‘Minamiyutaka’, a non-shattering indica rice cultivar, was developed from the easy-shattering cultivar ‘Moretsu’ by mutation breeding via gamma-ray irradiation. In present study, we observed significant differences in shattering habit, breaking tensile strength, and abscission zone structure between ‘Moretsu’ and ‘Minamiyutaka’. Whole-genome mutation analysis of ‘Minamiyutaka’ newly identified a 13-bp deletion causing defective splicing in exon 3 of the OsSh1 gene which has previously been referred to as a candidate for controlling seed shattering. Using CRISPR/Cas9 gene editing, we demonstrated that loss-of-function mutation in OsSh1 causes non-shattering in rice. Furthermore, gene expression analysis suggests that OsSh1 may function downstream of qSH1, a known key gene involved in abscission zone differentiation. Nucleotide diversity analysis of OsSh1 in wild rice accessions and cultivars revealed that OsSh1 has been under strong selection during rice domestication, and a missense mutation might have contributed to the reduction of seed shattering from the wild progenitors to cultivated rice.
Comparison of seed shattering characteristics in the rice cultivars ‘Moretsu’ and ‘Minamiyutaka’. (a) Seed shattering habits of rice panicles in ‘Moretsu’ (Left) and ‘Minamiyutaka’ (Right). Photos were taken after grasping rice panicles. Bars = 5 cm. (b) Comparison of pulling strength (PS). P values were determined by Student’s t test. In the violin plots, the violin shape indicates the kernel-density curve, the white node in the center indicates the average value, and the black box inside the violin indicates a box-and-whisker plot. Violin plots were created using R software62 and ggplot2 package63. (c) Comparison of bending strength (BS). P values were determined by Welch’s t test. (d) Longitudinal Sects. (2-μm) across the abscission zone of ‘Moretsu’ (Left) and ‘Minamiyutaka’ (Right). The sections were stained by toluidine blue. Bars = 100 μm. AZ abscission zone, P pedicel, SL sterile lemma, VB vascular bundle. (e) shows scanning electron microscopy photos of the fracture surface of the grain base of ‘Moretsu’ (Left) and ‘Minamiyutaka’ (Right) after detachment of grains. Bars = 100 μm. (f) shows close-up scanning electron microscopy photos corresponding to the yellow boxes in (e). Bars = 10 μm.