Construction of a high-resolution linkage map and chromosomal localization of the loci determining major qualitative traits in onion (Allium cepa L.)

A yellow inbred line (SP3B) and a red doubled haploid line (H6) were used to produce a F₂ mapping population of onion (Allium cepa L.). Initially, insertion/deletion and cleaved amplified polymorphic sequence markers were developed based on polymorphisms in the reference transcriptome. To improve efficiency of marker development, RNA-seq was carried out to identify single nucleotide polymorphisms (SNPs) between parental lines. High-quality SNPs were selected via customized screening process, and 344 high resolution melting (HRM) markers were developed. In addition, 161 HRM markers were developed based on the SNPs detected using genotyping-by-sequencing. A linkage map consisting of 652 molecular markers distributed in eight linkage groups was constructed. The total length of the linkage map was 749.8 cM, and the average interval between markers was 1.91 cM, the highest resolution among onion linkage maps reported so far. All eight linkage groups were assigned to onion chromosomes by identifying the common homologous loci in other linkage maps. Four major loci (C, I, R, and L) determining onion bulb colors were located on separate chromosomes. Analysis of ‘Santero’, a F₁ cultivar resistant to downy mildew, revealed that the length of the chromosome fragment introgressed from Allium roylei, harboring the resistance gene estimated at 27.6 cM at the end of chromosome 3. The high-resolution linkage map constructed in this study and chromosomal locations of major qualitative loci will be used to design an effective selection strategy for onion breeding programs.