Figure 2.

Identification of candidate sRNAs controlling the dominance–recessivity relationships: class IV > (class III, class II, class I). (a) Schematic diagrams of the S locus in the S₂₀ haplotype (HQ379628), S₃₉ haplotype (KJ772418–KJ772419), and S₅₀ haplotype (HQ379631). Green, yellow, and red boxes indicate SP11, SRK, and AlSMI1, respectively. (b) Massively parallel sequencing analysis of sRNA expression from the AlSMI1 inverted repeat sequence. sRNAs that obtained at least 10 reads were mapped against the AlSMI1 inverted repeat sequence. Arrows indicate mapped sRNAs and their directions. Numbers at the tips of arrows indicate the number of obtained sRNA reads, and numbers at the ends of arrows indicate the length of each sRNA (in nucleotides). Bases in red represent the 24-nt AlSmi1-a region. (c) Stem-loop structures of AlSMI1 of the S₂₀, S₃₉, and S₅₀ haplotypes predicted by RNAfold [20]. The predicted mature 24-nt AlSmi1-a region is shown in red. (d) Schematic diagrams of the S₂₀, S₅₀, S₁₃, S₁₆, S₁₄, S₁₈, and S₁-SP11 genomic regions. Black boxes indicate exon regions of SP11 genes, orange boxes indicate regions with high sequence similarity to AlSmi1-a. (e) Sequence similarity between AlSmi1-a and SP11. Each number shows the mispair score between the class IV (S₂₀, S₃₉, S₅₀)-AlSmi1-a and the SP11 introns of class-IV, class-III, class-II, and class-I S haplotypes. N.D., not detected. Mispair scores < 5.5 are shown in red.