The anaerobic germination 1 (AG1) locus, which confers tolerance to the anaerobic germination of rice seed, has been previously identified and a gel-based InDel DNA marker developed for marker-assisted selection (MAS). However, there is a need for marker development for high-throughput genotyping in order to increase the breeding efficiency. Single nucleotide polymorphisms (SNPs)-based Kompetitive Allele Specific PCR (KASP) markers enable high-accuracy and high-throughput analyses for the genotyping of AG1 locus. In the present study, we developed one AG1 InDel-specific and four flanking KASP markers, which can be used as the foreground and recombination markers, respectively, for the AG1 locus. Of those, three KASP markers developed were validated with Dasan-AG1 (BC₃F₂) segregating lines; the AG1 InDel-specific KASP marker was 100% consistent with the existing AG1 gel-based marker, while the two flanking markers showed 70.3 and 66.7 percent consistency to the AG1 gel-based marker, respectively. In addition, the five KASP markers developed were further used to genotype 78 Korean and 95 foreign rice varieties. The genotyping results with 172 varieties revealed that most of the Korean varieties possessed the AG1 locus; however, a wide variation was observed in the foreign varieties for AG1 locus. Hence, the KASP markers developed for AG1 locus show promise as useful tools for expediting the breeding of varieties tolerant to anaerobic germination stress via high-throughput genotyping.

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• KASP: a high-throughput genotyping system and its applications in major crop plants for biotic and abiotic stress tolerance
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Milk thistle (Silybum marianum Gaertn.) is a well-known medicinal plant which has been used for more than 2,000 years around the world. It produces silymarin, which cures the liver from hepatitis and toxin damages. In this study, a selfed and purified breeding line of the milk thistle from the Korean environment was used as a source of chloroplast genome construction. It showed high concentration of silybin B (3.50 mg/g) in its dried seeds. The complete chloroplast genome of S. marianum acc. ‘912036’ is 152,556 bp in length and G+C content is 37.69%. A total of 87 protein coding genes with 104 exons were annotated. Chloroplast genomes of five accessions from different countries were compared with that of ‘912036’, and no sequence polymorphism among them was identified. Thus, the chloroplast genome from this study can be used to develop S. marianum-specific DNA markers when compared with other diverse S. marianum accessions and Asteraceae species.

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• The genetics and genomics of milk thistle: unlocking its therapeutic potential through modern breeding and biotechnological innovations
  Priskila Tolangi, Jeehyoung Shim, Raña Mae Sumabat, Sunghan Kim, Hyun-Seung Park, Kyung Do Kim, Hyun Uk Kim, Sanghyun Lee, Joong Hyoun Chin
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• Analysis of silybin A and silybin B in different accessions of Silybum marianum seeds
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  Journal of Applied Biological Chemistry.2024;[Epub]     CrossRef
• Agricultural phenotype and silymarin content variations of cultivated milk thistle in Korea
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• A Genomic Evaluation of Six Selected Inbred Lines of the Naturalized Plants of Milk Thistle (Silybum marianum L. Gaertn.) in Korea
  Jeehyoung Shim, Su Young Hong, Jae-Hyuk Han, Yeisoo Yu, Eunae Yoo, Jungsook Sung, Joong Hyoun Chin, O New Lee
  Plants.2023; 12(14): 2702.     CrossRef
• The complete chloroplast genome of Elephantopus scaber L. (Vernonioideae, Asteraceae), a useful ethnomedicinal plant in asia
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  Mitochondrial DNA Part B.2023; 8(9): 936.     CrossRef
• Assembly and Comparative Analysis of Complete Mitogenome of Silybum marianum (L.) Gaertner
  Jeongwoo Lee, Yedomon Ange Bovys Zoclanclounon, Hwajin Jung, Taeho Lee, Jeonggu Kim, Guhwang Park, Keunpyo Lee, Kwanghoon An, Jeehyoung Shim, Joonghyoun Chin, Suyoung Hong
  Korean Journal of Breeding Science.2022; 54(4): 294.     CrossRef

Saltol is one of the most well-known quantitative loci (QTLs) for salinity tolerance in rice. It has been used to develop highly tolerant rice varieties in saline and coastal areas in Southeast Asia, South Asia, and Africa. However, the functional activity of Saltol is not well known, and the molecular marker application of readily developed linked markers in Saltol has not always been successful in the rice breeding programs for salinity tolerance improvement. Interestingly, two BC₂F₉ sister backcrossed inbred lines (BILs), which have been developed by marker-assisted backcrossing utilized the linked markers of Saltol to improve the salinity tolerance of MS11 (a temperate japonica growing in tropical condition). The BILs showed very different phenotypic and stress tolerance, although both contained the Saltol QTL. The genomic similarity of the two BILs was 73%, and we have identified the genomic sites of different genic constitutions between the lines utilizing background genotyping. The stress response of the two BILs showed difference in survival rate, grain yield under highly saline field condition, and SPAD, SES in hydroponic conditions. MS11-SaltolA showed salinity tolerance through Na⁺/K⁺ homeostasis with relatively high K⁺ ion uptake and low Na⁺ ion uptake in the seedling stage. Further genomic analyses with whole genome resequencing is ongoing to study on gene interactions. The developed highly tolerant MS11-SaltolA can be used as an improved donor in rice molecular breeding for high salinity tolerance.

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• Chromosome-level genome assembly of IR64 near-isogenic line harboring Saltol reveals novel genomic regions associated with salinity tolerance in rice (Oryza sativa L.)
  Jae-Hyuk Han, Ji-Hun Hwang, Na-Hyun Shin, Sunghan Kim, Hyun-Sook Lee, Tobias Kretzschmar, Kyung Do Kim, Il-Ryong Choi, Joong Hyoun Chin
  Plant Physiology and Biochemistry.2025; 229: 110669.     CrossRef
• Harnessing the power of genomics to develop climate-smart crop varieties: A comprehensive review
  K.T. Ravikiran, R. Thribhuvan, C. Anilkumar, Jayanth Kallugudi, N.R. Prakash, Sandeep Adavi B, N.C. Sunitha, Krishnan P. Abhijith
  Journal of Environmental Management.2025; 373: 123461.     CrossRef
• Marker-Assisted Introgression of the Salinity Tolerance Locus Saltol in Temperate Japonica Rice
  Caterina Marè, Elisa Zampieri, Viviana Cavallaro, Julien Frouin, Cécile Grenier, Brigitte Courtois, Laurent Brottier, Gianni Tacconi, Franca Finocchiaro, Xavier Serrat, Salvador Nogués, Mireia Bundó, Blanca San Segundo, Noemi Negrini, Michele Pesenti, Gia
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• DECUSSATE network with flowering genes explains the variable effects of qDTY12.1 to rice yield under drought across genetic backgrounds
  Jacobo Sanchez, Pushpinder Pal Kaur, Isaiah C. M. Pabuayon, Naga Bhushana Rao Karampudi, Ai Kitazumi, Nitika Sandhu, Margaret Catolos, Arvind Kumar, Benildo G. de los Reyes
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• Integrative Approach for Precise Genotyping and Transcriptomics of Salt Tolerant Introgression Rice Lines
  Mireia Bundó, Héctor Martín-Cardoso, Michele Pesenti, Jorge Gómez-Ariza, Laia Castillo, Julien Frouin, Xavier Serrat, Salvador Nogués, Brigitte Courtois, Cécile Grenier, Gian Attilio Sacchi, Blanca San Segundo
  Frontiers in Plant Science.2022;[Epub]     CrossRef
• QTL Analysis of Rice Grain Size Using Segregating Populations Derived from the Large Grain Line
  Ja-Hong Lee, Jeonghwan Seo, San Mar Lar, Seong-Gyu Jang, Hongjia Zhang, Ah-Rim Lee, Fang-Yuan Cao, Na-Eun Kim, Joohyun Lee, Soon-Wook Kwon
  Agriculture.2021; 11(6): 565.     CrossRef
• Genetic diversity in Bambara groundnut {Vigna subterranea (L.) Verdc.}
  Nwakuche Chinenye Onwubiko
  Agricultura Tropica et Subtropica.2021; 54(1): 89.     CrossRef

The yield related traits are controlled by multiple quantitative trait loci (QTLs) and influenced by environmental change in rice. We analyzed QTLs for 15 yield related traits using two backcross populations, derived from crosses between IR64 as recurrent parent and Koshihikari as donor parent, through two years. A total of 67 backcross inbred lines (BILs) and 40 chromosome segment substitution lines (CSSLs) were genotyped using 183 SNP markers using a high-throughput genotyping system. Some genomic gaps between markers were identified in two populations. For fifteen traits in this study, 36 major QTLs (mQTLs) for 12 traits and 16 digenic epistatic QTLs (EpQTLs) for culm length were detected in BILs. On the other hand, 17 mQTLs were detected for nine traits in CSSLs. Among them, six mQTLs for grain yield traits were collocated on chromosome 10 in both years. For spikelet fertility, six putative QTLs were detected under high temperature conditions in 2018. The QTLs identified in this study could be used for the development of rice varieties conferring inter-subspecific combinations of yield-related traits.

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• Haplotype-based multi-locus genome-wide association study reveals genomic regions associated with reproductive stage high temperature stress tolerance in rice
  Adhip Das, Madan Pal, Adam H. Price, Sukumar Taria, Ayushman Mallick, Megha Sharma, Sudhir Kumar, Ranjith Kumar Ellur, S. Gopala Krishnan, Lekshmy Sathee, Pradeep Kumar Jain, Monika Dalal, Annamalai Anandan, Siddharth Panda, Anita Kumari, Manu Agarwal, Vi
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• Decrypting molecular mechanism of heat stress tolerance in rice to tackle climate change challenges through recent approaches
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• ‘Drimi9ho’, A Lodging Tolerance with Mid-late Maturing, Improved White-backed Planthopper (Sogatella furcifera) and Cultivation Stability
  Jae-Ryoung Park, Eun-Gyeong Kim, Yoon-Hee Jang, Kyung-Min Kim
  Korean Journal of Breeding Science.2025; 57(4): 493.     CrossRef
• Climate-driven trends in rice grain appearance: a 2023–2024 comparative study using Korea field data
  Jae-Ryoung Park, Su-Kyung Ha, Hyun-Sook Lee, Gileung Lee, Seung Young Lee, Kyeong Min Kang, Jung-Pil Suh, Mina Jin, Hyun-Su Park, Chang-Min Lee, Jeonghwan Seo, Songhee Park, Keon-Mi Lee, O-Young Jeong
  Journal of Crop Science and Biotechnology.2025; 28(5): 657.     CrossRef
• Natural variation of HTH5 from wild rice, Oryza rufipogon Griff., is involved in conferring high‐temperature tolerance at the heading stage
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• QTL Analysis of Rice Grain Size Using Segregating Populations Derived from the Large Grain Line
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  Agriculture.2021; 11(6): 565.     CrossRef
• A trait specific QTL survey identifies NL44, a NERICA cultivar as a novel source for reproductive stage heat stress tolerance in rice
  K. T. Ravikiran, S. Gopala Krishnan, K. K. Vinod, Gaurav Dhawan, Priyanka Dwivedi, Pankaj Kumar, Vijay Prakash Bansal, M. Nagarajan, Prolay K. Bhowmick, Ranjith K. Ellur, Haritha Bollinedi, Madan Pal, Amitha C. R. Mithra, A. K. Singh
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• Genetic and Phenotypic Characterization of Rice Backcrossed Inbred Sister Lines of Saltol in Temperate Saline Reclaimed Area
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  Plant Breeding and Biotechnology.2020; 8(1): 58.     CrossRef
• Characterization of the Common Japonica-Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice (Oryza sativa L.)
  Jeonghwan Seo, So-Myeong Lee, Jae-Hyuk Han, Na-Hyun Shin, Yoon Kyung Lee, Backki Kim, Joong Hyoun Chin, Hee-Jong Koh
  Genes.2020; 11(5): 562.     CrossRef

Seedling vigor in drought stress conditions is an important characteristic of the dry direct-seeded rice system. The drought stress in the seedling stage disrupts seed germination and delays the establishment of seedlings. However, little is known about the genetic mechanism of seedling vigor in drought conditions. The identification of quantitative trait loci (QTL) was conducted using 162 recombinant inbred lines (RILs) derived from a cross between two rice varieties—a Tongil-type Milyang23 and a temperate japonica Tong88-7. The seedling vigor of these RILs was characterized by measuring 10 morphological traits of the seedlings grown under drought conditions. The Tong88-7 seedlings showed significantly higher values than the Milyang23 seedlings for all traits. The genotyping-by-sequencing method was used to construct a map of 6140 single nucleotide polymorphisms. Six main-effect QTLs (M-QTLs) associated with seedling vigor traits under drought stress were identified on chromosomes 9 and 11. In particular, five out of these six QTLs were located on chromosome 11, explaining the phenotypic variances of 4.3% through 10.1%. In addition, 21 epistatic QTLs (E-QTLs) were detected, and the 27 loci involved in this interaction were distributed on 11 chromosomes. Both M-QTLs and E-QTLs detected in this study would be useful in breeding programs to develop elite rice varieties especially adapted to dry direct-seeded rice system.

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• Analysis of Seed Vigor and Grain Quality Traits under Accelerated Aging Treatment in japonica Rice
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  Korean Journal of Breeding Science.2025; 57(3): 217.     CrossRef
• The resilience of rice under water stress will be driven by better roots: Evidence from root phenotyping, physiological, and yield experiments
  Sadiah Shafi, Insha Shafi, Aaqif Zaffar, Sajad Majeed Zargar, Asif B. Shikari, Anuj Ranjan, P.V. Vara Prasad, Parvaze A. Sofi
  Plant Stress.2023; 10: 100211.     CrossRef
• Hydraulic conductance and xylem vessel diameter of young maize roots subjected to sustained water‐deficit
  Nahid Jafarikouhini, Thomas R. Sinclair
  Crop Science.2023; 63(4): 2458.     CrossRef
• Shaping the root system architecture in plants for adaptation to drought stress
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• Genetics and genomics of root system variation in adaptation to drought stress in cereal crops
  Md Nurealam Siddiqui, Jens Léon, Ali A Naz, Agim Ballvora, Miriam Gifford
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• Phenotyping Root Systems in a Set of Japonica Rice Accessions: Can Structural Traits Predict the Response to Drought?
  Paulo Henrique Ramos Guimarães, Isabela Pereira de Lima, Adriano Pereira de Castro, Anna Cristina Lanna, Patrícia Guimarães Santos Melo, Marcel de Raïssac
  Rice.2020;[Epub]     CrossRef

Supplying sufficient rice to growing populations is a global challenge. Hybrid indica rice varieties exploiting heterosis have increased yields, but inter-subspecific crosses between indica and japonica varieties are hampered by sterility. Examination and genetic understanding of yield heterosis in indica/japonica crosses addressing yield barriers are basic requirements. In this study, QTLs for heterosis of yield traits were identified in indica-japonica recombinant inbred lines (RILs) using a total of 178 RILs originating from Dasanbyeo (indica) × TR22183 (japonica) (DT-RILs) and their backcrossed populations. Nine of sixty-six major quantitative trait loci (QTLs) identified in DT-RILs exhibited heterosis. Heterosis QTLs clustered with other traits on chromosomes 1, 4, and 8, and clusters were conserved between different RILs. The clusters contained several known yield enhancement genes/QTLs. Specific heterotic allele combinations contributed to four major heterosis QTLs, particularly for panicle and spikelet number traits. Heterosis for yield and yield-related traits was explained by the harmonized effects of overdominance, dominance, and epistatic interactions in inter-subspecific breeding populations.

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• Exploring environmentally stable and novel genetic factors influencing rice grain shape and yield attributes
  Sadia Gull, Zulqarnain Haider, Houwen Gu, Saleem Uddin, Muhammad Qasim, Rana Ahsan Raza Khan, Adil Altaf, Sajid Fiaz, Mona S. Alwahibi, Mohamed S. Elshikh, Rashid Iqbal, Jun Miao, Guohua Liang
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• Quantitative Trait Loci Analysis of Leaf Size Traits Using the Recombinant Inbred Lines Derived from a Cross between ‘Odae’ and ‘Unbong40’
  Eunchan Lee, Mihyun Cho, Soojin Jun, Hwayoung Kim, Seon-Hwa Bae, Myeongjin Kang, Hyoja Oh, Jae-Hyeon Oh, HwangWeon Jeong, Il-Pyung Ahn, Jae Il Lyu, Hyeonso Ji
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• Analysis of Agricultural Traits of O. sativa and O. glaberrima under Korean Climatic Conditions
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  Korean Journal of Breeding Science.2024; 56(2): 97.     CrossRef
• Association Analysis of Yield-Related Traits in Rice Following the Introduction of Brown Planthopper Resistant Genes
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  Korean Journal of Breeding Science.2024; 56(4): 381.     CrossRef
• Genetic mechanism of heterosis for rice milling and appearance quality in an elite rice hybrid
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• Genetic dissection of grain traits and their corresponding heterosis in an elite hybrid
  Sundus Zafar, Hui You, Fan Zhang, Shuang Bin Zhu, Kai Chen, Congcong Shen, Hezhou Wu, Fangjin Zhu, Conghe Zhang, Jianlong Xu
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• Mapping QTLs for yield and photosynthesis-related traits in three consecutive backcross populations of Oryza sativa cultivar Cottondora Sannalu (MTU1010) and Oryza rufipogon
  Venkateswara Rao Yadavalli, Divya Balakrishnan, Malathi Surapaneni, Krishnamraju Addanki, Sukumar Mesapogu, Kavitha Beerelli, Subrahmanyam Desiraju, Sitapati Rao Voleti, Sarla Neelamraju
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• Genomic Architecture of Yield Performance of an Elite Rice Hybrid Revealed by its Derived Recombinant Inbred Line and Their Backcross Hybrid Populations
  Fan Zhang, Conghe Zhang, Xiuqin Zhao, Shuangbing Zhu, Kai Chen, Guixiang Zhou, Zhichao Wu, Min Li, Tianqing Zheng, Wensheng Wang, Zhi Yan, Qinyong Fei, Zhikang Li, Jinjie Chen, Jianlong Xu
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• A meta-quantitative trait loci analysis identified consensus genomic regions and candidate genes associated with grain yield in rice
  Kelvin Dodzi Aloryi, Nnaemeka Emmanuel Okpala, Aduragbemi Amo, Semiu Folaniyi Bello, Selorm Akaba, Xiaohai Tian
  Frontiers in Plant Science.2022;[Epub]     CrossRef
• Mapping of QTLs for Yield Traits Using F2:3:4 Populations Derived From Two Alien Introgression Lines Reveals qTGW8.1 as a Consistent QTL for Grain Weight From Oryza nivara
  Kavitha Beerelli, Divya Balakrishnan, Krishnam Raju Addanki, Malathi Surapaneni, Venkateswara Rao Yadavalli, Sarla Neelamraju
  Frontiers in Plant Science.2022;[Epub]     CrossRef
• Mapping novel QTLs for yield related traits from a popular rice hybrid KRH-2 derived doubled haploid (DH) population
  Swapnil Ravindra Kulkarni, S. M. Balachandran, K. Ulaganathan, Divya Balakrishnan, A. S. Hari Prasad, G. Rekha, M. B. V. N. Kousik, S. K. Hajira, Ravindra Ramarao Kale, D. Aleena, M. Anila, E. Punniakoti, T. Dilip, K. Pranathi, M. Ayyappa Das, Mastanbee S
  3 Biotech.2021;[Epub]     CrossRef
• Genetic dissection of heterosis of indica–japonica by introgression line, recombinant inbred line and their testcross populations
  Wenqing Yang, Fan Zhang, Sundus Zafar, Junmin Wang, Huajin Lu, Shahzad Naveed, Jue Lou, Jianlong Xu
  Scientific Reports.2021;[Epub]     CrossRef
• Molecular mapping of QTLs for yield related traits in recombinant inbred line (RIL) population derived from the popular rice hybrid KRH-2 and their validation through SNP genotyping
  Swapnil Ravindra Kulkarni, S. M. Balachandran, K. Ulaganathan, Divya Balakrishnan, M. Praveen, A. S. Hari Prasad, R. A. Fiyaz, P. Senguttuvel, Pragya Sinha, Ravindra R. Kale, G. Rekha, M. B. V. N. Kousik, G. Harika, M. Anila, E. Punniakoti, T. Dilip, S. K
  Scientific Reports.2020;[Epub]     CrossRef
• Mapping and Validation of QTLs for the Amino Acid and Total Protein Content in Brown Rice
  Su Jang, Jae-Hyuk Han, Yoon Kyung Lee, Na-Hyun Shin, Yang Jae Kang, Chang-Kug Kim, Joong Hyoun Chin
  Frontiers in Genetics.2020;[Epub]     CrossRef
• Identification of Yield and Yield-Related Quantitative Trait Loci for the Field High Temperature Condition in Backcross Populations of Rice (Oryza sativaL.)
  Jeonghwan Seo, So-Myeong Lee, Jae-Hyuk Han, Na-Hyun Shin, Hee-Jong Koh, Joong Hyoun Chin
  Plant Breeding and Biotechnology.2019; 7(4): 415.     CrossRef

Rice varieties developed through the inter-specific crosses between Asian (Oryza sativa L.) and African cultivated rice (O. glaberrima Steud.) have contributed to yield enhancement of African rice. However, the genetic diversity and genetic structure of the African varieties have rarely been reported. In this study, we characterized 40 rice varieties including rice released in Africa based on eleven yield related agronomic traits and 96 single nucleotide polymorphism (SNP) markers. They were grouped into three categories based on the cluster analysis using agronomic traits. Meanwhile, they were grouped into two distinct clusters, indica- and japonica-type, based on the genetic distance using 96 SNP markers. CG14, which belongs to O. glaberrima, was found to be an admixture type between indica and japonica. The number of secondary branches (SBs) was the only agronomic trait which was significantly different between two groups. The results of this study provide basic agronomic and genomic information of cultivated and tested rice varieties for Africa, that would be helpful for further rice varietal improvement in Africa.

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• Analysis of Agricultural Traits of O. sativa and O. glaberrima under Korean Climatic Conditions
  Jae-Ryoung Park, Hyun-Su Park, Jeonghwan Seo, Chang-Min Lee, Songhee Park, Mina Jin, Keon Mi Lee, Keunpyo Lee, Sukyeung Lee, Ebrima Jallow, O-Young Jeong
  Korean Journal of Breeding Science.2024; 56(2): 97.     CrossRef
• QTL Analysis of Rice Grain Size Using Segregating Populations Derived from the Large Grain Line
  Ja-Hong Lee, Jeonghwan Seo, San Mar Lar, Seong-Gyu Jang, Hongjia Zhang, Ah-Rim Lee, Fang-Yuan Cao, Na-Eun Kim, Joohyun Lee, Soon-Wook Kwon
  Agriculture.2021; 11(6): 565.     CrossRef
• Development and application of indica–japonica SNP assays using the Fluidigm platform for rice genetic analysis and molecular breeding
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