As recent advances in gene editing technologies have enabled rapid and accurate modification of target genes, new varieties are being developed through the application of gene editing technologies in various crop species. In particular, the CRISPR/Cas9 system has become a tool of choice for gene editing because it is much more economical and efficient than previous tools such as ZFN and TALEN, and is being actively used to improve various breeding traits, including biotic and abiotic stress tolerance to overcome the limitations of conventional plant breeding technologies. In this review, we retrieved 210 papers describing the utilization of CRISPR/Cas9 in rice published between 2013 and 2021 and classified them according to the field of study and traits of interest. Further case studies were conducted on 21 and 12 research papers that reported the enhancement of biotic and abiotic stress tolerance, respectively. This demonstrated that CRISPR/Cas9-based gene editing can be highly effective in improving resistance to bacterial (bacterial leaf blight and bacterial leaf streak), fungal (blast, sheath blight), and viral (rice tungro spherical virus, rice black streak virus) diseases as well as various abiotic stresses, including drought, salinity, cold, and heat, in many cases, without diminishing important agronomic traits. As recent technological advances have begun to overcome the major limitations of CRISPR/Cas9 gene editing, such as low HDR efficiency and off-target effects, it is expected that more research on gene function and cultivar development will adopt CRISPR/Cas9 as a major gene editing tool in the future. To effectively apply such innovative technologies in crop improvement, much effort is required to establish more reasonable and detailed policies for regulating crops developed through new breeding technologies.

A dwarf mutant rice line was selected from an Ac/Ds insertion mutant population and named dwf1. The phenotype of F₁ and F₂ plants derived from a cross between dwf1 and Dongjin indicated that a single recessive gene is responsible for the mutant phenotype, and we named this gene dwf1. Resequencing of the dwf1 line and Dongjin (wild type) revealed 42,386 homozygous single nucleotide polymorphisms (SNPs) between dwf1 line and Dongjin. MutMap analysis was performed by sequencing a DNA pool prepared from 100 mutant type plants in the dwf1/Dongjin F₂ population, and it was found that the dwf1 gene was located in the 23 ~ 30 Mbp region on chromosome 4. In this region, we found a non-synonymous SNP in the Os04g0469800 gene, which was reported as D11 gene encoding a cytochrome P450 family protein involved in the biosynthesis of brassinosteroids (BRs). This SNP was regarded as the causative SNP for the dwf1 phenotype, and the dwf1 gene is a novel allele of D11. We performed mapping of the dwf1 gene with five SNP markers on chromosome 4 with 190 dwf1/Dongjin F₂ plants. The phenotype of F₂ plants was completely co-segregated with genotypes of the J10402 marker, which was developed based on the non-synonymous SNP in the D11 gene. These results will contribute to the study of the molecular biological functions of the D11 gene and BRs.

Seed dormancy is an important adaptive mechanism to protect seeds under the unfavorable environments. Unlike to wild type species, the seed dormancy trait of cultivated crops has been weakened by breeding programs during the domestication period. Weak seed dormancy often causes preharvest sprouting (PHS) problem in many cereal crops that result in significant economic loss. The seed dormancy is a quantitative trait loci (QTL) controlled by multiple genetic and environmental factors. So far, many QTLs for seed dormancy have been identified from rice and wheat as well as in the model plant Arabidopsis. Unveiling of QTL genes and complex mechanisms underlying seed dormancy is accelerated by the rapid progress of crop genomics. In the present study, we reviewed current status of research progress on the seed dormancy QTLs and correlated genes in Arabidopsis and cereal crops.