Direct identification of a mutation in OsSh1 causing non-shattering in a rice (Oryza sativa L.) mutant cultivar using whole-genome resequencing

Feng Li,Akira Komatsu,Miki Ohtake,Heesoo Eun,Akemi Shimizu,Hiroshi Kato

doi:10.1038/s41598-020-71972-1

Abstract

Loss of seed shattering has been regarded as a key step during crop domestication. Mutagenesis contributes to the development of novel crop cultivars with a desired seed-shattering habit in a relatively short period of time, but also to uncovering the genetic architecture of seed shattering. ‘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.

Highlights

Loss of seed shattering has been regarded as a key step during crop domestication
It should be noted that the pulling strength (PS) and bending strength (BS) values may be affected by the health status of a pedicel
We found remarkable improvement of resistance to shattering in ‘Minamiyutaka’ compared to its original cultivar ‘Moretsu’ (Fig. 1)

Summary

Introduction

Loss of seed shattering has been regarded as a key step during crop domestication. Mutagenesis contributes to the development of novel crop cultivars with a desired seed-shattering habit in a relatively short period of time, and to uncovering the genetic architecture of seed shattering. Wild rice has a complete layer of abscission cells, while the SH4 domestication allele contributes to absent abscission cells near the vascular bundle, leading to incomplete development of the abscission zone in cultivated rice[2]. Another mutation is a single nucleotide polymorphism (SNP) in the 5′ regulatory region of the qSH1 gene, an ortholog of the Arabidopsis homeobox gene REPLUMLESS (RPL)[5,17]. Domestication-related Q gene, involved in controlling seed shattering, is an AP2-like g ene[27] These results suggest that the regulatory network controlling seed shattering is extensively conserved in grain crops, and that mutagenesis can facilitate the uncovering of the complex genetic architecture of seed shattering

Methods

Results

Conclusion