Genomic Approaches for Gene Identification

SHOREmap is a recently introduced method that utilizes whole-genome sequencing data from bulked mapping populations for rapid one-step identification of mutations with phenotypic effects. Our method relies on a full-length reference sequence and many-fold of genome coverage. Thus, applying the original SHOREmap to large and un-sequenced genomes is not straightforward. Using whole-genome sequencing data of a recessive Arabidopsis thaliana mutant I will outline how SHOREmapping can be performed using only a small fraction of a reference genome (e.g. sequence-based genetic maps) and how targeted enrichment sequencing compensates for the decrease in the number of markers while using only parts of the reference. However, using partial reference sequences only, ultimate identification of the causal mutation requires further fine-mapping. To minimize the workload for this step, we introduced a new usage of likelihood ratio test statistics, transforming local allele frequency estimations into a confidence interval substituting conventional mapping intervals. BSA combined with deep sequencing has also proved to be efficient for mapping QTLs in yeast and Drosophila. But as this requires large number of generations, this has not been attempted in species that hardly allow for generating large numbers of recombinants. Using the legume model Lotus japonicus, two nodulation traits were subjected to SHOREmapping analysis. After introducing novel QTL-seq statistics we identified major nodulation QTLs. To add further resolution and to identify QTNs, we whole-genome sequenced 30 L. japonicus accessions with extreme phenotypes. This resulted in the identification of candidate alleles, which were previously shown to be involved in nodulation.