De Novo SNP Discovery and Genotyping of Iranian Pimpinella Species Using ddRAD Sequencing

The species of Pimpinella, one the largest genera family Apiaceae, are traditionally cultivated for medicinal purposes. In this study, high-throughput double digest restriction-site associated DNA sequencing technology (ddRAD-seq) was used to identify single nucleotide polymorphisms (SNPs) in eight Pimpinella from Iran. After double-digestion with enzymes HpyCH4IV and HinfI, a total 334,702,966 paired-end reads were de novo assembled into 1,270,791 loci an average 28.8 per locus. stringent filtering, 2440 high-quality SNPs identified downstream analysis. Analysis genetic relationships population structure, based on these retained SNPs, indicated presence three major groups. Gene ontology pathway analysis determined by using comparison SNP-associated flanking sequences public non-redundant database. Due lack genomic resources genus, our present study is first report provide pipeline ddRAD-seq. This data will enhance molecular knowledge genus important source information breeders research community breeding programs support management resources.