Development of a new S locus haplotyping system based on three tightly linked genes in the S locus controlling self-incompatibility in radish (Raphanus sativus L.)

To develop an efficient and reliable haplotype identification system of the S locus controlling self-incompatibility (SI) in radish (Raphanus sativus L.), polymorphic sequences of the SLL2 and SP6 genes, which were located at each border of the S core regions, were used together with those of the SRK gene, the female determinant of SI. Partial sequences of the SP6 and SRK genes were isolated from 35 diverse breeding lines that showed differential self-incompatibility responses. A total of 25 SP6 and 29 SRK alleles were isolated in this study, and 29 SLL2 alleles isolated from the previous study were included for the S haplotyping. Whereas the phylogenetic tree of the SP6 alleles showed species-specific clustering patterns, the phylogenetic tree of the SRK alleles revealed intergeneric pairing of some SRK alleles, although the others showed species-specific clustering. Among 35 breeding lines, 13 had combinations of the unique SLL2, SRK, and SP6 alleles, but the others shared a common allele of either SLL2 or SP6 genes. Except for two breeding lines that contained the same SLL2, SRK, and SP6 alleles, all breeding lines were shown to harbor unique haplotypes that consisted of different combinations of SLL2, SRK, and SP6 alleles. When 73 additional diverse breeding lines were analyzed by this new S locus haplotyping system, the haplotypes of all breeding lines were clearly identified. In addition, eight new combinations that contained different combinations of the SLL2, SRK, and SP6 alleles were identified.