B. Weisshaar: Genome Research
Plant Genetics and Crop Genomics
Structural and functional genomics, next generation sequencing and bioinformatics, classical genetics and molecular biology – these are our tools to investigate plant regulatory networks and to generate knowledge that can be transferred from model systems to agronomically relevant crops.
Previous and Current Research
Plants are essential. They bind carbon and produce oxygen, they preserve soils and water, they serve as food and feed, they provide wood and fibre as well as starch and biofuels – to name just a few aspects of their importance. Deciphering plant genomes and unraveling their functions is key to understand plant development, responses to the environment and to the application of knowledge to crops. The Chair of Genome Research is dedicated to structural and functional genomics in plants. For many of our projects we use the model system Arabidopsis thaliana, a small crucifer and one of the first eukaryotes whose genome was fully sequenced back in the year 2000. Gene functions in plants are, however, not accessible by targeted knock out via homologous recombination. Instead, collections of sequence-indexed insertion mutants are used for reverse genetic experimental approaches. With the GABI-Kat project we host the largest population of such T-DNA mutants in Europe and the second worldwide. Scientists can search the project database for lines with insertions in their genes of interest and place orders for relevant lines via the Internet. For about 2,800 A. thaliana genes insertion alleles are available from GABI-Kat only. Alleles from the GABI-Kat population make a significant contribution to saturate the A. thaliana genome, which contains about 27,000 protein-coding genes, with NULL mutations. In some of our other projects we use these alleles to identify new gene activities and to unravel regulatory networks of transcription factors with a focus on flavonoid biosynthesis control and seed coat development. As a non transgenic tool we have also established the TILLING technology for the detection of point mutations in A. thaliana and crop species like rapeseed.
Future Projects and Aims
In the last few years, tremendous progress was made in the development of new DNA sequencing technologies. We are part of a project to determine the structure and the sequence of the genome of sugar beet, and this project has profited from these technological advances. The rapidly increasing number of available plant genome sequences and the affordability to produce them offers great opportunities for comparative genomics. In cooperation with German grape breeding experts, we will use this approach to understand mechanisms that provide pathogen resistance in grape. We address this by comparing the genomes of resistant and susceptible varieties. RNAseq will be used to compare vegetative and reproductive structures as well as early and late flowering cultivars to identify the genes that control flowering time in grape. We will make use of ChipSeq to determine new transcription factor targets and characterize regulons in flavonoid biosynthesis on a genome wide scale. The ShoreMap approach will be applied to directly characterize mutants by sequencing without mapping and cloning. The ultimate goal of our projects is to transfer knowledge from A. thaliana to crop species.