Onion (Allium cepa) pseudoreference genome

Onion (Allium cepa) is not highly tractable for development of molecular
markers due to its large (16 gigbases per 1C) nuclear genome. 
Single nucleotide polymorphisms (SNPs) are useful for genetic
characterization and marker-aided selection of onion because of
codominance and common occurrence in elite germplasm.  We
completed genotyping by sequencing (GBS) to identify SNPs in onion using
46 F2 plants, parents of the F2 plants (Ailsa Craig 43 and Brigham Yellow
Globe 15-23), two doubled haploid (DH) lines (DH2107 and DH2110), and
plants from 94 accessions in the USDA National Plant Germplasm System
(NPGS).  SNPs were called using the TASSEL 3.0 Universal Network
Enabled Analysis (UNEAK) bioinformatics pipeline.  Sequences from
the F2 and DH plants were used to construct a pseudo-reference genome
against which genotypes from all accessions were scored.  Quality
filters were used to identify a set of 284 high quality SNPs which were
placed onto an existing genetic map for the F2 family. 
Accessions showed a moderate level of diversity (mean He = 0.341) and
evidence of inbreeding (mean F = 0.592).  GBS is promising for
SNP discovery in onion, although lack of a reference genome required
extensive custom scripts for bioinformatics analyses to identify high
quality markers.