Genetical genomics of plant stresses

Growth and development of an organism is regulated by a wide range of genes. During the past decade, the use of natural variation and quantitative trait locus (QTL) analysis has been proven to be very fruitful in unraveling genes (and/or more alleles) that play a role in such complex multigenic processes. Shortly, naturally occurring accessions (ecotypes), preferably differing for the trait under investigation, are crossed; the resulting progeny is genotypes by molecular markers, and trait(s) are quantified. Then, marker-trait association are studied using appropriate statistical software, resulting in QTL, being genetic region that significantly affect the trait under investigation. As a follow-up the underpinning genes may be identified, and the (nucleotide) polymorphism, responsible for the variation between the parental accessions, can be revealed.

Initially, QTL analyses focused on single traits. Recently, it was shown that large scale (so-called ‘omics’ technologies) may be used for large-scale QTL studies, not only revealing loci regulating individual traits, but also networks of interconnected traits. For instance, Keurentjes et al. (2006) showed that combining large-scale untargeted metabolites analyses, in combination with QTL mapping, reveal metabolic networks. Similarly, it was shown that transcriptomic data may be used to build regulatory gene networks (Keurentjes et al., 2007). Collectively, these approaches are named ‘genetical genomics’ (Jansen and Nap, 2001).

Applied approaches include simple correlation analyses but also more sophisticated large-scale QTL analyses and regulatory network construction. Particular attention is given to the role of natural variation in the regulation of traits related to plant adaptation and ecology. An important element of the work involves technological and mathematical improvements for comprehensive analyses of large sample sets (e.g. mapping populations). For this, long lasting collaborations have been established with technology oriented and mathematic research groups.

Selected references
  • Alonso-Blanco, C., Aarts, M.G., Bentsink, L., Keurentjes, J.J.B., Reymond, M., Vreugdenhil, D.and Koornneef, M. (2009). What Has Natural Variation Taught Us about Plant Development, Physiology, and Adaptation? Plant Cell 10.1105/tpc.109.068114
  • El-Lithy, M.E., Clerkx, E.J., Ruys, G.J., Koornneef, M., and Vreugdenhil, D. (2004). Quantitative trait locus analysis of growth-related traits in a new Arabidopsis recombinant inbred population. Plant Physiol 135, 444-458.
  • Keurentjes, J.J.B., Fu, J., de Vos, C.H., Lommen, A., Hall, R.D., Bino, R.J., van der Plas, L.H.W., Jansen, R.C., Vreugdenhil, D., and Koornneef, M. (2006). The genetics of plant metabolism. Nat Genet 38, 842-849.