Partnership Green Genetics
Title: Finding key phenotypic markers by genome interrogation
Abstract
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. 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. 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.
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”.
Names and addresses:
Dr. Bert J. van der Zaal
Institute of Biology Leiden (IBL), Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE Leiden (tel:
071-5274760)
Dr. Young H. Choi (same address, tel:071-52704510)
Dr. Christiaan Henkel (same address, tel: 071-5274750)
Preliminary budget forecast:
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1 AIO (4 years): 187,000
1 Postdoc (4 years): 250,000
Materials, travels, etc. : 4x10,000 each = 80,000
Extra costs RNA seqs / NMR time: 40,000
Total: 560,000