Targeted Resequencing in maize using Ampliseq

Cost remains a prohibitory factor in obtaining whole genome sequencing across a large number of samples. Genotyping-by-sequencing is a cost-effective alternative for obtaining a large number of markers across a large sample size, but markers are randomly distributed throughout the genome. Alternately, enrichment coupled with next generation sequencing is a cost-effective strategy for obtaining sequence information for loci of interest across a large sample. We will present our results using Ampliseq, a system for amplicon-based enrichment coupled with semi-conductor sequencing, on a validation set consisting of maize inbred lines, hybrids and landrace accessions. We report the use of a multiplexed panel of 319 PCR assays that target 20 candidate regions for photoperiod sensitivity and requires less than 25 ng of starting DNA. Enriched regions had an average sequencing depth of 105X coverage with 98.67% of bases mapping to the B73 reference genome. We were successfully able to call heterozygotes in the hybrid materials and identified novel variation in the landrace accessions. In summary, we have validated Ampliseq for genotyping diverse maize germplasm.