| Summary: | Anthocyanins, the pigmented flavonoids responsible for red and blue colors in horticultural products, promote human health by preventing cancers and lowering the risk of cardiovascular disease. Red onions contain several cyanidin- and peonidin-based anthocyanins. In this study, we constructed a single-nucleotide polymorphism (SNP)-based genetic linkage map in an F<sub>2</sub> segregating population derived from a cross between the inbred line ‘SP3B’ (yellow bulb) and the doubled haploid line ‘H6′ (red bulb) to identify quantitative trait loci (QTLs) for total anthocyanin content of onion bulbs using a genotyping-by-sequencing (GBS) analysis based on a reference gene set. A total of 101.9 Gbp of raw sequences were generated using an Illumina HiSeq 2500 system and a total of 1625 SNP loci were identified with the criteria of 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 319 GBS-based SNP loci and 34 high-resolution melting (HRM) markers was constructed with eight linkage groups and a total genetic distance of 881.4 cM. In addition, the linkage groups were assigned to corresponding chromosomes by comparison with the reference genetic map OH1×5225 through marker development based on common transcripts. The analysis revealed one major QTL, <i>qAS7.1</i>, for anthocyanin synthesis and two significant QTLs, <i>qAC4.1</i> and <i>qAC4.2</i>, for anthocyanin content. The QTL <i>qAS7.1</i>, located on chromosome 7 with a phenotypic variation of 87.61%, may be a dihydroflavonol 4-reductase (<i>DFR</i>) gene that determines whether the bulb color is red or yellow. The QTLs <i>qAC4.1</i> and <i>qAC4.2</i> are separately positioned on chromosome 4 with <i>R<sup>2</sup></i> values of 19.43% and 26.28%, respectively. This map and QTL information will contribute to marker development and breeding for high anthocyanin content in bulb onion.
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