Available_upon_publication.txt

This effort is an attempt to develop a cost-effective genotyping system by using the Tecan Allegro Targeted Resequencing V2 kit. This provides customed probe design, whcich can be modified by adding or dropping target sequences. SNPs obtained from previous peanut next generation sequencing data were pre-filtered and selected as targets. These SNP targets were polymorphic among different tetraploid accessions and were selected to be distinguishable from paralogs. A total of 5,154 probes were designed to detect 2,770 SNP targets and were tested on 48 accessions, which include some closely related sister lines from a breeding population. The results indicated that this genotyping by targeted resequencing approach reduced the cost from around $28 (SNP chip and GBS) to $18 per sample, while providing polymorphic markers with accurate SNP calls. With this cost-effective genotyping platform, pre-selected SNP markers can be used effectively and routinely for more breeding programs. The data set includes raw reads and a variant call (vcf) file of 48 peanut accessions, sequenced from both ends.