three extreme
RILs (Fold change of >2; p-value<0.05). In addition, Quantitative Trait Loci (QTL) for
bolting time were mapped in the complete set of RILs. Five QTL were mapped in the
cold environment and three QTL were mapped in the no-cold environment explaining
40% and 30% of the observed phenotypic variation, respectively. QTL underlying
variation in bolting time were screened for differentially expressed genes from the
microarray study to identify candidate genes. Ninety-three of the identified genes colocalized
to bolting time QTL, with kinesis and transferases being overrepresented in the
expressed QTLs. Few studies have combined microarray and QTL data, and this study
will offer insight into the genetic mechanism of phenotypic plasticity.
Subject
DNA microarrays
Climatic changes
Gene mapping
Arabidopsis thaliana
Phenotypic plasticity
Permanent Link
http://digital.library.wisc.edu/1793/56882Description
A Thesis Submitted In Partial Fulfillment of the Requirements For the Degree of Master of Science - Biology