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 scientists: Annelies Vercauteren, Inge Van Daele
Ph.D. Students: Iris Pinheiro, Ives Vanstechelman, Katrijn Vannerum, Stephanie De Vos, Valerie Devos
Support personnel: Ilse Vercauteren

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 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 such as microarrays and next generation sequencing technology, however, allows 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.

Association mapping in Arabidopsis
Over the last years, large-scale genome-wide (candidate gene) association analyses (GWAS) of major human diseases have proven successful. The same strategy can now be exploited in some plant species where genomic tools become available and affordable. Currently, we are applying structured association mapping in a set of 240 Arabidopsis accessions to find the  gene underlying the major chrom1 QTL for seed size, identified previously by classical linkage mapping in a LerCvi RIL mapping population (Alonso-Blanco et al. 1999). We also apply a candidate gene association mapping approach to identify genes underlying the natural variation in mitosis-related phenotypes such as endoreduplication and root length elongation endoreduplication. The large number of cell cycle (CC) genes identified through molecular and bioinformatic approaches makes CC related phenotypes particularly attractive traits for this candidate gene association mapping study. For this purpose, we resequenced a set of 96 A. thaliana accessions at a predefined set of CC genes to infer haplotypes across the genes. Associations between haplotypes and variation for endoreduplication and other CC related phenotypes in the population of 96 accessions is currently examined.

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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