Joohyun Lee

Weed control is among the principal challenges limiting the wider adoption of direct-seeded rice cultivation. Glufosinate is an effective non-selective herbicide, although its use in rice fields is limited by the high sensitivity of cultivated rice to this compound. However, a previously identified OsGS1;1 6-bp insertion allele (GCCTTC) has been established to confer glufosinate tolerance in rice, and in this study, using a dual-pegRNA prime editing strategy, we precisely introduced this allele into the Korean japonica rice cultivar Dongjin. Sanger sequencing of regenerated T0 plants identified the predicted homozygous 6-bp insertion in 14 of the 23 analyzed lines, corresponding to a homozygous precise editing frequency of 61%. Compared with the wild-type plants, when subjected to 2.5 mg/L glufosinate treatment, T2 plants derived from the homozygous line PE-gs1-1 were characterized by significantly greater shoot and root lengths, whereas only minor differences were observed in the absence of the herbicide. These findings reveal that the 6-bp OsGS1;1 insertion allele confers glufosinate tolerance in Dongjin following prime editing, thereby providing a transgene-free edited genetic resource for weed management and a strategy that is potentially applicable to other Korean rice cultivars.

Leaf rolling is a key component of rice canopy architecture that affects light interception, microclimate formation, and planting density. The contribution of naturally occurring allelic variation to quantitative variation in leaf rolling within cultivated rice remains poorly understood, while extreme leaf rolling caused by loss-of-function mutations often results in detrimental pleiotropic effects. Herein, we examined how multi-locus allelic variation contributes to natural variation in leaf rolling within japonica rice. Leaf rolling was quantified based on the leaf rolling index (LRI) using a panel of 201 japonica accessions. The phenotype was transformed using the Yeo–Johnson method to reduce strong right skewness and improve the distributional properties of the data, thereby facilitating subsequent regression modeling. Haplotype analyses were performed for previously reported leaf rolling-associated genes and genome-wide association study (GWAS) lead loci, leading to the identification of five loci exhibiting substantial haplotype-dependent phenotypic variation. Phenotypically defined allelic groups represented these loci were subsequently evaluated using multiple linear regression (MLR), with the first two principal components derived from genome-wide SNP data included as covariates to account for population structure. The final MLR model identified four loci ( qALR1 , OsYABBY1 , OsSLL2 , and OsSRL10 ) as the independent contributors to leaf rolling variation, collectively explaining 21% of the variance in the transformed phenotype after accounting for population structure. Model diagnostics and ten-fold cross-validation supported the statistical validity of the framework and indicated stable model performance across validation folds. Analysis of multi-locus allelic combinations showed 13 distinct configurations that clustered into three phenotypically differentiated groups. This reflected the cumulative dosage of high-leaf rolling alleles. Thus, the natural variation in leaf rolling in japonica rice is governed by the additive effects of multiple moderate-impact loci. The multi-locus allelic framework established here provides a statistically sound and biologically interpretable basis for dissecting polygenic canopy traits and practical guidance for developing genetic materials aimed at optimizing rice plant architecture.

Key message Combined association and selection sweep analyses identified OsCTD2 and OsLTPL159 as key candidate genes associated with cold tolerance at both germination and seedling stages. Abstract Cold sensitivity in rice leads to significant yield losses. Identifying cold-tolerant germplasm and uncovering cold tolerance genes are essential for developing resilient rice varieties. Kam Sweet Rice (KSR) is notable for strong cold tolerance, which is an invaluable genetic resource for identifying such genes. In this study, we phenotyped cold tolerance across various growth stages using 104 KSR accessions and 268 other rice landraces. Genome-wide association studies (GWAS) identified 89 loci significantly associated with cold tolerance: 57 loci at the germination stage, 9 at the bud stage, and 28 at the seedling stage, with 61 loci (69%) being newly discovered. Through association and selection sweep analyses, we identified two high-confidence candidate genes, OsCTD2 and OsLTPL159, associated with cold tolerance at both germination and seedling stages. Haplotype analysis revealed significant differences in cold tolerance grade and survival rate among various haplotypes of these genes, with superior haplotypes predominantly present in KSR. RNA-seq and qRT-PCR results showed that the superior haplotypes of OsCTD2 and OsLTPL159 exhibited significantly higher expression in cold-tolerant accessions under cold stress, whereas no significant differences were observed in cold-sensitive accessions with the inferior haplotypes. These results indicated that OsCTD2 and OsLTPL159 are involved in cold stress response in rice. Additionally, we identified two other promising candidate genes and their superior haplotypes for cold tolerance: OsGRS7 at the germination stage and OsBSR6 at the bud stage. Our findings provide a solid foundation for cloning cold tolerance genes and offer insights for designing molecular breeding strategies.

Rice cold tolerance is an important breeding target, particularly for Tongil-type rice. In this study, six molecular markers were developed for cold tolerance-related genes using five rice cultivars. dCAPS markers targeted OsCTK1 and OsSAPK6, tetra-primer ARMS-PCR markers targeted COLD1, LTG1, and HAN1, and a KASP marker targeted OsLUX. The markers discriminated allelic variation among cultivars. COLD1, LTG1, and HAN1 markers targeted characterized functional polymorphisms, whereas OsCTK1 targeted a haplotype-linked SNP and OsSAPK6 and OsLUX targeted parental polymorphisms. These markers may facilitate parental allele tracking and marker-assisted selection for cold-tolerance breeding in rice.

Pre-harvest sprouting (PHS) of rice (Oryza sativa L.) causes severe economic problems due to reduced grain quality and yield. Fine mapping was carried out to identify genes associated with PHS; the detected quantitative trait locus (QTL) was narrowed down to 50 Kbp using F_3:4 populations, four polymorphic insertion and deletion (InDel) markers, and two cleaved amplified polymorphic sequence (CAPS) markers. In one region, five candidate genes were detected, and the SNP and InDel in each gene (Os01g0111400 and Os01g0111600) were confirmed to show the differences and resulting amino acid changes between parent plants. Based on haplotype, expression, and co-segregation analysis, the InDel in Os01g0111600 was confirmed to be associated with the PHS trait. The results of this study could be applied to improve the PHS tolerance of Japonica rice varieties, and they also improved our understanding of the genetic basis underlying PHS tolerance.

Genetic transformation has emerged as an important tool for the genetic improvement of valuable plants by incorporating new genes with desirable traits. These strategies are useful especially in crops to increase yields, disease resistance, tolerance to environmental stress (cold, heat, drought, salinity, herbicides, and insects) and increase biomass and medicinal values of plants. The production of healthy plants with more desirable products and yields can contribute to sustainable development goals. The introduction of genetically modified food into the market has raised potential risks. A proper assessment of their impact on the environment and biosafety is an important step before their commercialization. In this paper, we summarize and discuss the risks and benefits of genetically modified plants and products, human health hazards by genetically transformed plants, environmental effects, Biosafety regulations of GMO foods and products, and improvement of medicinal values of plants by the genetic transformation process. The mechanisms of action of those products, their sources, and their applications to the healthcare challenges are presented. The present studies pointed out the existence of several controversies in the use of GMOs, mainly related to the human health, nutritions, environmental issues. Willingness to accept genetically modified (GM) products and the adoption of biosafety regulations varies from country to country. Knowledge about the gene engineering technology, debate between the government agencies, scientist, environmentalist and related NGOs on the GM products are the major factors for low adoptions of biosafety regulation. Therefore, the genetic transformation will help in the advancement of plant species in the future; however, more research and detailed studies are required.

Following the development of electric and hybrid vehicles, permanent-magnet synchronous machines (PMSMs) have been widely used as traction motors. In most PMSM drives, the rotor position sensor is required for reliable torque control. A variable reluctance resolver has been adopted as a position sensor in automotive industries thanks to its mechanical reliability in a harsh environment. Because the resolver signal is analog, the signal is vulnerable to the noise caused by electromagnetic interference such as common-mode voltage and external magnetic field. In this paper, the source of electromagnetic noise in the target motor system is identified experimentally. From finite element analysis (FEA), the noise path to the position signal of the resolver is identified. Furthermore, a strategy to suppress the noise is devised and evaluated with FEA and verified experimentally with an actual motor.

Direct seeding is considered an efficient cultivation technology that reduces water use and labor costs. Mesocotyl length is one of the significant traits in cultivation; long mesocotyl is beneficial for the rate and uniformity of seedling emergence. In this study, we used a core collection of 137 rice accessions to identify quantitative trait loci (QTL) for mesocotyl elongation. A genome-wide association study (GWAS), combined with a principal component analysis (PCA) and a kinship matrix analysis, was conducted for the genotype analysis of 2 million, high-quality single nucleotide polymorphisms (SNPs). Through this GWAS analysis, 11 lead SNPs were confirmed to be associated with mesocotyl length, and a linkage disequilibrium (LD) decay analysis identified the 230 kb exploratory range for the detection of QTLs and candidate genes. Based on the gene expression database and haplotype analysis, five candidate genes (Os01g0269800, Os01g0731100, Os08g0136700, Os08g0137800, and Os08g0137900) were detected to be significantly associated with phenotypic variation. Five candidate gene expressions are reported to be associated with various plant hormone responses. Interestingly, two biotic stress response genes and two copper-containing redox proteins were detected as the candidate genes. The results of this study provide associated SNPs in candidate genes for mesocotyl length and strategies for developing direct seeding in breeding programs.

Jeonghwan Seo, Hongjia Zhang, Ah-Rim Lee, Wondo Lee, Yoo-Hyun Cho, Soon-Wook Kwon, and Joohyun Lee. Korean J. Breed. Sci. 2021;53:424-31. https://doi.org/10.9787/KJBS.2021.53.4.424

Oxidative stress is a pathological condition occurring due to an imbalance between the oxidants and antioxidant defense systems in the body. Nuclear factor E2-related factor 2 (NRF2), encoded by the gene NFE2L2, is the master regulator of phase II antioxidant enzymes that protect against oxidative stress and inflammation. NRF2/ARE signaling has been considered as a promising target against oxidative stress-mediated diseases like diabetes, fibrosis, neurotoxicity, and cancer. The consumption of dietary phytochemicals acts as an effective modulator of NRF2/ARE in various acute and chronic diseases. In the present review, we discussed the role of NRF2 in diabetes, Alzheimer’s disease (AD), Parkinson’s disease (PD), cancer, and atherosclerosis. Additionally, we discussed the phytochemicals like curcumin, quercetin, resveratrol, epigallocatechin gallate, apigenin, sulforaphane, and ursolic acid that have effectively modified NRF2 signaling and prevented various diseases in both in vitro and in vivo models. Based on the literature, it is clear that dietary phytochemicals can prevent diseases by (1) blocking oxidative stress-inhibiting inflammatory mediators through inhibiting Keap1 or activating Nrf2 expression and its downstream targets in the nucleus, including HO-1, SOD, and CAT; (2) regulating NRF2 signaling by various kinases like GSK3beta, PI3/AKT, and MAPK; and (3) modifying epigenetic modulation, such as methylation, at the NRF2 promoter region; however, further investigation into other upstream signaling molecules like NRF2 and the effect of phytochemicals on them still need to be investigated in the near future.