The final products of a breeding process are in fact the selected
genotypes sold to customers. In advanced breeding programs, with
lots of complex genetic interactions, the prediction of the final
phenotypes gets more and more problematic. At the same time
the genetic variation of the selected plant lines decreases. The
aim of the project is to explore the phenotypic flexibility of
a selected plant genotype by a brute force method coined genome interrogation.

Goal

The method depends on large-scale gene expression changes brought about by the introduction of genes encoding artificial transcription factors. In that manner, lots of different epigenetic phenotypes - including different metabolite profiles - can be observed in collections of plants sharing the same selected genotype. By selecting for plants with newly gained traits of interest, highly focused transcriptome and/or metabolome analyses can subsequently link a molecular signature to an observed phenotype, without being confused by genetic variation between different races or cultivars. Genome interrogation proved to be a very successful strategy in the model plant Arabidopsis.

Expected Results

By using Arabidopsis, we can link gained traits of interest to signature ratios of mRNA expression levels as well as to metabolomic markers, likely to be universal for many different plant species. The tools for genome interrogation are in principle generic, so genome interrogation can also be applied by breeders when their preferred species is amenable to genetic transformation.

Results

However, for many interesting traits, such as resistance to drought or other environmental cues, data from the model plant system can be guiding. By providing novel insights for fast and accurate phenotyping and prediction of phenotypes from genetic information, the project fits very well within the defined area “Genetics: Breeding by design”. By using genome interrogation to explore phenotypic variation of a given genotype under different conditions, the project also connects to the area “Environment: the plant in its environment”.