Climate change-induced instability in cultivation environments poses a major threat to rice productivity, highlighting the need to develop climate-adaptive rice cultivars. The identification of favorable alleles from diverse genetic resources is therefore essential for broadening the genetic basis of breeding materials and improving agronomic performance under variable environments. In this study, 147 rice accessions derived from the International Rice Research Institute’s 3 K Rice Genomes Project, consisting primarily of japonica accessions showing relatively early heading under temperate field conditions, were evaluated for days to heading (DTH), culm length (CL), and panicle length (PL) across three environments. A genome-wide association study (GWAS) was performed using the FarmCPU model with 926,373 single nucleotide polymorphisms (SNPs). Three stable QTLs, qDTH3, qCL9, and qPL11, were identified for DTH, CL, and PL, respectively, and their lead SNPs showed significant phenotypic differences between allelic groups. Haplotype analyses further suggested Os03g0401200 (LHD3) and Os09g0422500 (BC6) as promising candidate genes underlying qDTH3 and qCL9, respectively. Specifically, qDTH3 may facilitate the adjustment of heading date with limited effects on culm and panicle development, whereas qCL9 suggests a potential link between culm length variation and cell wall biosynthesis. These findings provide useful genetic resources and molecular breeding targets for the development of climate-resilient rice cultivars.

Directional selection within elite breeding pools has narrowed the genetic base, yet phenotypic diversity persists among modern cultivars. Here, we analyzed 257 Korean japonica rice cultivars to dissect the genetic and environmental determinants of heading date. A genome-wide association study (GWAS) identified Hd1, Ghd7, OsPRR37, and Hd16 as major-effect genes in the population. Given the central role of Hd1 in variation of heading date, subpopulation-specific GWAS based on Hd1 functionality was performed to uncover minor-effect variants. Regression models using alleles identified in GWAS explained a substantial portion of phenotypic variance and achieved higher predictive accuracy than genome-wide SNP-based prediction within this population. Allele-specific genomic prediction with the additive linear model LASSO closely matched the nonparametric machine learning model XGBoost, indicating that additive effects largely accounted for variation in heading date. A redefined accumulated temperature index (ATI) model further enabled estimation of cultivar-specific thermal requirements within an optimized developmental window. We also discuss how the Hd1-Type14 allele was preferentially utilized for developing early maturing cultivars in Korean breeding programs. These findings demonstrate that integrating allele-based and environment-based prediction provides an effective framework for improving breeding precision for regional adaptation.

ROC5, an HD-ZIP IV transcription factor, negatively regulates bulliform cell development and leaf rolling in rice (Oryza sativa L.). Its molecular partners in epidermal cell fate are well characterised, but its broader effects on agronomic performance and gene expression remain largely unexplored. We evaluated a CRISPR/Cas9-generated roc5 loss-of-function line in the Korean elite japonica cultivar 'Samkwang' over two field seasons, with comparative RNA-seq analysis of flag leaf and panicle tissues at the heading stage. The roc5 line exhibited abaxial leaf rolling; reductions in culm and panicle length, grain number per panicle, and spikelet fertility, resulted in a 32.9

Abstract Fine‐tuning heading date is critical for optimizing yield, grain quality, and local adaptation in rice (Oryza sativa L.). QTL‐seq (where QTL is quantitative trait locus), which integrates bulked segregant analysis with whole‐genome resequencing, provides a rapid and cost‐effective approach for identifying QTLs underlying complex traits. Shinpyeong and Haedeul are elite Korean rice cultivars that carry identical alleles at four major heading date genes (Hd1, OsPRR37, Ghd7, and DTH8), yet differ by approximately 7 days in heading under natural long‐day conditions. To elucidate the genetic basis of this difference, we applied allele‐informed QTL‐seq to an F2 population derived from a cross between Shinpyeong and Haedeul. A single prominent QTL peak with the highest ΔSNP‐index (where SNP is single nucleotide polymorphism) was consistently detected across both field and greenhouse environments and co‐localized with Hd18, identifying it as the most likely causal gene. The underlying polymorphism was a previously reported missense A/G variant. Genotyping of the Hd18 A/G SNP using a dCAPS (derived cleaved amplified polymorphic sequence) marker revealed that F2 plants homozygous for the A allele headed 4.1 days earlier in the field and 6.2 days earlier in the greenhouse than those homozygous for the G allele. Analysis of 290 Korean rice cultivars further demonstrated that the Hd18 A allele was associated with approximately 2 days earlier heading under a nonfunctional hd1 background. Evaluation of two recombinant inbred line populations showed that Hd18 had minimal effects on major agronomic traits, while exhibiting background‐dependent effects on specific traits. These results establish Hd18 as a minor effect modifier of heading date with utility for fine‐scale phenological adjustment in rice breeding.

Recent climate change and frequent extreme weather events during the maturation period of rice exacerbate lodging and threaten stable production. Samkwang, a widely cultivated rice variety in Korea, is particularly vulnerable to lodging due to its tall stature. To improve lodging tolerance while preserving Samkwang’s elite genetic background, we identified an SMXL4-edited line (smxl4) with reduced culm length and stable growth from a CRISPR/Cas9-edited Samkwang population. The biological function of SMXL4, a clade Ⅳ member of the SMXL (SUPPRESSOR OF MAX2 1-LIKE) family, has not been well characterized in rice. Compared to Samkwang, the smxl4 plants showed reduced plant height, internode length, panicle length, grain number per panicle, and grain weight, while panicle number per plant increased. Transcriptome profiling of elongating internodes at booting and heading stages revealed upregulation of genes associated with cell wall remodeling and defense responses in smxl4 relative to Samkwang. These findings highlight the broad involvement of SMXL4 in rice growth and development and provide insights for breeding lodging tolerant rice cultivars.

Enhancing productivity is a crucial objective in rice breeding programs. As genes for increased yield are present in indica and japonica subspecies distinctively, pyramiding favorable alleles from the two subspecies can increase yield effectively. In this study, 117 doubled haploid lines derived from the cross between 93–11 (indica) and Milyang352 (japonica) were evaluated for their yield-related traits under three different environments. QTL analysis with this population identified two and four stable QTLs for panicle length and thousand-grain weight, respectively. qPL3 and qPL7 increased panicle length with the 93–11 alleles, with significant pyramiding effects. For thousand grain weight, qTGW2, qTGW5, and qTGW10 increased the trait with the Milyang352 allele, while qTGW3 with the 93–11 allele, with beneficial pyramiding effects. In the long panicle background (qPL393−11 + qPL793−11), the pyramiding of MY352 alleles at qTGW2 and qTGW5 resulted in an increase in thousand-grain weight, while maintaining panicle length and grain number per panicle, indicating that using this QTL combination can be used for yield improvement. These findings provide valuable insights for developing high-yielding rice varieties and optimizing allele combinations for improved productivity.

The present study aimed to identify genetic loci associated with days to heading (DTH) in wheat under autumn-sowing conditions in Korea, where early heading is critical owing to the overlap between the wheat harvest and the rainy season. We evaluated 530 wheat core collections over five years, focusing on known heading date genes VRN-1 and PPD-1, and conducted a genome-wide association study (GWAS) to identify new genetic loci related to DTH. The results revealed that Korean accessions exhibited the earliest DTH, with modern Korean varieties heading even earlier, reflecting a strong breeding focus on early heading. Among the existing heading date genes, VRN-1 and PPD-D1 were significantly associated with DTH in the wheat core collection. However, all Korean varieties carried the same alleles for each of VRN-A1, PPD-A1, and PPD-D1, resulting in low genetic diversity, which rendered the existing heading date genes insufficient to fully account for the variation in DTH within the Korean varieties. GWAS identified nine single nucleotide polymorphisms (SNPs) associated with DTH in Group A (entire collection filtered, n=518) and six in Group B (accessions with genotypes identical to Korean varieties filtered, n=231). Four key SNPs (AX-95222044 and AX-94685526 in Group A, and AX-94550996 and AX-94970315 in Group B) were selected based on their effect sizes on DTH. In both groups, accessions with alleles for early heading at both of the selected SNPs exhibited the earliest DTH, advancing by 7.7 to 8.9 days. These findings suggest that the selected SNPs, particularly those reflecting the genotypes of Korean varieties, effectively explain the variations in DTH among Korean varieties and could enhance wheat breeding efficiency in Korea. Further research is needed to validate the four selected SNPs and identify the underlying genes, which could serve as valuable markers for developing early-heading wheat varieties suited to Korean autumn-sowing conditions.

Rice yield is a complex trait influenced by genotype-by-environment interactions (GEI), with climate change further intensifying these effects. Therefore, evaluating crop productivity and adaptability in diverse environments is essential in plant breeding. Here, we evaluated the yield-related traits and yield performance of 25 Korean rice cultivars under early- and late-season transplanting in two consecutive years. By utilizing GEI analysis and machine learning (ML) models, we aimed to identify superior genotypes for each trait based on transplanting seasons and assess trait contribution to rice yield. On average, in the late season compared to the early-season, days to heading were significantly promoted by 25 days, grain filling rate increased by 5

Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) poses a serious threat to rice production. The pathogen promotes infection by targeting effector binding elements in the promoter regions of rice susceptibility genes such as SWEET (Sugars Will Eventually be Exported Transporters) genes. Previous studies have shown that natural or induced variations in SWEET genes can effectively enhance BB resistance in rice. However, the effects of variations in SWEET genes on disease resistance and agronomic performance vary depending on the Xoo strains and the genetic background of rice cultivars, highlighting the need for precise evaluations in breeding applications. In this study, we developed a CRISPR/Cas9-edited OsSWEET14 knockout line (SK-s14) in the background of the elite Korean rice cultivar Samkwang. The SK-s14 line exhibited enhanced resistance against the Xoo strain KACC10859. Transcriptomic analysis revealed that defense-related genes, including pathogenesis-related genes and salicylic acid signaling genes, were downregulated in SK-s14 relative to Samkwang under Xoo inoculation. These results suggest that the enhanced resistance may result from pathogen starvation due to restricted sugar efflux to apoplast, rather than from classical defense activation. Field evaluations showed that SK-s14 plants headed 1–7 days earlier, had longer panicles (+ 8.0

Rice blast is a destructive fungal disease affecting rice plants at various growth stages, significantly threatening global yield stability. Development of resistant rice cultivars stands as a practical means of disease control. Generally, association mapping with a diversity panel powerfully identifies new alleles controlling trait of interest. On the other hand, utilization of a breeding panel has its advantage that can be directly applied in a breeding program. In this study, we conducted a genome-wide association study (GWAS) for blast resistance using 296 commercial rice cultivars with low population structure but large phenotypic diversity. We attempt to answer the genetic basis behind rice blast resistance among early maturing cultivars by subdividing the population based on its Heading date 1 (Hd1) functionality. Subpopulation-specific GWAS using the mixed linear model (MLM) based on blast nursery screening conducted in three years revealed a total of 26 significant signals, including three nucleotide-binding site leucine-rich repeat (NBS-LRR) genes (Os06g0286500, Os06g0286700, and Os06g0287500) located at Piz locus on chromosome 6, and one at the Pi-ta locus (Os12g0281300) on chromosome 12. Haplotype analysis revealed blast resistance associated with Piz locus was exclusively specific to Type 14 hd1 among japonica rice. Our findings provide valuable insights for breeding blast resistant rice and highlight the applicability of our elite cultivar panel to detect superior alleles associated with important agronomic traits.

Kyeong-Min Kim, Sumin Hong, Myung-Goo Choi, Changhyun Choi, Myoung Hui Lee, Mira Yoon, Chon-Sik Kang, Ki-Chang Jang, Youngjun Mo, and Chul Soo Park. Korean J. Breed. Sci. 2024;56:113-24. https://doi.org/10.9787/KJBS.2024.56.2.113

Abstract Introduction Optimal intrinsic capacity (IC) is crucial for preserving the functional abilities of older adults. The presence of multimorbidity is closely associated with IC impairments. Various multimorbidity indices have been developed for diverse health outcomes. This study aimed to compare the performance of six commonly used multimorbidity indices to discriminate IC impairments among community-dwelling older adults. Method We used data from a multidimensional geriatric assessment program including 627 community-dwelling older adults in five cities of Hunan, China. Six multimorbidity indices were extracted from the data, including disease counts, Functional Comorbidity Index (FCI), the Deyo Charlson comorbidity index, two indices (total score and comorbidity index) derived from the Cumulative Illness Rating Scale-Geriatric (CIRS-G), and medication counts. The IC was measured with five individual domains, i.e., locomotion, vitality, sensory, cognition, and psychological capacity. Individuals were regarded as having IC impairments if they had impairments in one or more domains. Associations between multimorbidity indices and IC impairments were examined using logistic regression analyses. The discriminative ability of multimorbidity indices for IC impairments was compared using the c-statistics. Results A total of 374 (59.6%) participants had IC impairments. All multimorbidity indices were significantly associated with IC impairments after adjusting for confounding factors. All indices showed acceptable discriminative power (c-statistic ranged from 0.711 to 0.759) for IC impairments. The comorbidity index derived from CIRS-G resulted in the highest c-statistic, followed by the total score of CIRS-G and FCI. Conclusions Our study results suggest that multimorbidity indices differed in their ability to discriminate IC impairments. The comorbidity index derived from CIRS-G performed better than other multimorbidity indices included in this study. The comorbidity index has the potential as a simple proxy measure of indicating the need for interventions to optimise IC for older adults in community settings.

Heading date is a critical agronomic trait that significantly affects grain yield and quality in rice. As early heading is typically associated with reduced yield due to shorter growth duration, it is essential to harness optimum heading date genes and their allelic combinations to promote heading while minimizing yield penalties. In this study, we identified quantitative trait loci (QTLs) for heading date and other major agronomic traits in a recombinant inbred line (RIL) population derived from a cross between Koshihikari and Baegilmi. Analyses on 3 major QTLs for heading date and their underlying genes (Hd1, Hd16, and Ghd7) revealed their pleiotropic effects on culm length, panicle length, and head rice percentage. Additionally, Ghd7 exhibited pleiotropic effects on panicle number and grain size. Among 8 different types of allelic combinations of the 3 heading date genes, RILs carrying a single nonfunctional hd16 or ghd7 under the functional background of the other 2 genes (Hd1hd16Ghd7 and Hd1Hd16ghd7) showed potential for maintaining yield and quality-related traits while accelerating heading. These results provide valuable insights for fine-tuning heading dates in rice breeding programs.

Wheat, one of the most important cereal crops globally, stands as the second most consumed crop in Korea following rice. However, the self-sufficiency rate of wheat is extremely low (1.1%, as of 2021) in Korea, leading to an excessive dependency on imports. Therefore, developing wheat varieties with high productivity and quality for Korean environments is crucial to improve self-sufficiency. As wheat breeding in Korea has mainly focused on developing early-maturing varieties suitable for the rice-wheat double cropping system, genetic diversity is highly limited. Hence, it is essential to establish a genetically diverse germplasm pool to discover and utilize valuable breeding materials for the development of competitive varieties. This study has two main objectives: (i) Assess genetic diversity among 359 underutilized wheat accessions from 45 countries based on a comparative analysis of nine key agronomic traits. (ii) Select superior accessions which can be utilized for building a breeding population. The agronomic traits of the 359 wheat accessions exhibited wide variation. Using principal component and k-means cluster analyses, the 359 accessions were classified into three groups, and characteristics among these groups were compared to analyze genetic diversity within the population. Based on the results, accessions with superior spikelet number per spike (SNS) and thousand grain weight (TGW) were selected for further use in breeding and genetic analysis.