High Resolution Skim Genotyping Assists in Chickpea (Cicer arietinum) Reference Genome Assessment and Improvement

Next generation sequencing technologies have enhanced sequence-based genotyping for genome assessment, validation, diversity and association studies. We applied a skim-based genotyping by sequencing approach to genotype the segregating Chickpea population ICC4958 (desitype) X PI489777 (wild type). SNPs were genotyped by sequencing 46 population individuals at less than 1x coverage (skim sequencing) and imputation performed to define the haplotypes. We demonstrate the application of these haplotypes to improve the quality of reference genome assembly. In addition, isolating individual chromosomes and sequencing with next generation sequencing permits the validation of genome assemblies. We isolated and sequenced all chickpea chromosomes individually to assess the quality of reference assembly.

Skim-GBS, combined with isolated chromosome methods, would be a powerful approach to assess and improve other crop reference genome assemblies.