Allele frequency profiling of candidate adaptive genes for landscape genomics in perennial ryegrass

Tom Ruttink, Kurt Lamour, Philippe Barre, Sabine Van Glabeke, Hilde Muylle, Anna Roschanski, Klaus Dehmer, Jean-Paul Sampoux, Isabel Roldán-Ruiz

    Onderzoeksoutput: Bijdrage aan congresPosterpeer review


    Dynamic changes in the genomic composition of populations can provide insight
    in the genetic response to short-term selection pressure, or the mechanisms
    underlying adaptation to a changing environment. To characterize such genetic
    responses, we have implemented a high-multiplex amplicon sequencing method
    to quantify allele frequencies in populations, based on the use of pooled leaf
    samples to represent populations. First, we used probe capture enrichment to resequence a panel of 550 genes in a diverse set of 736 perennial ryegrass
    (Lolium perenne) genotypes. From this catalogue of genetic diversity we
    identified highly divergent regions in 26 candidate genes expected to drive
    adaptation to differing environmental conditions, and developed primers in
    flanking conserved domains to amplify 85 DNA fragments of around 500 bp. Next, we split these primers over two multiplex sets and used unique sample-
    indexes for the parallel sequencing of thousands of pool-samples in a single
    HiSeq2500 lane. We validated the method by comparing allele frequencies determined in pool-samples versus those determined using the individual plant
    s. We used the same strategy to develop a multiplex set targeting six regio
    ns in the chloroplast genome. This set allows determining phylogeographic re
    lations in perennial ryegrass. Finally, we used these three multiplex sets to es
    timate allele frequencies of 26 candidate adaptive genes and six chloroplast regions in 576 natural populations covering the European distribution range of
    L. perenne. These data are used to determine phylogeographic relationships and
    genetic signatures of adaptation of the species across Europe as part of the Eur
    opean network research project GrassLandscape (
    Oorspronkelijke taalEngels
    PublicatiestatusGepubliceerd - 17-mrt.-2016
    EvenementApplied Bioinformatics in Life Sciences - Leuven, België
    Duur: 17-mrt.-201618-mrt.-2016


    CongresApplied Bioinformatics in Life Sciences


    • B110-bioinformatica


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