Fine-Mapping of a Red-Skinned Taproot Gene in Radish (Raphanus sativus L.)

The skin color of radish taproots is an important commodity character that directly affects the choice behavior of consumers. Here, we identified a skin color gene carried by a red-skinned inbred line, SXAU-R2. Genetic population was constructed by the crossing of SXAU-R2 and a white-skinned inbred line, SXAU-W2, and the taproots of F₁ plants exhibited intermediate color. In the F₂ population, the separation ratio of taproot skin color indicated that the phenotype was controlled by one major locus, named <i>RST1</i> (<i>Red-Skinned Taproot 1</i>). Combined with bulked segregant analysis and RNA sequencing (BSA-seq), 2640 single nucleotide polymorphisms (SNPs) were detected between the annotated genes of the red skin bulk and white skin bulk. Molecular markers were developed in the SNP-enriched 27~32 Mbp region of chromosome 7, and then <i>RST1</i> was mapped in the genetic interval between flanking markers <i>SSR-14</i> and <i>SSR-22</i>. Using F_2:3 lines derived from a key F₂ heterozygote, <i>RST1</i> was narrowed down into a 530 Kbp interval. There were 46 expressed annotated genes in the fine-mapping region, and a gene encoding MYB was selected as the candidate of <i>RST1</i>. Finally, based on Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and RT-qPCR, we identified the potential interacting genes <i>RsbHLH</i> and <i>RsWD</i>, as well as the latent target genes <i>RsDFR</i> and <i>RsANS</i> of RST1 in the anthocyanin synthesis pathway. These results provide an understanding of the genetic mechanisms regulating anthocyanin synthesis and offer an efficient molecular marker for the radish breeding of skin color.