Amylose content is a key factor affecting the eating and cooking qualities of rice. In our previous study, protein disulfide isomerase like 1-1 (PDIL1-1) on chromosome 11 was a candidate gene for amylose content (AC) trait. Based on whole genome sequencing, polymorphisms were identified between Dodamssal and Hwayeong on PDIL1-1. In this study, the association of PDIL1-1 on AC was characterized. Haplotype analysis of 79 KNU accessions highlighted the presence of allelic patterns identifiable by the sequence variants between Dodamssal and Hwayeong. Identified SNPs and InDel were used to develop gene-based molecular markers for PDIL1-1. The 29 F₂ plants and 160 Korean japonica cultivars were classified into two and three groups, respectively, based on the G/A SNP at position -4973180 and ATTCG/G at position -4974161. Our findings revealed that the G/A SNP at position -4973180 of PDIL1-1 plays a role in regulating the AC in japonica rice. This suggested that PDIL1-1 would be useful for fine-tuning the rice AC. To our knowledge, no studies of the allelic variation of the PDIL1-1 gene regulating AC have been reported worldwide. Furthermore, no research had reported the development of PDIL1-1 gene-based molecular markers.

Cold stress is one of the serious abiotic stresses for stable rice production especially in high-latitude temperate region and high-altitude tropical area. Improving cold tolerance at seedling stage led stable seedling growth with yield stability. In this study, QTLs for cold tolerance at seedling stage were identified using the 96 introgression lines (ILs) derived from an inter-specific cross between Hwaseong (Oryza sativa) and Oryza rufipogon. Three QTLs were detected and the O. rufipogon alleles at two QTL (qCTS1 and qCTS12) improved cold tolerance in the Hwaseong genetic background whereas the O. rufipogon allele at qCTS10 on chromosome 10 decreased cold tolerance. Among these three QTLs, a major QTL qCTS12 explained 27.5% of phenotypic variation. Fine-mapping indicated that qCTS12 was different from those QTL reported in previous studies based on the map location suggesting that qCTS12 might be a new allele and is not associated with deleterious genes such fertility reduction. Among the 96 introgression lines, two lines, CR60 and CR61 were selected based on enhanced cold tolerance at seedling stage. qCTS12, therefore, provides a valuable allele for breeding rice with improved cold tolerance.

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• Stage-specific screening reveals differential resilience response to cold stress in rice
  Fahamida Akter, Partha S. Biswas, Abul Kalam Mohammad Aminul Islam, Mohammad Sharif Raihan, Md. Mizanur Rahman, Khandakar Md. Iftekharuddaula, Mohammad Rafiqul Islam, John Damien Platten, Md Ashrafuzzaman
  PLOS One.2026; 21(4): e0338290.     CrossRef
• Genome-wide Association Study for Cold Tolerance at Seedling Stage Using a Core Collection of Korean Rice
  Sa-Eun Park, Ngoc Ha Luong, Sang-Nag Ahn, Kyu-Chan Shim
  Journal of Agriculture & Life Science.2025; 59(2): 13.     CrossRef
• Identification of QTLs Related to Plant Growth at Low Temperatures in the Seedling Stage of Tongil Type Rice after Transplanting
  Seong-Gyu Jang, Ji-Yoon Lee, Ju-Won Kang, Youngho Kwon, So-Myeong Lee, Sais-Beul Lee, Jun-Hyeon Cho, Dong-Soo Park, Jong-Hee Lee, Soon-Wook Kwon, Sumin Jo
  Korean Journal of Breeding Science.2024; 56(3): 225.     CrossRef

We conducted transcriptome profiling analysis of O. glaberrima root using RNA-Seq at the control (OCR) and 100 mM NaCl treatment (OTR) at two time points (6 and 24 hours after treatment) to detect genes induced by salt stress. RNA-Seq analysis generated 102,690,698 sequence reads representing 30,388 predicted transcripts including 6,189 unannotated in Rice Annotation Project database. A total of 539 and 424 of differentially expressed genes (DEGs) were detected between OCR_6hours vs OTR_6hours and between OCR_24hours vs OTR_24hours, respectively (P < 0.001, q < 0.05). Among these DEGs, 262 genes showed constant differential expression at both 6 hours and 24 hours, and these included a bHLH containing protein, WRKY transcription factor, serine/threonine kinase, R2R3 MYB protein, and amino acid transporters. Interestingly, an enhanced seedling salt tolerant introgression line IL55 from a cross between a salt sensitive indica cultivar “Milyang23” and O. glaberrima harbors one DEG, Os02g0787300 encoding a mitogen activated protein kinase kinase (MAPKK) on chromosome 2. Analysis of the salt tolerance of the F_2:3 lines from a cross between IL55 and Milyang23 indicated that the O. glaberrima segment on chromosome 2 containing the MAPKK gene was responsible for better shoot growth under salt stress at the seedling stage. The salt inducible genes will be evaluated in introgression lines (ILs) to understand whether the expression of these genes is associated with salt tolerance in ILs having the Milyang23 genetic background. Transcriptome sequence information in this study may be useful for developing DNA markers linked to salinity tolerance for MAS breeding.

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• Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages
  Taikui Zhang, Weichen Huang, Lin Zhang, De-Zhu Li, Ji Qi, Hong Ma
  Nature Communications.2024;[Epub]     CrossRef
• Grain protein function prediction based on self-attention mechanism and bidirectional LSTM
  Jing Liu, Xinghua Tang, Xiao Guan
  Briefings in Bioinformatics.2023;[Epub]     CrossRef

Genetic analysis of genes that regulate the color pigmentation of sterile lemma and apiculus has been conducted. “Josaengjado” has small and round grains with purple leaf, sterile lemma and apiculus. In the F₂ population from a cross between Josaengjado and Daeribbyeo 1, 246 and 182 plants exhibited purple and straw-white sterile lemma, respectively. It fitted a 9:7 segregation ratio indicating that two complementary genes control the pigmentation in sterile lemma and apiculus. Genetic analysis was performed using the F_2:3 and KASP (Kompetitive Allele-Specific PCR) markers. Genes for the coloration of leaf sheath, ligule, sterile lemma, and apiculus were detected on chromosomes 1 and 6. Sequence comparison showed a single nucleotide substitution C (Josaengjado) to A (Daeribbyeo 1) in the second exon of the Rd gene on chromosome 1 leading to a premature stop in Daeribbyeo 1. In C1, a 3-bp deletion in the second exon was detected in Daeribbyeo 1. Haplotype analysis was performed in the Rd and C1 genes of the 78 rice accessions. 78 accessions were divided into 14 groups. A total of 11 and 1 mutation sites were detected in OsC1 and Rd, respectively. The haplotype analysis also confirmed that two complementary genes, Rd and OsC1 are necessary to express anthocyanin pigmentation in sterile lemma and apiculus. To our knowledge, this is the first report to identify genes for the coloration of sterile lemma in rice.

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• Genetic dissection and transcriptomic analysis of a novel high‐tillering phenotype in rice derived from weedy rice (Hapcheonaengmi3) and Tongil‐type Rice (Milyang23)
  Kyu‐Chan Shim, Donghyun Jeon, Yun‐A Jeon, Cheryl Adeva, Hyun‐Sook Lee, Ju‐Won Kang, Sa‐Eun Park, Sang‐Nag Ahn, Inkyu Park
  The Plant Genome.2026;[Epub]     CrossRef
• Identification of a novel mutant allele of the LIKE EARLY STARVATION 1 gene in rice (Oryza sativa L.) using QTL-seq
  Kyu-Chan Shim, HyunJung Kim, Mi-Ra Yoon, Sung-Ho Na, Sa-Eun Park, Sang-Nag Ahn, Thomas H Tai, J Holland
  G3: Genes, Genomes, Genetics.2026;[Epub]     CrossRef
• Spontaneous mutation in OsABCI8 caused an albino rice mutant induced by transplanting
  Kyu-Chan Shim, Yun-A Jeon, Hyun-Sook Lee, Sang-Nag Ahn, Inkyu Park
  Scientific Reports.2025;[Epub]     CrossRef
• Genetic analysis and gene mapping of the purple glume tip trait in rice (Oryza sativa)
  Gang Jin, Zhongquan Cai, Yanxi Chen, Ying Ling, Liping Wang, Deyuan Mo
  Crop Breeding and Applied Biotechnology.2024;[Epub]     CrossRef
• T-DNA insertion mutants of Arabidopsis DA1 orthologous genes displayed altered plant height and yield-related traits in rice (O. sativa L.)
  Kyu-Chan Shim, Ngoc Ha Luong, Thomas H. Tai, Gyu-Ri Lee, Sang-Nag Ahn, Inkyu Park
  Genes & Genomics.2024; 46(4): 451.     CrossRef
• A Frameshift Mutation in the Mg-Chelatase I Subunit Gene OsCHLI Is Associated with a Lethal Chlorophyll-Deficient, Yellow Seedling Phenotype in Rice
  Kyu-Chan Shim, Yuna Kang, Jun-Ho Song, Ye Jin Kim, Jae Kwang Kim, Changsoo Kim, Thomas H. Tai, Inkyu Park, Sang-Nag Ahn
  Plants.2023; 12(15): 2831.     CrossRef
• Identification of QTLs for Cold Tolerance at Seedling Stage Using a Population Derived from an Inter-specific Cross in Rice
  Kyu-Chan Shim, Yeo-Tae Yun, Ju-Won Kang, Sang-Nag Ahn
  Plant Breeding and Biotechnology.2022; 10(4): 282.     CrossRef

Quantitative trait loci (QTLs) for the starch-related traits amylose content (AC) and resistant starch (RS) content have received much attention due to the potential benefits of grains high in these starch levels. In this study, QTLs associated with AC and RS content were identified using 92 recombinant inbred lines (RILs) developed from a cross between two closely related japonica cultivars ‘Dodamssal’ and ‘Hwayeong’. One QTL on chromosome 2 for RS content and 2 QTLs for AC on chromosomes 2 and 6 were detected. The F₂ population derived from a cross between Hwayeong and two selected RILs were used to analyze the interaction between starch branching enzyme 3 (SBE3) and granule-bound starch synthase 1 (GBSS1). The combined effect of SBE3 and GBSS1 in the F₂ population suggested that these two genes behaved in an additive manner in increasing AC. Haplotype analysis based on two SNPs in GBSS1 classified 117 rice accessions into three groups. At the first SNP site, all indica, Korean landrace, and weedy rice accessions had the Wx^a allele at the 5ʹ splice site of intron 1, whereas japonica accessions had the mutated Wx^b allele. This suggests that this splice-donor mutation is prevalent in japonica cultivars, but rare or absent in landrace and weedy rice cultivars. Landrace or weedy rice accessions harboring the Wx^a allele could be employed in breeding programs to manipulate AC in cultivated japonica rice considering the difficulty and time to introduce desirable indica traits into japonica due to reproductive barriers.

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• Improved Processing Quality in a tongil-type Waxy Rice Cultivar Associated with a Rare granule-bound starch synthase I Allele
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  Korean Journal of Breeding Science.2026; 58(2): 123.     CrossRef
• Evaluation of glycemic response and starch digestibility in Korean rice toward the development of low GI rice
  Chang-Min Lee, O-Young Jeong, Hyun-Su Park, Jeonghwan Seo, Songhee Park, Keon-Mi Lee, Mina Jin, Il-Ryong Choi, Jae-Hyuk Han
  Frontiers in Plant Science.2025;[Epub]     CrossRef
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  Xia Li, Xiaomeng Yang, Li’e Yang, Hafiz Ghulam Muhu-Din Ahmed, Chunlian Yao, Jiazhen Yang, Luxiang Wang, Tao Yang, Xiaoying Pu, Yawen Zeng
  Biologia.2024; 79(7): 2203.     CrossRef
• Allelic Diversity at Protein Disulfide Isomerase Like 1-1 (PDIL1-1) Gene is Associated with Amylose Content in Japonica Rice
  Cheryl Adeva, Ju-Won Kang, Kyu-Chan Shim, Ngoc Ha Luong, Hyun-Sook Lee, Jong-Hee Lee, Sang-Nag Ahn
  Plant Breeding and Biotechnology.2023; 11(1): 56.     CrossRef
• Quality Characteristics of Rice-Based Ice Creams with Different Amylose Contents
  Gi-Un Seong, Ji-Yoon Kim, Jung-Soo Kim, Sae-Ul Jeong, Jun-Hyeon Cho, Ji-Yoon Lee, Sais-Beul Lee, Nkulu-Rolly Kabange, Dong-Soo Park, Kwang-Deog Moon, Ju-Won Kang
  Foods.2023; 12(7): 1518.     CrossRef
• Molecular Breeding of Zheyou810, an Indica–Japonica Hybrid Rice Variety with Superior Quality and High Yield
  Jian Song, Yongtao Cui, Honghuan Fan, Liqun Tang, Jianjun Wang
  Agriculture.2023; 13(9): 1807.     CrossRef
• Interaction of starch branching enzyme 3 and granule-bound starch synthase 1 alleles increases amylose content and alters physico-chemical properties in japonica rice (Oryza sativa L.)
  Kyu-Chan Shim, Cheryl Adeva, Ju-Won Kang, Ngoc Ha Luong, Hyun-Sook Lee, Jun-Hyeon Cho, HyunJung Kim, Thomas H. Tai, Sang-Nag Ahn
  Frontiers in Plant Science.2022;[Epub]     CrossRef
• QTL Mapping of Mineral Element Contents in Rice Using Introgression Lines Derived from an Interspecific Cross
  Cheryl Adeva, Yeo-Tae Yun, Kyu-Chan Shim, Ngoc Ha Luong, Hyun-Sook Lee, Ju-Won Kang, Hyun-Jung Kim, Sang-Nag Ahn
  Agronomy.2022; 13(1): 76.     CrossRef
• Evaluation of Hardness and Retrogradation of Cooked Rice Based on Its Pasting Properties Using a Novel RVA Testing
  Sumiko Nakamura, Junji Katsura, Yasuhiro Maruyama, Ken’ichi Ohtsubo
  Foods.2021; 10(5): 987.     CrossRef

Previously, we mapped the qSPP7 QTL affecting the number of spikelets per panicle (SPP) on rice chromosome 7 using near-isogenic line (NIL WH29001) derived from an interspecific cross between the japonica ‘Hwaseong’ and Oryza minuta. In the present study, we confirmed this QTL using progeny derived from a cross between IL102, a WH29001 sister line and Hwaseong. Genetic analysis determined that qSPP7 was located between a KASP marker KJ07–049 and RM21605. The O. minuta segment on chromosome 7 introgressed into the Hwaseong background was associated with an increase in SPP. The panicle structure of IL102 revealed that not only the number of SPP increased significantly, but also the number of branches per panicle increased as compared to Hwaseong suggesting that the donor allele of qSPP7 promotes branching in the genetic background of Hwaseong. Linkage analysis indicated that qEhd1 on chromosome 10 is involved in the difference in heading date of IL102 and Hwaseong. Experiments under 3 different day length conditions revealed that IL102 always showed earlier heading and higher SPP as compared to Hwaseong indicating that the effect of qSPP7 in the Hwaseong background was not dependent on photoperiod, and SPP increased in proportion to the number of days to heading.

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• Assessment of mutant rice genotypes on growth cycle length and response to reduced water availability
  Luis Herminio Chairez Tejeda, Raymond Joseph, Eduardo Venske, Viviane Kopp da Luz, Andrés Eloy Chacón-Ortiz, Ariano Martins de Magalhães Júnior, Luciano Carlos da Maia, Antonio Costa de Oliveira, Camila Pegoraro
  Scientia Agricola.2024;[Epub]     CrossRef
• Molecular Breeding of Zheyou810, an Indica–Japonica Hybrid Rice Variety with Superior Quality and High Yield
  Jian Song, Yongtao Cui, Honghuan Fan, Liqun Tang, Jianjun Wang
  Agriculture.2023; 13(9): 1807.     CrossRef
• Genetic Structure and Geographical Differentiation of Traditional Rice (Oryza sativa L.) from Northern Vietnam
  Ngoc Ha Luong, Le-Hung Linh, Kyu-Chan Shim, Cheryl Adeva, Hyun-Sook Lee, Sang-Nag Ahn
  Plants.2021; 10(10): 2094.     CrossRef

Low-temperature germinability (LTG) is an important trait for rice direct seeding at temperate and high-altitude region. Previously, five QTLs (quantitative trait loci) for LTG were detected using an interspecific cross population between the Korea japonica cultivar Hwaseong and Oryza rufipogon (IRGSP#105491). O. rufipogon alleles at all loci increased the germination rate at the 13°C condition. In this study, we tried to confirm and fine-map qLTG1 located on the short arm of chromosome 1. To map the qLTG1, two introgression lines, TR5 and TR20 were crossed to Hwaseong to develop F_2:3 populations. QTL analysis confirmed the existence of the qLTG1 and it explained 55.5% and 29.9% of phenotypic variation in two populations, respectively. Substitution mapping using informative recombinant lines indicated that qLTG1 was located in 167-kb region between two SSR markers RM10310 and RM10326. This segment harbored 18 genes with nine of them were annotated with specific gene function. In addition, the O. rufipogon introgression in this region was associated with an increase in spikelets per panicle in the Hwaseong background. The results strongly indicate that the O. rufipogon alleles will be a valuable source of genes in improving japonica rice for low-temperature germinability and yield. To our knowledge, this is the first report to fine-map qLTG1 associated with LTG in rice considering that no QTL for LTG has not been reported near this QTL region from other biparental populations.

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• Genetic dissection and transcriptomic analysis of a novel high‐tillering phenotype in rice derived from weedy rice (Hapcheonaengmi3) and Tongil‐type Rice (Milyang23)
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  The Plant Genome.2026;[Epub]     CrossRef
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• Spontaneous mutation in OsABCI8 caused an albino rice mutant induced by transplanting
  Kyu-Chan Shim, Yun-A Jeon, Hyun-Sook Lee, Sang-Nag Ahn, Inkyu Park
  Scientific Reports.2025;[Epub]     CrossRef
• Cold-Tolerance Candidate Gene Identification in Maize Germination Using BSA, Transcriptome and Metabolome Profiling
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  Plants.2024; 13(5): 643.     CrossRef
• A Frameshift Mutation in the Mg-Chelatase I Subunit Gene OsCHLI Is Associated with a Lethal Chlorophyll-Deficient, Yellow Seedling Phenotype in Rice
  Kyu-Chan Shim, Yuna Kang, Jun-Ho Song, Ye Jin Kim, Jae Kwang Kim, Changsoo Kim, Thomas H. Tai, Inkyu Park, Sang-Nag Ahn
  Plants.2023; 12(15): 2831.     CrossRef
• Genome-wide identification and expression reveal the involvement of the FCS-like zinc finger (FLZ) gene family in Gossypium hirsutum at low temperature
  JunDuo Wang, Zhiqiang Li, Yajun Liang, Juyun Zheng, Zhaolong Gong, Guohui Zhou, Yuhui Xu, Xueyuan Li
  PeerJ.2023; 11: e14690.     CrossRef
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  Jing Yang, Aie Chen, Ji Wei, Jifen Xu, Shengnan Chen, Wei Tang, Jing Liu, Hongyang Wang
  Food and Energy Security.2023;[Epub]     CrossRef
• Interaction of starch branching enzyme 3 and granule-bound starch synthase 1 alleles increases amylose content and alters physico-chemical properties in japonica rice (Oryza sativa L.)
  Kyu-Chan Shim, Cheryl Adeva, Ju-Won Kang, Ngoc Ha Luong, Hyun-Sook Lee, Jun-Hyeon Cho, HyunJung Kim, Thomas H. Tai, Sang-Nag Ahn
  Frontiers in Plant Science.2022;[Epub]     CrossRef
• A Novel Embryo Phenotype Associated With Interspecific Hybrid Weakness in Rice Is Controlled by the MADS-Domain Transcription Factor OsMADS8
  Sun Ha Kim, Shi-Dong Ji, Hyun-Sook Lee, Yun-A Jeon, Kyu-Chan Shim, Cheryl Adeva, Ngoc Ha Luong, Pingrong Yuan, Hyun-Jung Kim, Thomas H. Tai, Sang-Nag Ahn
  Frontiers in Plant Science.2022;[Epub]     CrossRef
• Brassinosteroid biosynthesis gene OsD2 is associated with low-temperature germinability in rice
  Sun Ha Kim, Kyu-Chan Shim, Hyun-Sook Lee, Yun-A Jeon, Cheryl Adeva, Ngoc Ha Luong, Sang-Nag Ahn
  Frontiers in Plant Science.2022;[Epub]     CrossRef
• Identification of QTLs for Cold Tolerance at Seedling Stage Using a Population Derived from an Inter-specific Cross in Rice
  Kyu-Chan Shim, Yeo-Tae Yun, Ju-Won Kang, Sang-Nag Ahn
  Plant Breeding and Biotechnology.2022; 10(4): 282.     CrossRef
• Mapping QTLs controlling low-temperature germinability in rice by using single segment substitution lines derived from 4 AA-genome species of wild rice
  Ruiqin Pei, Zhengao Zhang, Mingchuan Huang, Guangshan Hou, Jijing Luo, Haitao Zhu, GuiFu Liu, Xuelin Fu, Guiquan Zhang, Shaokui Wang
  Euphytica.2021;[Epub]     CrossRef
• Natural variation in rice ascorbate peroxidase gene APX9 is associated with a yield-enhancing QTL cluster
  Yun-A Jeon, Hyun-Sook Lee, Sun-Ha Kim, Kyu-Chan Shim, Ju-Won Kang, Hyun-Jung Kim, Thomas H Tai, Sang-Nag Ahn, Christine Foyer
  Journal of Experimental Botany.2021; 72(12): 4254.     CrossRef
• Deployment of wild relatives for genetic improvement in rice (Oryza sativa)
  Kiran B. Gaikwad, Naveen Singh, Parampreet Kaur, Sushma Rani, Prashanth Babu H, Kuldeep Singh, Sang Nag Ahn
  Plant Breeding.2021; 140(1): 23.     CrossRef
• Characterization of Quantitative Trait Loci for Germination and Coleoptile Length under Low-Temperature Condition Using Introgression Lines Derived from an Interspecific Cross in Rice
  Mirjalol Akhtamov, Cheryl Adeva, Kyu-Chan Shim, Hyun-Sook Lee, Sun Ha Kim, Yun-A Jeon, Ngoc Ha Luong, Ju-Won Kang, Ji-Yoon Lee, Sang-Nag Ahn
  Genes.2020; 11(10): 1200.     CrossRef
• Characterization of a New qLTG3–1 Allele for Low-temperature Germinability in Rice from the Wild Species Oryza rufipogon
  Kyu-Chan Shim, Sun Ha Kim, Hyun-Sook Lee, Cheryl Adeva, Yun-A Jeon, Ngoc Ha Luong, Woo-Jin Kim, Mirjalol Akhtamov, Yong-Jin Park, Sang-Nag Ahn
  Rice.2020;[Epub]     CrossRef
• A RING-Type E3 Ubiquitin Ligase, OsGW2, Controls Chlorophyll Content and Dark-Induced Senescence in Rice
  Kyu-Chan Shim, Sun Ha Kim, Yun-A Jeon, Hyun-Sook Lee, Cheryl Adeva, Ju-Won Kang, Hyun-Jung Kim, Thomas H Tai, Sang-Nag Ahn
  International Journal of Molecular Sciences.2020; 21(5): 1704.     CrossRef

In this study, two near-isogenic lines (NILs) were selected from a series of chromosome segment substitution lines developed from an interspecific cross between Oryza sativa ssp. japonica cultivar ‘Hwaseongbyeo’ as a recipient parent and wild rice (Oryza grandiglumis) as the donor parent. Compared with Hwaseongbyeo control, one NIL (CR222) had reduced plant height and the other NIL (CR7501) displayed thicker basal and first internodes leading to increased lodging tolerance in the field condition. QTL analysis using progeny from crosses between Hwaseongbyeo and the NILs indicated that QTL for culm length and internode diameter leading to erect panicle were located on chromosomes 1 and 2, respectively. The major QTL for culm length on chromosome 1 was allelic to sd1 locus and the NIL showed the same sequence as the sd1 mutant cultivar ‘Reimei’. The QTL for the internode diameter was delimited to a 1-Mbp region on chromosome 2 and this QTL region harbors GW2 gene controlling grain width. The NIL with thick internode trait showed no undesirable pleiotropic effects and therefore has potential value for rice breeding for increasing lodging resistance.

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• Brassinosteroid biosynthesis gene OsD2 is associated with low-temperature germinability in rice
  Sun Ha Kim, Kyu-Chan Shim, Hyun-Sook Lee, Yun-A Jeon, Cheryl Adeva, Ngoc Ha Luong, Sang-Nag Ahn
  Frontiers in Plant Science.2022;[Epub]     CrossRef
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