Molecular characterization of a 313-kb genomic region containing the self-incompatibility locus of Ipomoea trifida, a diploid relative of sweet potato [Ipomoea batatas]

Diploid Ipomoea trifida is an ancestral wild species of the cultivated hexaploid sweet potato, and displays a sporophytic self-incompatibility (SI) that is controlled by a single multiallelic S-locus. To characterize the genomic region of the S-locus using a map-based cloning method, a BAC library consisting of approximately 40,000 clones was constructed from genomic DNA of S1-homozygote, and screened using S-linked DNA markers which were mapped in our previous study. We constructed a contig covering the S-locus region with additional screening of fosmid and λ phase libraries. RFLP analysis of recombinant plants using terminal end sequences of the BAC clones as probes indicated that the S-locus region was delimited within a map distance of 0.57 cM, spanning approximately 300 kb in physical distance. Remarkable suppression of genetic recombination was detected in the S-locus region. From sequence analysis of the 313-kp region, 43 ORFs, many repetitive sequences and 5 transposable elements were predicted. None of the ORFs, however, showed a high homology with the SI genes reported to date at the S-locus of other plant families, suggesting that a unique molecular mechanism is involved in the SI system of the Convolvulaceae family.