SNP discovery of Korean short day onion inbred lines using double digest restriction site-associated DNA sequencing

• DOI: 10.1371/journal.pone.0201229
• Publication Date: 2018-08-07T17:42:00Z
• Authors: Ji-Hee Lee; Sathishkumar Nata...; Manosh Kumar Biswas; Kenta Shirasawa; Sachiko Isobe; Hoy-Taek Kim; Jong-In Park; Chi-Nam Seong; Ill-Sup Nou
• Keywords: Molecular breeding; SNP array; SNP; Restriction site

Onion (Allium cepa L.) is an economically important vegetable crop around the world. Genetic and genomic research into various onion accessions will provide insights genome to enhance breeding strategies improve crops. However, onion's large size means that studies of molecular markers are limited in onion. This study aimed discover high quality single nucleotide polymorphisms (SNPs) from 192 inbred lines relating short-day cultivation Korea. Paired-end (PE) double digested restriction site-associated DNA sequencing (ddRAD-seq) was used SNPs A total 538,973,706 reads (25.9 GB), with average 2,658,491 high-quality reads, were generated using ddRAD-seq. With stringent filtering, 1904 discovered based on reference scaffolds. Further, population structure genetic relationship suggested two well-differentiated sub-populations exist lines. SNP-associated flanking sequences also compared a public non-redundant database for gene ontology pathway analysis. To our knowledge, this first report identify ddRAD-seq platform. The SNP identified be useful breeders community deepen their understanding, programs, support management resources.