Deletion of a 236 kb region around S 4-RNase in a stylar-part mutant S 4sm-haplotype of Japanese pear

Japanese pear (Pyrus pyrifolia Nakai) has a gametophytic self-incompatibility (GSI) mechanism controlled by a single S-locus with multiple S-haplotypes, each of which contains separate genes that determine the allelic identity of pistil and pollen. The pistil S gene is the S-ribonuclease (S-RNase) gene, whereas good candidates for the pollen S gene are the F-box protein genes. A self-compatible (SC) cultivar, ‘Osa-Nijisseiki’, which is a bud mutant of ‘Nijisseiki’ (S 2 S 4), has a stylar-part mutant $$ S^{{sm}}_{4} $$ -haplotype, which lacks the S 4-RNase gene but retains the pollen S gene. To delineate the deletion breakpoint in the $$ S^{{sm}}_{4} $$ -haplotype, we constructed a bacterial artificial chromosome (BAC) library from an S 4-homozygote, and assembled a BAC contig of 570 kb around the S 4-RNase. Genomic PCR of DNA from S 4- and $$ S^{{sm}}_{4} $$ -homozygotes and the DNA sequence of the BAC contig allowed the identification of a deletion of 236 kb spanning from 48 kb upstream to 188 kb downstream of S 4-RNase. The $$ S^{{sm}}_{4} $$ -haplotype lacks 34 predicted open reading frames (ORFs) including the S 4-RNase and a pollen-specific F-box protein gene (termed as S 4 F-box0). Genomic PCR with a primer pair designed from the deletion junctions yielded a product specific for the $$ S^{{sm}}_{4} $$ -haplotype. The product could be useful as a maker for early selection of SC cultivars harboring the $$ S^{{sm}}_{4} $$ -haplotype.