Figure 2

Whole-genome resequencing identified a 13-bp deletion in OsSh1 as candidate causal mutation leading to loss of seed shattering in ‘Minamiyutaka’. (a) Integrative Genomics Viewer screenshot of the region containing the 13-bp deletion for ‘Moretsu’ (Upper Graph) and ‘Minamiyutaka’ (Lower Graph). Genome position and gene annotation are shown at the top and bottom, respectively. The 13-bp deletion causes defective splicing in exon 3. (b) Sanger sequencing chromatograms of the region containing the 13-bp deletion for ‘Moretsu’ (Upper Graph) and ‘Minamiyutaka’ (Lower Graph). (c) Sequence alignment of the deduced amino acid sequences of OsSh1 in ‘Moretsu’ and ‘Minamiyutaka’. The 13-bp deletion causes exon 3 skipping and a reading frameshift leading to a putative translational termination codon. Zinc finger domain and YABBY domain are underlined in red and green, respectively. (d) Seed shattering and genotype of the OsSh1 gene in an F₂ population derived from the cross between ‘Moretsu’ and ‘Minamiyutaka’. W/W (n = 21) represents a homozygous allele for ‘Moretsu’, m/m (n = 27) represents a homozygous allele for ‘Minamiyutaka’, and W/m (n = 52) for a heterozygous allele.