Fig. 1

Cloning of Sc reveals variations in genomic structure and copy number. a Pollen phenotypes of T65, E5, and their F₁. Arrows indicate smaller, sterile pollen grains (scale bars, 50 μm). The self-fertilized F₂ family shows a severely distorted segregation of the alleles (P  < 0.001 for the chi-square test). b Fine-mapping of Sc using F₂ plants of the T65/E5 cross. The markers indicate the positions (kb) in the BAC of the japonica cultivar (cv) Nipponbare (Nip). c Genomic configurations of the Sc alleles in japonica lines (from GenBank except for T65) and indica lines (determined in this study). The Sc-i allele variants have three or two tandemly duplicated segments, each containing the gene homologous to Os03g0247300. T1 (2016 bp) and T2 (9087 bp) are transposon insertions (a DDE-type and a Rim2/Hipa-type, respectively). The Sc-i paralogous genes have recombinant promoter/upstream sequences different from that of Sc-j. d Fiber-FISH images of the MH63 BAC (~ 180 kb) and the E5 chromatin (genomic) DNA (gDNA). For the BAC fiber-FISH, Probes I and II were labeled for red fluorescence, and the whole BAC DNA was labeled for green fluorescence. The labeled Probe I (or Probe II) was mixed with the labeled BAC for the hybridization. For fiber-FISH of E5 gDNA, Probes I and II were labeled for red and green fluorescence, respectively, and mixed for hybridization. Scale bars, 2 μm. Note that the BAC and chromatin DNA fibers for the same segments had different extension levels, similar to the previous observations³⁴. FF full fertility, SS semi-sterility