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Thursday, September 14, 2017
Thursday, September 14, 2017
  • 03:00pm - 04:00pm  Rice Breeding and Strategic Innovation Joint Platform Seminar by Dr. Richard Mott PB and GB Joint Division Seminar
    (Please click “Add to calendar” to mark it in your calendar. We will not circulate reminders)

    Richard Mott
    Weldon Professor of Computational and Statistical Genetics
    UCL Genetics Institute, Gower Street, London WC1E 6BT


    Title: Sequencing Populations to Find Causal Genetic Variants

    Abstract:
    We describe two approaches, based on sequencing a population at low coverage, to impute single nucleotide polymorphisms (SNPs) in the absence of a haplotype reference panel, and to detect structural variation (SVs). These methods are applicable to any species including crops, and in particular populations descended from known inbred lines such as MAGIC populations. The first approach is described in (Davies et al 2016 Nat Genetics.48:965-969 PMID: 2737623). It assumes an unknown set of haplotypes (the reference panel) segregate at each locus in the population, and that each chromosome is a mosaic of these unknown haplotypes. It then simultaneously estimates the panel and the individual chromosome mosaics using a hidden Markov model that utilises features of low-coverage sequence data. The number of unknown haplotypes at each locus is a variable dependent on the population history. We apply this method to humans, mice and Arabidopsis MAGIC and show that common variants can be imputed accurately using only modest levels of sequence coverage (between 0.1x an 1.5x depending on the population history). The second approach also uses low-coverage sequence to identify regions that are structurally variant, and if they are due to a transposition, the originating locus of the transposition. Applying this method to the Arabidopsis MAGIC population (Imprialou et al 2017 Genetics 205:1425-1441. PMID: 28179367) identified thousands of SVs of which about a quarter were transpositions, and mapped SVs that were likely to be functional for fungal resistance and germination. Of interest, for some phenotypes structural variation explains more heritability than does SNP variation. :: IRRI Events