2018 ASHS Annual Conference

Genetic linkage maps of bulb onion (Allium cepa L.) remain relatively rudimentary despite its economic significance as one of the most important vegetable crops globally. It is very difficult to study on genomics and genetic mapping of onion due to large genome size (16.3 Gbp), biennial life cycle, cross-pollinated habit, and high inbreeding depression. High-density genetic maps of onion are inevitably required for completion of its whole genome reference and development of molecular markers associated with traits of interest. In this study, we attempted to generate a high-density genetic map of onion using an F₂ segregating population derived from a cross between a DH line ‘H6’ and an inbred line ‘SP3B’, and using genotyping-by-sequencing (GBS) analysis. First of all, 101.8 Gbp of raw sequence data and 1 G of reads were generated by Illumina HiSeq 2500. Clean reads of each sample were mapped to the onion transcriptome reference sequences. When the filtering condition was set to the minimum depth of 3, a total of 8,431 SNPs were detected. Of them, 704 SNPs were positioned on the genetic linkage map consisting of 8 linkage groups, and the entire genetic distance was 928.3 cM. In addition, each chromosome number of 8 linkage groups was assigned by comparing with the previously reported onion genetic linkage map, OH1×5225. A total of 248 primer sets for high-resolution melting (HRM) analysis were designed based on common SNPs between H6×SP3B and OH1×5225. A total of 35 polymorphic HRM markers were mapped on the onion genetic map of this study and used for comparison of two genetic maps. Finally, the genetic map covered 8 chromosomes with a total genetic distance of 870.4 cM, and contained total 736 markers consisting of 701 SNPs by GBS and 35 HRM markers. This high-density genetic linkage map of bulb onion will be helpful to develop molecular markers for important traits and to accelerate the improvement of onion.