Marnik Vuylsteke
Quantitative Genomics 
VIB Department of Plant Systems Biology, UGent

PhD: Univ. of Wageningen, Wageningen, The Netherlands, '99 Principal Investigator VIB since 2001

e-mail phone +32 9 331 38 60 ADDRESS

Current team members
Group leader: Marnik Vuylsteke
Postdoctoral scientist: Inge Van Daele
Ph.D. Students: Iris Pinheiro, Ives Vanstechelman, Katrijn Vannerum, Naïra Naouar, Stephanie De Vos, Valerie Devos
Support personnel: Ilse Vercauteren, Lien De Smet

Keywords
heterosis - gene expression profiling - haplotype

Science

Bridging the gap between heterozygosity and heterosis by quantifying transcriptional variation 
In the context of heterosis, there are a number of fundamental issues that we will explore with the quantitative gene expression profiling. The first is documentation of the heritability and degree of dominance of gene expression. The availability of genomic tools however, will allow us to address the additivity and the lack thereoff of gene expression in a systematic manner at the transcriptional level. The second issue deals with an explanation for heterosis. Classical quantitative genetic theory has formulated hypotheses and models for heterosis without regard to the molecular events (transcription, translation and protein interactions) that relate genotype to phenotype. Therefore, they may be of diminished utility for describing the molecular parameters that accompany heterosis. To build gene expression models to explain heterosis, one needs to assess the relative contributions of cis- and trans-acting factors to the expression of a gene and their identification. If transcription is controlled predominantly by cis-regulatory regions of a particular gene, then transcript abundance might often be expected to be additive. By contrast, transcription factors that vary in activity level between the parents are more likely to interact to produce a range of degrees of dominance.
Extensive sampling in the form of an Arabidopsis diallel cross, will be required not only to assess the generality of additive and non-additive gene expression but also to identify genes of which the expression is either strictly cis- or trans-regulated, or regulated by a combined action of both factors. Identification of cis- and trans-elements will allow us to develop an expression model underlying the transcript abundance in hybrids.

Reverse quantitative genetics of biomass production
Rather than applying a classical QTL-approach to identify genes underlying natural trait variation, it is becoming more and more desirable to focus on known genes which are likely to play a major role in determining a specific phenotype based on prior molecular and physiological studies. Given the growing evidence that altering cell cycle (CC) gene expression results in growth phenotypes, we considered 61 CC genes as candidate genes underlying variation in growth phenotypes. For this purpose, we resequenced a predefined set of 30 A. thaliana accessions at these 61 CC genes to infer haplotypes across the genes. Associations between haplotype variation for growth phenotypes in the population of 30 accessions will be examined. This will likely provide us more insight and a better understanding of the role of CC genes in plant growth.

Naouar N, Vandepoele K, Lammens T, Casneuf T, Zeller G, Van Hummelen P, Weigel D, Rätsch G, Inzé D, Kuiper M, De Veylder L, Vuylsteke M
Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes
PLANT J 57, 184-94, 2009



Sterken R, Kiekens R, Coppens E, Vercauteren I, Zabeau M, Inzé D, Flowers J, Vuylsteke M
A population genomics study of the Arabidopsis core cell cycle genes shows the signature of natural selection
PLANT CELL 21, 2987-98, 2009



Vuylsteke M, Peleman J, Van Eijk M
AFLP-based transcript profiling (cDNA-AFLP) for genome-wide expression analysis
Nat Protoc 2, 1399-413, 2007



Vuylsteke M, Peleman J, Van Eijk M
AFLP technology for DNA fingerprinting
Nat Protoc 2, 1387-98, 2007



Kiekens R, Vercauteren A, Moerkerke B, Goetghebeur E, Van Den Daele H, Sterken R, Kuiper M, Van Eeuwijk F, Vuylsteke M
Genome-wide screening for cis-regulatory variation using a classical diallel crossing scheme
NUCLEIC ACIDS RES 34, 3677-86, 2006

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