Physical size of the S locus region defined by genetic recombination and genome sequencing in Ipomoea trifida, Convolvulaceae
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- Rahman, M.H., Tsuchiya, T., Suwabe, K. et al. Sex Plant Reprod (2007) 20: 63. doi:10.1007/s00497-007-0044-x
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Sporophytic self-incompatibility (SSI) in the genus Ipomoea (Convolvulaceae) is controlled by a single polymorphic S locus. We have previously analyzed genomic sequences of an approximately 300 kb region spanning the S locus of the S1 haplotype and characterized the genomic structure around this locus. Here, we further define the physical size of the S locus region by mapping recombination breakpoints, based on sequence analysis of PCR fragments amplified from the genomic DNA of recombinants. From the recombination analysis, the S locus of the S1 haplotype was delimited to a 0.23 cM region of the linkage map, which corresponds to a maximum physical size of 212 kb. To analyze differences in genomic organization between S haplotypes, fosmid contigs spanning approximately 67 kb of the S10 haplotype were sequenced. Comparison with the S1 genomic sequence revealed that the S haplotype-specific divergent regions (SDRs) spanned 50.7 and 34.5 kb in the S1 and S10 haplotypes, respectively and that their flanking regions showed a high sequence similarity. In the sequenced region of the S10 haplotype, five of the 12 predicted open reading frames (ORFs) were found to be located in the divergent region and showed co-linear organization of genes between the two S haplotypes. Based on the size of the SDRs, the physical size of the S locus was estimated to fall within the range 34–50 kb in Ipomoea.