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SUMMARY:Genome- and species-wide analysis of sequence variation and its fu
 nctional consequences - Professor Detlef Weigel\, MPI for Developmental Bi
 ology\, Tübingen
DTSTART:20071108T160000Z
DTEND:20071108T170000Z
UID:TALK8079@talks.cam.ac.uk
CONTACT:3901
DESCRIPTION:Comprehensive polymorphism data are a prerequisite for the sys
 tematic identification of sequence variants affecting phenotypes. In the f
 irst part of my talk\, I will discuss our efforts to provide a whole genom
 e resource for the study of population level evolutionary processes in an 
 experimentally tractable\, multicellular organism\, Arabidopsis thaliana. 
 In collaboration with several groups\, we interrogated 20 different strain
 s with high-density arrays comprising close to 1 billion (109) unique olig
 onucleotide probes. We identified over 1 million non-redundant single nucl
 eotide polymorphisms (SNPs) at various levels of precision\, and ~4% of th
 e genome was identified as being highly dissimilar or missing relative to 
 the reference genome. A large number of SNPs is predicted to have a major 
 effect on gene function\; for example\, over 1\,000 introduce premature st
 op codons\, while about 200 replace stop codons in the reference with amin
 o acid codons. However\, while knockouts are common\, the allele frequency
  spectrum suggests that they are often associated with fitness costs. We a
 re now expanding these studies using Illumina/Solexa 1G technology.\n\nThr
 ough our work on natural variation\, we have also become involved in more 
 general questions of species-wide evolution. To understand mechanisms unde
 rlying nascent incompatibilities that may lead to speciation\, we performe
 d an extensive survey for hybrid incompatibilities within A. thaliana. We 
 identified numerous independent F1 incompatibilities with a range of pheno
 typically related abnormalities. Each case is attributable to two to three
  epistatic loci. A common autoimmune mechanism -- activation of pathogen r
 esponses in the absence of pathogens -- underlies the majority of incompat
 ibilities. Detailed characterization of one hybrid interaction identified 
 an NB-LRR gene as causal. NB-LRR genes are the most common class of diseas
 e resistance (R) genes\, which loosely speaking encode pathogen detectors.
  Since NB-LRR genes constitute the family with the highest allelic diversi
 ty in plants\, this suggests that such incompatibilities arise frequently 
 as a by-product of natural selection\, and that they make an important con
 tribution to the process of speciation in plants. \n\nhttp://www.weigelwor
 ld.org/research
LOCATION:Department of Plant Sciences\, Large Lecture Theatre
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