Genome-wide discovery and deployment of insertions and deletions markers provided greater insights on species, genomes, and sections relationships in the genus Arachis

Summary

Small insertions and deletions (InDels) are the second-most prevalent and the most abundant structural variations in plant genomes. In order to deploy these genetic variations for genetic analysis in genus Arachis, we conducted comparative analysis of the draft genome assemblies of both the diploid progenitor species of cultivated tetraploid groundnut (Arachis hypogaea L.), i.e. Arachis duranensis (A subgenome), and Arachis ipaënsis (B subgenome), and identified 515,223 InDels. These InDels include 269,973 insertions identified in A. ipaënsis against A. duranensis and 245,250 deletions in A. duranensis against A. ipaënsis. The majority of the InDels were of single bp (43.7%) and 2–10 bp (39.9%), while the remaining were >10 bp (16.4%). Phylogenetic analysis using genotyping data for 86 (40.19%) polymorphic markers grouped 96 diverse Arachis accessions into 8 clusters, mostly by the affinity of their genome. This study also provided evidence for the existence of ‘K’ genome, which was distinct from the ‘A’ and ‘B’ genomes but more similar to the ‘B’ genome. The complete homology between A. monticola and A. hypogaea tetraploid taxa showed a very similar genome composition. The above analysis has provided greater insights into the phylogenetic relationship among accessions, genomes, sub species, and sections. These InDel markers are a useful resource for the groundnut research community for genetic analysis and breeding applications.

Open resource Download resource Access resource on external site