University of Cambridge > > Plant Sciences Departmental Seminars > Genome- and species-wide analysis of sequence variation and its functional consequences

Genome- and species-wide analysis of sequence variation and its functional consequences

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Comprehensive polymorphism data are a prerequisite for the systematic identification of sequence variants affecting phenotypes. In the first part of my talk, I will discuss our efforts to provide a whole genome 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 strains with high-density arrays comprising close to 1 billion (109) unique oligonucleotide probes. We identified over 1 million non-redundant single nucleotide polymorphisms (SNPs) at various levels of precision, and ~4% of the 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 stop codons, while about 200 replace stop codons in the reference with amino acid codons. However, while knockouts are common, the allele frequency spectrum suggests that they are often associated with fitness costs. We are now expanding these studies using Illumina/Solexa 1G technology.

Through our work on natural variation, we have also become involved in more general questions of species-wide evolution. To understand mechanisms underlying nascent incompatibilities that may lead to speciation, we performed an extensive survey for hybrid incompatibilities within A. thaliana. We identified numerous independent F1 incompatibilities with a range of phenotypically related abnormalities. Each case is attributable to two to three epistatic loci. A common autoimmune mechanism—activation of pathogen responses in the absence of pathogens—underlies the majority of incompatibilities. Detailed characterization of one hybrid interaction identified an NB-LRR gene as causal. NB-LRR genes are the most common class of disease resistance® genes, which loosely speaking encode pathogen detectors. Since NB-LRR genes constitute the family with the highest allelic diversity in plants, this suggests that such incompatibilities arise frequently as a by-product of natural selection, and that they make an important contribution to the process of speciation in plants.

This talk is part of the Plant Sciences Departmental Seminars series.

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