Construction of a linkage map flanking the I locus controlling dominant white bulb color and analysis of differentially expressed genes between dominant white and red bulbs in onion (Allium cepa L.)

White bulb colors of onion (Allium cepa L.) are determined by the C and I loci which control the so-called recessive and dominant white bulb colors, respectively. To identify the causal gene responsible for the I locus, a combined approach of bulked segregant analysis and RNA-Seq was used in the present study. A total of 68 contigs containing homozygous single nucleotide polymorphisms (SNPs) between red and dominant white bulked RNAs were identified. The position of I locus was found to be located at chromosome 3 by performing comparative analysis of these contigs and using a previously constructed linkage map. After verification of homozygous SNPs by sequencing of PCR products, 12 high resolution melting, one cleaved amplified polymorphic sequence, and one InDel markers were developed. A linkage map flanking the I locus was constructed using these markers. Two tightly linked markers (DW51596 and DW35019) flanking the I locus were identified by analyzing 1457 F-4 individuals. A total of 104 and 39 contigs showing more than tenfold increase of expression in red and dominant white bulks, respectively, were identified. Transcriptions of all structural genes encoding enzymes in flavonoid biosynthesis pathway were significantly reduced in the dominant white bulk. Transcription levels of most contigs showing more than tenfold reduced expression in dominant white were also significantly reduced in the recessive white bulbs controlled by the C locus. Genomic DNA sequences of 12 genes encoding transcription factors assumed to regulate flavonoid biosynthesis were analyzed. However, the causal gene for the I locus could not be identified.