Onion (2n = 2x = 16) has been a nutritional, medicinal and economically valuable vegetable crop all over the world since ancient times. To accelerate the molecular breeding in onion, genetic linkage maps are prerequisite. However, construction of genetic linkage maps of onion remains relatively rudimentary due to a large genome (about 16.3 Gbp) as well as biennial life cycle, cross-pollinated nature, and high inbreeding depression. In this study, we constructed single nucleotide polymorphism (SNP)-based genetic linkage map of onion in an F2 segregating population derived from a cross between the doubled haploid line ‘16P118′ and inbred line ‘Sweet Green’ through genotyping by sequencing (GBS). A total of 207.3 Gbp of raw sequences were generated using an Illumina HiSeq X system, and 24,341 SNPs were identified with the criteria based on three minimum depths, lower than 30% missing rate, and more than 5% minor allele frequency. As a result, an onion genetic linkage map consisting of 216 GBS-based SNPs were constructed comprising eight linkage groups spanning a genetic length of 827.0 cM. Furthermore, we identified the quantitative trait loci (QTLs) for the sucrose, glucose, fructose, and total sugar content across the onion genome. We identified a total of four QTLs associated with sucrose (qSC4.1), glucose (qGC5.1), fructose (qFC5.1), and total sugar content (qTSC5.1) explaining the phenotypic variation (R2%) ranging from 6.07–11.47%. This map and QTL information will contribute to develop the molecular markers to breed the cultivars with high sugar content in onion.

The control of bolting time in onion is an important approach for bulb and seed production, as onion plants which bolt do not produce marketable bulbs and seed yields are dependent on floral induction. However, genetic and molecular studies about bolting time in onion plants have not been examined yet to date. In order to understand the regulation of bolting time in onion plants, we conducted the genetic crosses between late bolting-type cultivar (MOS8) and very early bolting-type cultivar (Guikum). Segregation ratio of late to very early in F 2 populations indicated that this lateness trait was determined by a dominant locus. We also analyzed protein profiles in onion plants with different bolting time by a proteomics approach. Interestingly, a protein spot with significant similarities to chromodomains of mammalian chromo-ATPase/helicase-DNA-binding 1 or heterochromatin protein 1, which is involved in the histone modifications, was identified. Histone methyltransferase activity was also observed in onion plants. Taken together, these results suggest that a genetic pathway may be involved in the modulation of bolting time in onion plants, though there is no direct evidence that this protein spot obtained by proteomics is relevant to vernalization.