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SUMMARY:The genotype-phenotype map in Arabidopsis - Magnus Nordborg (The G
 regor Mendel Institute\, Vienna)
DTSTART:20131017T120000Z
DTEND:20131017T130000Z
UID:TALK47368@talks.cam.ac.uk
CONTACT:Ian Henderson
DESCRIPTION:Understanding how genetic variation translates into phenotypic
  variation\, and how this translation depends on the environment\, is fund
 amental to many fields of biology. We have been attempting to tackle this 
 problem using A. thaliana as a model for many years. Because it naturally 
 exists as inbred lines\, A. thaliana can be brought into the laboratory an
 d grown\, in replicate\, under different environmental conditions. As part
  of the 1\,001 Genomes Project\, we have sequenced 200 Swedish lines\, and
  are generating multiple phenotypes\, in the field as well as in the lab. 
 We are also generating “in-between-ome” data\, such as genome-wide tra
 nscription and DNA methylation data\, in order to gain insight into the me
 chanism whereby particular polymorphisms lead to phenotypic variation. The
  sequencing has revealed massive variation in genome-size\, mostly due to 
 variation in 45S rDNA clusters\, and evidence for strong selective sweeps.
  GWAS results vary greatly between phenotypes due to difference in the und
 erlying genetic architecture.  Compared to efforts in other organisms\, we
  find much greater effects of individual loci. At the transcriptome level\
 , a very high proportion of genes show evidence of strong cis-regulation i
 n GWAS\, with effects peaking close to transcription start sites\, while t
 rans-effects appear to be smaller\, and typically interact with the enviro
 nment. In terms of DNA methylation\, most of the genome is unmethylated\, 
 with methylation concentrated in repetitive parts of the genome. Methylati
 on patterns vary between genotypes\, but are largely conserved across envi
 ronments\, although differences in overall level are seen and appear to ha
 ve a genetic basis. We are now attempting to connect all layers of data to
  create a genotype-phenotype map.
LOCATION:Sainsbury Laboratory
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