Genetic and genomic variation in plants (Weigel)

by admin last modified Jul 23, 2013 06:20 PM

A key question in biology is how organisms adapt to their environment, which eventually leads to the invention of new structures or organs. Many developmental biologists are trying to answer this question by comparing complex structures between distantly related taxa. The difficulties inherent in such an approach were already apparent to Darwin: “To suppose that the eye with all its inimitable contrivances … could have been formed by natural selection, seems, I freely confess, absurd to the highest degree.” An alternative to the study of macroevolutionary events is to investigate variation that occurs within a species or between sister species that can still interbreed.

One of the models that is used in the department to address such questions is phenotypic variation among different strains of Arabidopsis thaliana. The geographical distribution of A. thaliana includes much of the Northern hemisphere, and plants can be found in very different habitats (Weigel, 2012). To enable the rapid discovery of functionally relevant variation, we spearheaded a collaboration to discover a large fraction of common SNPs in 19 wild strains of Arabidopsis thaliana, using array-based whole-genome variation scans (Clark et al., 2007). The 250k SNP chip that was developed based on this work has been used by our collaborators to type hundreds of strains, setting the stage for genome-wide association studies in A. thaliana (Atwell et al., 2010).

As a next step, we embarked on more extensive genome sequencing using Illumina  technology. Because few computational tools were available when we started to use short read sequencing, we produced  the SHORE pipeline for the analysis of such data. Based on our early success with this technology, we initiated the 1001 Genomes Project for A. thaliana; see the project website for more information. The results from the first major phase of the project have been published (Cao et al., 2011). To understand the patterns of sequence variation in natural strains, it is important to both know the rate and spectrum of spontanenous mutation (Ossowski et al., 2010), and to have outgroup information (Hu et al., 2011). In addition, we are looking at spontaneous variation in the methylome of A. thaliana (Becker et al., 2011).

We use these resources to study a range of traits. In the course of these studies, we discovered the first example of a naturally occurring genetic defect associated with a triplet repeat expansion outside humans (Sureshkumar et al., 2009) and we documented natural variation in the efficieny of miRNA processing (Todesco et al., 2012).

However, our major effort in this area is the analysis of fitness tradeoffs in immunity. A while ago, we developed A. thaliana as a model for hybrid necrosis, a syndrome that is characterized by inappropriate activation of the immune system due to self-recognition (Bomblies et al., 2007). We have identified dozens of hybrid necrosis cases in A. thaliana and have cloned the causal loci underlying four genetically distinct interactions. Most encode highly polymorphic immune receptors, and an important part of our efforts is the description of species- and genome-wide variation at NB-LRR immune receptor genes.

While most hybrid necrosis systems involve two loci, autoimmunity can also be caused by inter-allelic interactions at a single locus, ACCELERATED CELL DEATH 6 (ACD6). We have shown that ACD6 is involved in a major fitness tradeoff between growth and pathogen resistance in inbred strains (Todesco et al., 2010). The ACD6 case is particularly interesting, because necrosis is relatively mild, and naturally occurring hybrids survive in the field. Thus, while divergence of pathogen recognition systems can potentially result in reproductive isolation, hyperactivation of the immune system in hybrids may in other cases promote outcrossing in a species that is otherwise predominantly selfing. To test these and related hypotheses, we have begun to relate microbial diversity in natural A. thaliana populations to the distribution of resistance gene alleles.

Key publications

 

 

Personnel

Dr. Detlef Weigel weigel@weigelworld.org
Director
Dr. Claude Becker
Postdoctoral fellow (also Small RNA group)
Dr. Eunyoung Chae
Postdoctoral fellow
Jörg Hagmann
Ph.D. student
Dino Jolic
Ph.D. student
Dr. Sang-tae Kim
Postdoctoral fellow
Dr. Dan Koenig
Postdoctoral fellow
Dr. Chan Liu
Postdoctoral fellow
Jonas Müller
Ph.D. student
Subhashini Muralidharan
Ph.D. student
Danelle Seymour
Ph.D. student
Dr. Patrice Salomé
Postdoctoral fellow
Dr. Lisa Smith
Postdoctoral fellow (also Small RNA group)
Diep Tran
Ph.D. student
Dr. François Vasseur
Postdoctoral fellow
Dr. George Wang
Postdoctoral fellow
Dr. Congmao Wang
Postdoctoral fellow
Dr. Xi Wang
Postdoctoral fellow
Maricris Zaidem
Ph.D. student

Major Collaborators

Dr. Jeffery Dangl
University of North Carolina, Chapel Hill
Dr. Daniel Huson
University Tübingen
Dr. Magnus Nordborg
Gregor Mendel Institute, Vienna
Dr. Korbinian Schneeberger
Max Planck Institute for Plant Breeding Research, Cologne
Top
Document Actions
Personal tools