Improving Genome Assemblies, Assessing Structural Variation and Trait Association using Chromosome Genomics and Illumina Skim Genotyping by Sequencing

The ability to isolate individual chromosomes, combined with Illumina next generation DNA sequencing, provides the ability to perform chromosome genomics, to validate genome assemblies and identify structural variation between varieties. When this approach is combined with high resolution skim based genotyping by sequencing (GBS), it is possible to resolve genome structures and map heritable traits at extremely high resolution.

Following the success of these approaches in wheat and Brassica, we are applying chromosomal genomics and skim GBS to the genome of chickpea. By sequencing isolated individual chromosome arms or groups of arms, we can identify regions of variation in the reference genome. Current skim sequencing of mapping populations will resolve this structural variation and permit the high resolution mapping of agronomic traits with outcomes for genomics based chickpea improvement.