The increased severity and frequency of flooding is causing greater yield reductions in most rice-growing areas. To address this, popular cultivars were improved through introgression of SUB1, an FR13A-derived QTL conferring submergence tolerance at the vegetative stage, using marker-assisted backcrossing (MABC). Ciherang-Sub1, one of these improved near isogenic lines (NILs), showed significantly higher tolerance compared to the original cultivar while retaining its desirable agronomic qualities. However, due to the current shift to direct seeding, seed germination may also be adversely affected by flooding; thus the addition of major QTLs which can confer anaerobic germination (AG) tolerance will be highly beneficial. The AG tolerance QTL, qAG-9-2, also referred to as AG1, derived from Khao Hlan On, a Myanmar landrace, has been introgressed into the elite cultivar IR64 to produce IR64-AG1. This research focused on the transfer of AG1 to Ciherang-Sub1 via MABC, using IR64-AG1, a closely-related donor. Introgression of AG1 and recovery of the Ciherang genome was done in two backcross generations followed by one generation of selfing. The use of a closely-related donor shortened the development period to two years which could have been further reduced if a larger BC₁F₁ population had been used. Phenotypic evaluation showed that introgression of AG1 significantly increased AG tolerance compared to Ciherang-Sub1, and that the newly developed Ciherang-Sub1+AG1 retained the submergence tolerance from SUB1. The approach is very promising for faster development of improved lines using closely-related cultivars or improved lines as donors for introducing key traits.

Citations

Citations to this article as recorded by  

• Removal of Transgenes and Evaluation of Yield Penalties in Genome Edited Bacterial Blight Resistant Rice Varieties
  Eliza P. I. Loo, José C. Huguet‐Tapia, Michael Selvaraj, Melissa Stiebner, Britta Killing, Marcel Buchholzer, Van Schepler‐Luu, Thomas Hartwig, Sandra P. Valdéz Gutierrez, Madlen I. Rast‐Somssich, Christian Paolo Balahadia, Inez H. Slamet‐Loedin, Ricardo
  Plant Biotechnology Journal.2026; 24(2): 939.     CrossRef
• Advances in Rice Coleoptile Elongation: Implications for Direct-Seeded Rice Adaptation
  Honghuan FAN, Jian SONG, Liqun TANG, Junmin WANG, Zhonghua SHENG, Guiai JIAO, Shaoqing TANG, Shikai HU, Peisong HU
  Rice Science.2026; 33(3): 327.     CrossRef
• Towards dual-stage flood resilience: merging anaerobic germination and submergence tolerance in rice
  Sagar Lamsal, Haru Hirano, Takeshi Fukao, Motoyuki Ashikari
  Journal of Experimental Botany.2026;[Epub]     CrossRef
• Natural Variation in OsTPP7 Affects the Root Traits in Combined Germination Under Submergence and Nutrient Deficiency in indica Rice
  Sabarinathan Selvaraj, Subhashree Nayak, Parameswaran Chidambaranathan, Priyadarsini Sanghamitra, Simanta Mohanty, Cayalvizhi Balasubramaniasai, Sanghamitra Samantaray
  Tropical Plant Biology.2026;[Epub]     CrossRef
• Genetic improvement from 50 years of rice breeding in Indonesia
  Trias Sitaresmi, Aris Hairmansis, Willy Bayuardi Suwarno, Aan Andang Daradjat, Yudhistira Nugraha
  Journal of Crop Improvement.2025; 39(6): 517.     CrossRef
• Genomic approaches and prospects for breeding flood-tolerant rice in Africa
  Victoria Bulegeya, Newton Kilasi, Waseem Hussain, Rosemary Murori, Atugonza Bilaro, Abdelbagi Ismail, Susan Nchimbi-Msolla
  Journal of Plant Interactions.2025;[Epub]     CrossRef
• Understanding anaerobic germination in direct-seeded rice: a genomic mapping approach
  Vikas Kumar Verma, Nitika Sandhu
  BMC Plant Biology.2024;[Epub]     CrossRef
• Selection of Rice Promising Lines Having Ciherang’s Idiotype for Improved Resistance of Main Pest and Diseases
  T Sitaresmi, H Safitri, Nafisah, U Susanto, A Hairmansis, C Gunarsih, Rahmini, C Roza, Y Nugraha
  IOP Conference Series: Earth and Environmental Science.2023; 1172(1): 012022.     CrossRef
• Sub1 and qDTY3.1 improved tolerance of rice (Oryza sativa L.) lines to drought and submergence stresses
  Asmuni Mohd Ikmal, Abd Aziz Shamsudin Noraziyah, Ratnam Wickneswari, Yusuf Opeyemi Oyebamiji
  Euphytica.2023;[Epub]     CrossRef
• Genomic landscape of the OsTPP7 gene in its haplotype diversity and association with anaerobic germination tolerance in rice
  Kyaw Myo Aung, Win Htet Oo, Thant Zin Maung, Myeong-Hyeon Min, Aueangporn Somsri, Jungrye Nam, Kyu-Won Kim, Bhagwat Nawade, Chang-Yong Lee, Sang-Ho Chu, Yong-Jin Park
  Frontiers in Plant Science.2023;[Epub]     CrossRef
• Genome-wide association study reveals novel genetic loci involved in anaerobic germination tolerance in Indica rice
  Kai Liu, Jing Yang, Kai Sun, Dongxiu Li, Lixin Luo, Taotao Zheng, Hui Wang, Zhiqiang Chen, Tao Guo
  Molecular Breeding.2023;[Epub]     CrossRef
• Flooding tolerance in Rice: adaptive mechanism and marker-assisted selection breeding approaches
  Md Azadul Haque, Mohd Y. Rafii, Martini Mohammad Yusoff, Nusaibah Syd Ali, Oladosu Yusuff, Fatai Arolu, Mohammad Anisuzzaman
  Molecular Biology Reports.2023; 50(3): 2795.     CrossRef
• Segregation of molecular markers associated with Bph3 gene in BC5F2 population derived from Ciherang rice variety as the recipient parent
  M Yunus, A Dadang, Slamet, A Warsun, D Satyawan, Chaerani
  IOP Conference Series: Earth and Environmental Science.2023; 1255(1): 012044.     CrossRef
• Genome-wide identification, expression pattern and genetic variation analysis of SWEET gene family in barley reveal the artificial selection of HvSWEET1a during domestication and improvement
  Wenhao Yue, Kangfeng Cai, Xue Xia, Lei Liu, Junmei Wang
  Frontiers in Plant Science.2023;[Epub]     CrossRef
• Mapping of QTLs for flood tolerance in rice using recombinant inbred lines of Indra and a new plant genetic resource AC 39416 A
  M. Girija Rani, P. V. Satyanarayana, N. Chamundeswari, P. V. Ramana Rao, M. Prabhakar, B. N. V. S. R. Ravikumar, P. Nagakumari, K. Kalpana
  Plant Genetic Resources: Characterization and Utilization.2022; 20(4): 270.     CrossRef
• Development of a Temperate Climate-Adapted indica Multi-stress Tolerant Rice Variety by Pyramiding Quantitative Trait Loci
  Na-Hyun Shin, Jae-Hyuk Han, Kieu Thi Xuan Vo, Jeonghwan Seo, Ian Paul Navea, Soo-Cheul Yoo, Jong-Seong Jeon, Joong Hyoun Chin
  Rice.2022;[Epub]     CrossRef
• Genetic Mapping by Sequencing More Precisely Detects Loci Responsible for Anaerobic Germination Tolerance in Rice
  John Carlos I. Ignacio, Maricris Zaidem, Carlos Casal, Shalabh Dixit, Tobias Kretzschmar, Jaime M. Samaniego, Merlyn S. Mendioro, Detlef Weigel, Endang M. Septiningsih
  Plants.2021; 10(4): 705.     CrossRef
• Improved Transformation and Regeneration of Indica Rice: Disruption of SUB1A as a Test Case via CRISPR-Cas9
  Yuya Liang, Sudip Biswas, Backki Kim, Julia Bailey-Serres, Endang M. Septiningsih
  International Journal of Molecular Sciences.2021; 22(13): 6989.     CrossRef
• Enriched-GWAS and Transcriptome Analysis to Refine and Characterize a Major QTL for Anaerobic Germination Tolerance in Rice
  Hedia Tnani, Dmytro Chebotarov, Ranjita Thapa, John Carlos I. Ignacio, Walter K. Israel, Fergie A. Quilloy, Shalabh Dixit, Endang M. Septiningsih, Tobias Kretzschmar
  International Journal of Molecular Sciences.2021; 22(9): 4445.     CrossRef
• The ins and outs of SWEETs in plants: Current understanding of the basics and their prospects in crop improvement
  Anjali Anjali, Urooj Fatima, Muthappa Senthil-Kumar
  Journal of Biosciences.2021;[Epub]     CrossRef
• Genetic variability for and tolerance to anaerobic germination in rice (Oryza sativa L.)
  Maxwell Darko Asante, Samuel Oluwasegun Ipinyomi, Ayodeji Abe, Kossi Lorimpo Adjah, Phyllis Aculey, Raphael Kwame Bam, Baboucarr Manneh
  Journal of Crop Improvement.2021; 35(6): 832.     CrossRef
• Reference-Guided De Novo Genome Assembly to Dissect a QTL Region for Submergence Tolerance Derived from Ciherang-Sub1
  Yuya Liang, Shichen Wang, Chersty L. Harper, Nithya K. Subramanian, Rodante E. Tabien, Charles D. Johnson, Julia Bailey-Serres, Endang M. Septiningsih
  Plants.2021; 10(12): 2740.     CrossRef
• An epigenetic pathway in rice connects genetic variation to anaerobic germination and seedling establishment
  Lina Castano-Duque, Sharmistha Ghosal, Fergie A Quilloy, Thomas Mitchell-Olds, Shalabh Dixit
  Plant Physiology.2021; 186(2): 1042.     CrossRef
• Growth, productivity and grain quality of AG1 and AG2 QTLs introgression lines under flooding in direct-seeded rice system
  Satyen Mondal, M. Iqbal R. Khan, Shalabh Dixit, Pompe C. Sta. Cruz, Endang M. Septiningsih, Abdelbagi M. Ismail
  Field Crops Research.2020; 248: 107713.     CrossRef
• Molecular mechanisms and future improvement of submergence tolerance in rice
  Takeshi Kuroha, Motoyuki Ashikari
  Molecular Breeding.2020;[Epub]     CrossRef
• Responses of AG1 and AG2 QTL introgression lines and seed pre-treatment on growth and physiological processes during anaerobic germination of rice under flooding
  Satyen Mondal, M. Iqbal R. Khan, Frederickson Entila, Shalabh Dixit, Pompe C. Sta. Cruz, M. Panna Ali, Barry Pittendrigh, Endang M. Septiningsih, Abdelbagi M. Ismail
  Scientific Reports.2020;[Epub]     CrossRef
• Submergence Tolerance in Rice: Review of Mechanism, Breeding and, Future Prospects
  Yusuff Oladosu, Mohd Y. Rafii, Fatai Arolu, Samuel Chibuike Chukwu, Ismaila Muhammad, Isiaka Kareem, Monsuru Adekunle Salisu, Ibrahim Wasiu Arolu
  Sustainability.2020; 12(4): 1632.     CrossRef
• Early Vigor of a Pyramiding Line Containing Two Quantitative Trait Loci, Phosphorus Uptake 1 (Pup1) and Anaerobic Germination 1 (AG1) in Rice (O. Sativa L.)
  Na-Hyun Shin, Jae-Hyuk Han, Su Jang, Kihwan Song, Hee-Jong Koh, Jong-Hee Lee, Soocheul Yoo, Joong Hyoun Chin
  Agriculture.2020; 10(10): 453.     CrossRef
• The Molecular Regulatory Pathways and Metabolic Adaptation in the Seed Germination and Early Seedling Growth of Rice in Response to Low O2 Stress
  Mingqing Ma, Weijian Cen, Rongbai Li, Shaokui Wang, Jijing Luo
  Plants.2020; 9(10): 1363.     CrossRef
• Climate change and the need for agricultural adaptation
  Robyn Anderson, Philipp E Bayer, David Edwards
  Current Opinion in Plant Biology.2020; 56: 197.     CrossRef
• Flood resilience loci SUBMERGENCE 1 and ANAEROBIC GERMINATION 1 interact in seedlings established underwater
  Rejbana Alam, Maureen Hummel, Elaine Yeung, Anna M. Locke, John Carlos I. Ignacio, Miriam D. Baltazar, Zhenyu Jia, Abdelbagi M. Ismail, Endang M. Septiningsih, Julia Bailey‐Serres
  Plant Direct.2020;[Epub]     CrossRef
• Pyramiding QTLs controlling tolerance against drought, salinity, and submergence in rice through marker assisted breeding
  Valarmathi Muthu, Ragavendran Abbai, Jagadeeshselvam Nallathambi, Hifzur Rahman, Sasikala Ramasamy, Rohit Kambale, Thiyagarajan Thulasinathan, Bharathi Ayyenar, Raveendran Muthurajan, Paul C. Struik
  PLOS ONE.2020; 15(1): e0227421.     CrossRef
• Yield Gap Management under Seawater Intrusion Areas of Indonesia to Improve Rice Productivity and Resilience to Climate Change
  Hasil Sembiring, Nuning A. Subekti, Erythrina, Dedi Nugraha, Bhakti Priatmojo, Alexander M. Stuart
  Agriculture.2019; 10(1): 1.     CrossRef
• Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq
  Jing Yang, Kai Sun, Dongxiu Li, Lixin Luo, Yongzhu Liu, Ming Huang, Guili Yang, Hong Liu, Hui Wang, Zhiqiang Chen, Tao Guo
  BMC Genomics.2019;[Epub]     CrossRef
• Marker Assisted Breeding to Develop Multiple Stress Tolerant Varieties for Flood and Drought Prone Areas
  Nitika Sandhu, Shalabh Dixit, B. P. M. Swamy, Anitha Raman, Santosh Kumar, S. P. Singh, R. B. Yadaw, O. N. Singh, J. N. Reddy, A. Anandan, Shailesh Yadav, Challa Venkataeshwarllu, Amelia Henry, Satish Verulkar, N. P. Mandal, T. Ram, Jyothi Badri, Prashant
  Rice.2019;[Epub]     CrossRef
• Genetic Analysis and QTL Mapping for Agronomic and Yield-Related Traits in Ciherang-Sub1 Rice Backcross Populations
  Estria F Pramudyawardani, Hajrial Aswidinnoor, Bambang S Purwoko, Willy B Suwarno, M R Islam, Holden Verdeprado, Bertrand CY Collard
  Plant Breeding and Biotechnology.2018; 6(3): 177.     CrossRef
• Optimizing Sowing and Flooding Depth for Anaerobic Germination-Tolerant Genotypes to Enhance Crop Establishment, Early Growth, and Weed Management in Dry-Seeded Rice (Oryza sativa L.)
  Buddhika Sampath Chamara, Buddhi Marambe, Virender Kumar, Abdelbagi M. Ismail, Endang M. Septiningsih, Bhagirath Singh Chauhan
  Frontiers in Plant Science.2018;[Epub]     CrossRef
• Agronomic manipulations can enhance the productivity of anaerobic tolerant rice sown in flooded soils in rainfed areas
  B. Lal, Priyanka Gautam, A.K. Nayak, R. Raja, M. Shahid, R. Tripathi, Sudhanshu Singh, Endang M. Septiningsih, Abdelbagi M. Ismail
  Field Crops Research.2018; 220: 105.     CrossRef
• IR64: a high-quality and high-yielding mega variety
  David J. Mackill, Gurdev S. Khush
  Rice.2018;[Epub]     CrossRef
• Combining drought and submergence tolerance in rice: marker-assisted breeding and QTL combination effects
  Shalabh Dixit, Anshuman Singh, Nitika Sandhu, Aditi Bhandari, Prashant Vikram, Arvind Kumar
  Molecular Breeding.2017;[Epub]     CrossRef
• Genetics, Physiological Mechanisms and Breeding of Flood-Tolerant Rice (Oryza sativaL.)
  Anuradha Singh, Endang M. Septiningsih, Harendra S. Balyan, Nagendra K. Singh, Vandna Rai
  Plant and Cell Physiology.2017; : pcw206.     CrossRef
• Identification of QTLs for yield and agronomic traits in rice under stagnant flooding conditions
  Anshuman Singh, Jerome Carandang, Zennia Jean C. Gonzaga, Bertrand C. Y. Collard, Abdelbagi M. Ismail, Endang M. Septiningsih
  Rice.2017;[Epub]     CrossRef
• Mapping additional QTLs from FR13A to increase submergence tolerance in rice beyond SUB1
  Zennia Jean C. Gonzaga, Jerome Carandang, Darlene L. Sanchez, David J. Mackill, Endang M. Septiningsih
  Euphytica.2016; 209(3): 627.     CrossRef
• A trehalose-6-phosphate phosphatase enhances anaerobic germination tolerance in rice
  Tobias Kretzschmar, Margaret Anne F. Pelayo, Kurniawan R. Trijatmiko, Lourd Franz M. Gabunada, Rejbana Alam, Rosario Jimenez, Merlyn S. Mendioro, Inez H. Slamet-Loedin, Nese Sreenivasulu, Julia Bailey-Serres, Abdelbagi M. Ismail, David J. Mackill, Endang
  Nature Plants.2015;[Epub]     CrossRef

Chloroplast DNA sequences are a versatile tool for species identification and phylogenetic reconstruction of land plants. Different chloroplast loci have been utilized for phylogenetic classification of plant species. However, there is no report for a short DNA sequence that can distinguish all plant species from each other. Molecular markers derived from the complete chloroplast genome can provide effective tools for species identification and phylogenetic resolution. Thus, the complete chloroplast genome sequence of Korean landrace “Subicho” pepper (Capsicum annuum var. annuum) has been determined here. The total length of the chloroplast genome is 156,878 bp, with 37.7% overall GC content. A pair of IRs (inverted repeats) of 25,801 bp was separated by a small single copy (SSC) region of 17,929 bp and a large single copy (LSC) region of 87,347 bp. The chloroplast genome harbors 132 known genes, including 87 protein-coding genes, 8 ribosomal RNA genes, and 37 tRNA genes. A total of seven of these genes are duplicated in the inverted repeat regions, nine genes and six tRNA genes contain one intron, while two genes and a ycf have two introns. Analysis revealed 144 simple sequence repeat (SSR) loci and 96 variants, mostly located in the intergenic regions. The types and abundances of repeat units in Capsicum species were relatively conserved and these loci will be useful for developing C. annuum cp genome vectors.

Citations

Citations to this article as recorded by  

• Ripening‐related metabolic changes in different chili pepper cultivars revealed by nuclear magnetic resonance spectroscopy
  Gi‐Un Seong, Dae‐Yong Yun, Jeong‐Seok Cho, Seul‐Ki Park, Gyu Seok Lee, Jeong Hee Choi, Kee‐Jai Park, Jeong‐Ho Lim
  Journal of the Science of Food and Agriculture.2025; 105(11): 6084.     CrossRef
• NMR-Based Metabolomic Analysis of Biotic Stress Responses in the Traditional Korean Landrace Red Pepper (Capsicum annuum var. annuum, cv. Subicho)
  Gi-Un Seong, Dae-Yong Yun, Dong-Hyeok Shin, Jeong-Seok Cho, Seul-Ki Park, Jeong Hee Choi, Kee-Jai Park, Jeong-Ho Lim
  International Journal of Molecular Sciences.2024; 25(18): 9903.     CrossRef
• Comparative 1H NMR-Based Metabolomics of Traditional Landrace and Disease-Resistant Chili Peppers (Capsicum annuum L.)
  Gi-Un Seong, Dae-Yong Yun, Dong-Hyeok Shin, Jeong-Seok Cho, Gyuseok Lee, Jeong Hee Choi, Kee-Jai Park, Kyung-Hyung Ku, Jeong-Ho Lim
  Foods.2024; 13(13): 1966.     CrossRef
• Chloroplast genome analysis of Angiosperms and phylogenetic relationships among Lamiaceae members with particular reference to teak (Tectona grandis L.f)
  P Maheswari, C Kunhikannan, R Yasodha
  Journal of Biosciences.2021;[Epub]     CrossRef
• Pan-plastome approach empowers the assessment of genetic variation in cultivated Capsicum species
  Mahmoud Magdy, Lijun Ou, Huiyang Yu, Rong Chen, Yuhong Zhou, Heba Hassan, Bihong Feng, Nathan Taitano, Esther van der Knaap, Xuexiao Zou, Feng Li, Bo Ouyang
  Horticulture Research.2019;[Epub]     CrossRef
• Next generation sequencing technologies for the development of molecular markers and the analysis of genome diversity in Capsicum spp.
  T. Cardi, N. D’Agostino, C. Cantarella, V. Colonna, B. Greco, R. Tamburino, F. Taranto, N. Scotti, P. Tripodi
  Acta Horticulturae.2019; (1242): 831.     CrossRef
• The Complete Plastome Sequences of Eleven Capsicum Genotypes: Insights into DNA Variation and Molecular Evolution
  Nunzio D’Agostino, Rachele Tamburino, Concita Cantarella, Valentina De Carluccio, Lorenza Sannino, Salvatore Cozzolino, Teodoro Cardi, Nunzia Scotti
  Genes.2018; 9(10): 503.     CrossRef
• The complete chloroplast genome of Capsicum frutescens (Solanaceae)
  Donghwan Shim, Sebastin Raveendar, Jung‐Ro Lee, Gi‐An Lee, Na‐Young Ro, Young‐Ah Jeon, Gyu‐Taek Cho, Ho‐Sun Lee, Kyung‐Ho Ma, Jong‐Wook Chung
  Applications in Plant Sciences.2016;[Epub]     CrossRef
• Complete chloroplast genome sequence of Capsicum baccatum var. baccatum
  Tae-Sung Kim, Jung-Ro Lee, Sebastin Raveendar, Gi-An Lee, Young-Ah Jeon, Ho-Sun Lee, Kyung-Ho Ma, Sok-Young Lee, Jong-Wook Chung
  Molecular Breeding.2016;[Epub]     CrossRef
• The Complete Chloroplast Genome of Capsicum annuum var. glabriusculum Using Illumina Sequencing
  Sebastin Raveendar, Young-Wang Na, Jung-Ro Lee, Donghwan Shim, Kyung-Ho Ma, Sok-Young Lee, Jong-Wook Chung
  Molecules.2015; 20(7): 13080.     CrossRef

Functional stay-green (FSG) delays leaf yellowing, maintaining photosynthetic competence, whereas nonfunctional stay-green (NFSG) retains only leaf greenness without sustaining photosynthetic activity. Retention of chlorophylls and photosynthetic capacity is important for increasing crop yield. We determined the main-effect quantitative trait loci (QTLs) for FSG traits in the japonica rice SNU-SG1 and isolated candidate genes. To identify QTLs influencing FSG, we analyzed eight traits: (1) 1 day after heading-degree of chlorophyll content of flag leaf, (2) 1 day after heading-degree of chlorophyll content of second leaf, (3) 1 day after heading-degree of chlorophyll content of flag and second leaves, (4) 50 day after heading-degree of chlorophyll content of flag leaf, (5) 50 day after heading-degree of chlorophyll content of second leaf, (6) 50 day after heading-degree of chlorophyll content of flag and second leaves, (7) relative decline degree of chlorophyll content of flag and second leaves, and (8) flowering time. We carried out QTL analysis with F₇ RIL from a cross of japonica rice ‘SNU-SG1’ and indica rice ‘Milyang23 (M23)’. Using 131 molecular markers, we identified 18 QTLs for the eight traits with a threshold LOD value > 2.8. Sequence analysis identified 16 candidate genes for 10 main-effect QTLs. Of these, we have chosen seven strong candidate genes for the 10 main-effect QTLs. These genetic resources will be useful for breeding high-yielding rice cultivars.

Citations

Citations to this article as recorded by  

• Quantitative trait loci for stay‐greenness and agronomic traits provide new insights into chlorophyll homeostasis and nitrogen use in rice
  Ramakrishnappa Archana, Kunnummal Kurungara Vinod, Subbaiyan Gopala Krishnan, Elangovan Devi Chandra Vadhana, Prolay Kumar Bhowmick, Vikram Jeet Singh, Ranjith Kumar Ellur, Lekshmy Sathee, Pranab Kumar Mandal, Haritha Bollinedi, Shekharappa Nanda Kumar,
  Plant Breeding.2023; 142(3): 312.     CrossRef
• Integrated transcriptomics and miRNAomics provide insights into the complex multi-tiered regulatory networks associated with coleoptile senescence in rice
  Jyothish Madambikattil Sasi, Cheeni VijayaKumar, Bharti Kukreja, Roli Budhwar, Rohit Nandan Shukla, Manu Agarwal, Surekha Katiyar-Agarwal
  Frontiers in Plant Science.2022;[Epub]     CrossRef
• Genetic analysis of stay‐green, yield, and agronomic traits in spring wheat
  J. P. Cook, R. K. Acharya, J. M. Martin, N. K. Blake, I. J. Khan, H.‐Y. Heo, K. D. Kephart, J. Eckhoff, L. E. Talbert, J. D. Sherman
  Crop Science.2021; 61(1): 383.     CrossRef
• Unraveling candidate genomic regions responsible for delayed leaf senescence in rice
  Uma Maheshwar Singh, Pallavi Sinha, Shilpi Dixit, Ragavendran Abbai, Challa Venkateshwarlu, Annapurna Chitikineni, Vikas Kumar Singh, Rajeev K. Varshney, Arvind Kumar, Reyazul Rouf Mir
  PLOS ONE.2020; 15(10): e0240591.     CrossRef
• A xylan glucuronosyltransferase gene exhibits pleiotropic effects on cellular composition and leaf development in rice
  Dawei Gao, Wenqiang Sun, Dianwen Wang, Hualin Dong, Ran Zhang, Sibin Yu
  Scientific Reports.2020;[Epub]     CrossRef
• Photosynthetic Metabolism under Stressful Growth Conditions as a Bases for Crop Breeding and Yield Improvement
  Fermín Morales, María Ancín, Dorra Fakhet, Jon González-Torralba, Angie L. Gámez, Amaia Seminario, David Soba, Sinda Ben Mariem, Miguel Garriga, Iker Aranjuelo
  Plants.2020; 9(1): 88.     CrossRef
• Mapping a leaf senescence gene els1 by BSR-Seq in common wheat
  Miaomiao Li, Beibei Li, Guanghao Guo, Yongxing Chen, Jingzhong Xie, Ping Lu, Qiuhong Wu, Deyun Zhang, Huaizhi Zhang, Jian Yang, Panpan Zhang, Yan Zhang, Zhiyong Liu
  The Crop Journal.2018; 6(3): 236.     CrossRef
• QTL Mapping for Grain Yield, Flowering Time, and Stay‐Green Traits in Sorghum with Genotyping‐by‐Sequencing Markers
  Sivakumar Sukumaran, Xin Li, Xianran Li, Chengsong Zhu, Guihua Bai, Ramasamy Perumal, Mitchell R. Tuinstra, P.V. Vara Prasad, Sharon E. Mitchell, Tesfaye T. Tesso, Jianming Yu
  Crop Science.2016; 56(4): 1429.     CrossRef

DNA methylation is a common and rapid evolving epigeneticmechanism among higher eukaryotic organisms including cytosine residues in CG and CNG sequences. NtROS2a gene isolated from tobacco plants (Nicotiana tabacum cv Xanthi nc) contains DNA glycosylase domain with significant similarities to Arabidopsis ROS1 and DME at the C-terminus. Purified NtROS2a protein gene is 5879 bp long and is designated as Nicotiana tabacum Repressor Of Silencing (NtROS: accession numbers; AB281588). RT-PCR analysis initially revealed the adaptive response of the lines overexpressing the gene in tobacco to various abiotic stresses. This was validated when phenotypic evaluation to cold, salt, simulated drought and osmotic stress tolerance was performed. Reduction in leaf wilting rate against high salinity treatment is remarkable in transgenic plants which showed at least 50% less wilting than the WT. Moreover, about 70% wilt rate difference was noted between the transgenic and WT in H₂O₂ treatment. This study showed that NtROS2a gene encoding DNA glycosylase which caused demethylation could regulate adaptive response of tobacco to various abiotic stress conditions.

Citations

Citations to this article as recorded by  

• How Selenium Alleviates Salt Stress in Tobacco Seedlings: Regulation of Osmotic Adjustment Substances, Antioxidation and Gene Expression
  Shiqi Cao, Yanqiu Wei, Xiuhua Li, Huifang Shao, Wei Jia, Zicheng Xu, Wuxing Huang, Dan Han
  Agronomy.2026; 16(12): 1184.     CrossRef
• Functional identification of DNA demethylase gene CaROS1 in pepper (Capsicum annuum L.) involved in salt stress
  Xuelian Ou, Qingzhu Hua, Jichi Dong, Kexian Guo, Minghua Wu, Yinjun Deng, Zhiming Wu
  Frontiers in Plant Science.2024;[Epub]     CrossRef
• Drought induces DNA methylation balance‐related genes in a stage-dependent manner during tomato fruit ripening
  Paulo H. G. A. de Oliveira, Ana C. O. Barbosa, Nathiele S. Araújo, Marcio G. C. Costa
  Theoretical and Experimental Plant Physiology.2024; 36(4): 717.     CrossRef
• The pattern of DNA methylation alteration, and its association with the expression changes of non-coding RNAs and mRNAs in Moso bamboo under abiotic stress
  Yiqian Ding, Long-Hai Zou, Jiajun Wu, Muthusamy Ramakrishnan, Yubang Gao, Liangzhen Zhao, Mingbing Zhou
  Plant Science.2022; 325: 111451.     CrossRef
• Genome-Wide Characterization of DNA Demethylase Genes and Their Association with Salt Response in Pyrus
  Chunxiao Liu, Hui Li, Jing Lin, Ying Wang, Xiaoyang Xu, Zong-Ming (Max) Cheng, Yonghong Chang
  Genes.2018; 9(8): 398.     CrossRef
• Current status and prospects of epigenetic information in sexual reproductive processes of plants
  Yu Jin Jung, Yong-Gu Cho, Kwon Kyoo Kang
  Journal of Plant Biotechnology.2017; 44(1): 19.     CrossRef
• Overexpression ofNtROS2agene encoding cytosine DNA demethylation enhances drought tolerance in transgenic rice
  Jang Sun Choi, In Hye Lee, Yong-Gu Cho, Yu Jin Jung, Kwon Kyoo Kang
  Journal of Plant Biotechnology.2016; 43(3): 376.     CrossRef
• DNA microarray analysis of RNAi plant regulated expression ofNtROS2agene encoding cytosine DNA demethylation
  Jang Sun Choi, In Hye Lee, Yu Jin Jung, Kwon Kyoo Kang
  Journal of Plant Biotechnology.2016; 43(2): 231.     CrossRef

Capsinoids are the class of secondary metabolites identified in non-pungent peppers exhibiting the same bioactive properties as capsaicinoid. Previously, it has been demonstrated that capsinoid production is controlled by the capsaicin synthase (CS) gene and the putative-aminotransferase (pAMT) gene. In this study, we report that C. chinense ‘SNU11-001’ containing high levels of capsinoid has an early stop codon in pAMT resulted from 403 bp and 8 bp insertions deletion in the third and sixth exons. In order to know whether CS expression is correlated with the level of capsinoid, CS and pAMT expressions were determined using SNU11-001 and four Capsicum accessions with different pungency level. RT-PCR analysis showed higher transcription levels of CS in pungent accessions but no clear differences in pAMT expression. To investigate the effect of the substitution of the pAMT allele of C. chinense ‘Habanero’ with the dysfunctional pAMT allele of SNU11-001, an F₂ population was constructed by a cross between aforementioned parental lines. Molecular markers were developed to distinguish CS and pAMT genotypes of SNU11-001 and Habanero and F₂ plants were genotyped. All F₂ plants having the pAMT genotype of SNU11-001 contained high levels of capsinoid while very low levels of capsaicinoid. There was no significant difference in levels of capsinoid among the F₂ plants regardless of CS genotypes. This may be due to strong CS expression of both parental lines. In conclusion, our results show that it is possible to develop a new Habanero cultivar with high capsinoid content by introducing a dysfunctional pAMT allele.

Citations

Citations to this article as recorded by  

• Impact of Low-Intensity Exercise and Capsinoid Supplementation on Blood Lipids in Overweight and Obese Women
  Tae Gyu Kim, Hyun Joo Kang
  The Asian Journal of Kinesiology.2026; 28(1): 73.     CrossRef
• Molecular mechanisms and genomic strategies for enhancing stress resilience in pepper crop
  Ikram Ullah, Ihteram Ullah, Huafeng Zhang, Manzoor R. Khan, Abdul Mateen, Yingping Pei, Adnan Shakeel, Aashaq Hussain Bhat, Chenglong Fu, Rugang Chen
  Scientia Horticulturae.2025; 352: 114403.     CrossRef
• Combined Exercise and HabaNova^TM (NET-2201, Capsicum chinense L. cv.) Supplementation Potentiates Improvements in Body Composition and Anthropometric Measures in Overweight/Obese Women: A Double-Blind Randomized Controlled Pilot Study
  Hyun Joo Kang
  Exercise Science.2025; 34(2): 170.     CrossRef
• Recent Understanding of the Biosynthesis of Capsaicinoids and Low-pungent Analogs towards Quality Improvement of Chili Pepper
  Yoshiyuki Tanaka
  The Horticulture Journal.2025; 94(2): 117.     CrossRef
• Effects of NET-2201 (Capsicum chinense L. cv.) on brown adipose tissue activation and white adipose tissue browning in high-fat-diet-induced obese mice
  Yoon-Young Han, Ha-Neul Jo, Bo-Mi Kim, Jae-Sun Lee, Ji-Min Kim, Dae-Ho Ryu, Dong-Hee Kim, Chan-Sung Park, Byoung-Cheorl Kang, Yong-Wook Lee
  Food Science and Biotechnology.2025; 34(3): 769.     CrossRef
• Combining Ability on Yields, Capsinoids and Capsaicinoids in Pepper Varieties (Capsicum annuum L.)
  Tanyarat Tarinta, Saksit Chanthai, Eiji Nawata, Suchila Techawongstien
  Horticulturae.2023; 9(9): 1043.     CrossRef
• Update on the genetic and molecular regulation of the biosynthetic pathways underlying pepper fruit color and pungency
  Jelli Venkatesh, Seo-Young Lee, Seungki Back, Tae-Gun Kim, Geon Woo Kim, Jung-Min Kim, Jin-Kyung Kwon, Byoung-Cheorl Kang
  Current Plant Biology.2023; 35-36: 100303.     CrossRef
• Breeding peppers for industrial uses: Progress and prospects
  Satyaprakash Barik, Naresh Ponnam, Anand C. Reddy, Lakshmana Reddy D.C, Koushik Saha, Acharya G.C., Madhavi Reddy K.
  Industrial Crops and Products.2022; 178: 114626.     CrossRef
• Breeding Capsicum chinense Lines with High Levels of Capsaicinoids and Capsinoids in the Fruit
  Siyoung Jang, Minjeong Park, Do-Gyeong Lee, Jung-Hyun Lim, Ji-Won Jung, Byoung-Cheorl Kang
  Agriculture.2021; 11(9): 819.     CrossRef
• Factors affecting the capsaicinoid profile of hot peppers and biological activity of their non-pungent analogs (Capsinoids) present in sweet peppers
  Virgílio Gavicho Uarrota, Marcelo Maraschin, Ângela de Fátima M. de Bairros, Romina Pedreschi
  Critical Reviews in Food Science and Nutrition.2021; 61(4): 649.     CrossRef
• Influence of Fruit Ripening on the Total and Individual Capsaicinoids and Capsiate Content in Naga Jolokia Peppers (Capsicum chinense Jacq.)
  Mercedes Vázquez-Espinosa, José Arturo Olguín-Rojas, Oreto Fayos, Ana V. González-de-Peredo, Estrella Espada-Bellido, Marta Ferreiro-González, Carmelo G. Barroso, Gerardo F. Barbero, Ana Garcés-Claver, Miguel Palma
  Agronomy.2020; 10(2): 252.     CrossRef
• Changes in Capsiate Content in Four Chili Pepper Genotypes (Capsicum spp.) at Different Ripening Stages
  Mercedes Vázquez-Espinosa, Oreto Fayos, Ana V. González-de-Peredo, Estrella Espada-Bellido, Marta Ferreiro-González, Miguel Palma, Ana Garcés-Claver, Gerardo F. Barbero
  Agronomy.2020; 10(9): 1337.     CrossRef
• Content of Capsaicinoids and Capsiate in “Filius” Pepper Varieties as Affected by Ripening
  Mercedes Vázquez-Espinosa, Oreto Fayos, Ana V. González-de-Peredo, Estrella Espada-Bellido, Marta Ferreiro-González, Miguel Palma, Ana Garcés-Claver, Gerardo F. Barbero
  Plants.2020; 9(9): 1222.     CrossRef
• A MYB transcription factor is a candidate to control pungency in Capsicum annuum
  Koeun Han, Siyoung Jang, Joung-Ho Lee, Do-Gyeong Lee, Jin-Kyung Kwon, Byoung-Cheorl Kang
  Theoretical and Applied Genetics.2019; 132(4): 1235.     CrossRef
• Positional differences of intronic transposons in pAMT affect the pungency level in chili pepper through altered splicing efficiency
  Yoshiyuki Tanaka, Takaya Asano, Yorika Kanemitsu, Tanjuro Goto, Yuichi Yoshida, Kenichiro Yasuba, Yuki Misawa, Sachie Nakatani, Kenji Kobata
  The Plant Journal.2019; 100(4): 693.     CrossRef
• Quantitation of capsiate and dihydrocapsiate and tentative identification of minor capsinoids in pepper fruits (Capsicum spp.) by HPLC-ESI-MS/MS(QTOF)
  Oreto Fayos, María Savirón, Jesús Orduna, Gerardo F. Barbero, Cristina Mallor, Ana Garcés-Claver
  Food Chemistry.2019; 270: 264.     CrossRef
• Assessment of Capsaicinoid and Capsinoid Accumulation Patterns during Fruit Development in Three Chili Pepper Genotypes (Capsicum spp.) Carrying Pun1 and pAMT Alleles Related to Pungency
  Oreto Fayos, Neftalí Ochoa-Alejo, Octavio Martínez de la Vega, María Savirón, Jesús Orduna, Cristina Mallor, Gerardo F. Barbero, Ana Garcés-Claver
  Journal of Agricultural and Food Chemistry.2019; 67(44): 12219.     CrossRef
• Synthesis of (±)-3,4-dimethoxybenzyl-4-methyloctanoate as a novel internal standard for capsinoid determination by HPLC-ESI-MS/MS(QTOF)
  O Fayos, GF Barbero, M Savirón, J Orduna, AG Durán, M Palma, JMG Molinillo, FA Macías, CG Barroso, C Mallor, A Garcés-Claver
  Open Chemistry.2018; 16(1): 87.     CrossRef
• Identification of a Novel Mutant pAMT Allele Responsible for Low-pungency and Capsinoid Production in Chili Pepper: Accession ‘No. 4034’ (Capsicum chinense)
  Yoshiyuki Tanaka, Shiho Fukuta, Sota Koeda, Tanjuro Goto, Yuichi Yoshida, Ken-ichiro Yasuba
  The Horticulture Journal.2018; 87(2): 222.     CrossRef
• QTL mapping and GWAS reveal candidate genes controlling capsaicinoid content in Capsicum
  Koeun Han, Hea‐Young Lee, Na‐Young Ro, On‐Sook Hur, Joung‐Ho Lee, Jin‐Kyung Kwon, Byoung‐Cheorl Kang
  Plant Biotechnology Journal.2018; 16(9): 1546.     CrossRef
• Screening old peppers (Capsicum spp.) for disease resistance and pungency-related traits
  Cristina Silvar, Carlos A. García-González
  Scientia Horticulturae.2017; 218: 249.     CrossRef
• Marker-assisted backcross breeding for development of pepper varieties (Capsicum annuum) containing capsinoids
  Hyeon-Seok Jeong, Siyoung Jang, Koeun Han, Jin-Kyung Kwon, Byoung-Cheorl Kang
  Molecular Breeding.2015;[Epub]     CrossRef

The allelic variations at the Rht-1, Vrn-1 and Ppd-1 of 410 Korean wheat cultivars, including 111 Korean experimental lines, 238 Korean landraces and 61 North Korean collections, were investigated to provide the information of plant height and heading date and to elucidate the relationship between those traits and allelic variation of these genes because earliness is major consideration in Korean wheat production. All Korean wheats displayed vrn-A1 and Ppd-A1b alleles, while Rht-B1a, Rht-D1a, vrn-B1, Vrn-D1, Ppd-B1b and Ppd-D1a alleles were also predominantly found. Most Korean wheats carried both Rht-B1a and Rht-D1a alleles, both vrn-B1 and Vrn-D1 alleles, or both Ppd-B1b and Ppd-D1a alleles. The Rht-B1a, vrn-D1, Ppd-B1b and Ppd-D1b alleles were found to exhibit longer culm and spike length than their counterpart alleles. The Rht-B1a allele also showed longer spike length than Rht-B1b. Vrn-B1b and vrn-D1 alleles exhibited longer days to heading date than their counterpart alleles at the Vrn-B1 and Vrn-D1 loci. Lines carrying both Rht-B1b and Rht-D1b alleles displayed shorter culm and longer spike length and days to heading date than any other combination of alleles at the Rht-B1 and Rht-D1 loci. In contrast, lines carrying both Ppd-B1b and Ppd-D1b alleles exhibited longer culm and spike length than any other combination of alleles at the Ppd-B1 and Ppd-D1 loci.

Citations

Citations to this article as recorded by  

• АЛМАТЫ ОБЛЫСЫ ЖАҒДАЙЫНДА ЖАЗДЫҚ ЖҰМСАҚ БИДАЙ ГЕНОТИПТЕРІНІҢ АБИОТИКАЛЫҚ СТРЕСС – ҚҰРҒАҚШЫЛЫҚҚА ЖӘНЕ БИОТИКАЛЫҚ СТРЕСС – ҚОҢЫР ТАТ (PUCCINIA RECONDITA) АУРУЫНА ТӨЗІМДІЛІГІН ФИТОПАТОЛОГИЯЛЫҚ БАҒАЛАУ
  Женис Кеишилов, Алма Кохметова, Ерлан Дутбаев, Мадина Кумарбаева, Фахим Шехзад Балоч
  Izdenister natigeler.2026; 28(1(109)): 83.     CrossRef
• Genome-wide association study to identify the genomic loci associated with wheat heading date variation under autumn-sowing conditions
  Yurim Kim, Myoung-Goo Choi, Myoung Hui Lee, Chuloh Cho, Jun Yong Choi, Suk-Jin Kim, Chon-Sik Kang, Chul Soo Park, Ki-Chang Jang, Youngjun Mo, Changhyun Choi, Harsh Raman
  PLOS One.2025; 20(4): e0322306.     CrossRef
• Genotypic Variation and Phenotypic Clustering of 515 Korean Wheat Germplasm Based on Agronomic and Grain Traits
  Seon Suk Kim, Sumin Hong, Myoung-Goo Choi, Chang-Hyun Choi, Chon-Sik Kang, Kyeong-Min Kim, Chul Soo Park
  Korean Journal of Breeding Science.2025; 57(3): 231.     CrossRef
• Allelic Variations in Phenology Genes in Club Wheat (Triticum compactum) and Their Association with Heading Date
  Bárbara Mata, Adoración Cabrera
  International Journal of Molecular Sciences.2025; 26(10): 4875.     CrossRef
• Evaluation of genetic characteristics and physicochemical property of Korean wheat landraces (Triticum aestivum L.)
  Yumi Lee, Sejin Oh, Seong-Wook Kang, Jaeyoung Ock, Gitak Ryu, Seul Lee, Jinhee Park, Jin-Young Moon, Kim Jin-Young, Jongtae Lee, Seong-Woo Cho
  Czech Journal of Genetics and Plant Breeding.2025; 61(4): 210.     CrossRef
• QTL Mapping for Heading Date and Yield-Related Traits in a Doubled Haploid Population Derived from Two Korean Wheat Cultivars
  Sumin Hong, Kyeong-Min Kim, Changhyun Choi, Seong-Woo Cho, Chul Soo Park, Youngjun Mo
  Plant Breeding and Biotechnology.2023; 11(3): 197.     CrossRef
• Mining novel genomic regions and candidate genes of heading and flowering dates in bread wheat by SNP- and haplotype-based GWAS
  Pengfang Qiao, Xuan Li, Dezheng Liu, Shan Lu, Lei Zhi, Aiman Rysbekova, Liang Chen, Yin-gang Hu
  Molecular Breeding.2023;[Epub]     CrossRef
• Diversity of Ppd-1 genotypes of spring and winter bread wheat (Triticum aestivum L.) of Ukraine
  V. Fait, I. Balashova
  Visnyk of Lviv University. Biological series.2022; (87): 32.     CrossRef
• Allelic Variations in Phenology Genes of Eastern U.S. Soft Winter and Korean Winter Wheat and Their Associations with Heading Date
  Fengyun Ma, Gina Brown-Guedira, Moonseok Kang, Byung-Kee Baik
  Plants.2022; 11(22): 3116.     CrossRef
• Unlocking the Yield Potential of Wheat: Influence of Major Growth Habit and Adaptation Genes
  
  Crop Breeding, Genetics and Genomics.2021;[Epub]     CrossRef
• Identification of the vernalization gene VRN-B1 responsible for heading date variation by QTL mapping using a RIL population in wheat
  Yuting Li, Hongchun Xiong, Huijun Guo, Chunyun Zhou, Yongdun Xie, Linshu Zhao, Jiayu Gu, Shirong Zhao, Yuping Ding, Luxiang Liu
  BMC Plant Biology.2020;[Epub]     CrossRef
• Flowering-time Genes and Flowering-time Pathways in Wheat (Triticum aestivum L.)
  Jeong Hwan Lee
  Korean Journal of Breeding Science.2019; 51(2): 65.     CrossRef
• The Photoperiod-Insensitive Allele Ppd-D1a Promotes Earlier Flowering in Rht12 Dwarf Plants of Bread Wheat
  Liang Chen, Yingying Du, Qiumei Lu, Hua Chen, Ruishuang Meng, Chunge Cui, Shan Lu, Yang Yang, Yongmao Chai, Juan Li, Lulu Liu, Xiangning Qi, Hang Li, Kohei Mishina, Fei Yu, Yin-Gang Hu
  Frontiers in Plant Science.2018;[Epub]     CrossRef
• Assessment of DNA Markers Related to Days to Heading Date, Tiller Number, and Yield in Korean Wheat Populations
  Seong-Woo Cho, Taek-Gyu Kang, Seong-Wook Kang, Chon-Sik Kang, Chul Soo Park
  Korean Journal of Breeding Science.2018; 50(3): 211.     CrossRef
• Genetic Mapping of the Leaf Number above the Primary Ear and Its Relationship with Plant Height and Flowering Time in Maize
  Min Cui, Bo Jia, Huanhuan Liu, Xin Kan, Yu Zhang, Ronghua Zhou, Zhipeng Li, Liang Yang, Dexiang Deng, Zhitong Yin
  Frontiers in Plant Science.2017;[Epub]     CrossRef

Simple sequence repeats (SSRs) have been the marker of choice for rice molecular breeding due to the high level of polymorphism, technical simplicity and low cost. Recent advances in rice genomics have led to the discovery of abundant single nucleotide polymorphism (SNPs) which have enormous potential for rice molecular breeding. To assess both marker systems for molecular breeding in rice, SSR and SNP markers were evaluated on a set of 23 genotypes representing indica germplasm for their usefulness in molecular research and breeding program. Seven hundred SSR and sequence tagged sites (STS) markers and 384 SNPs were screened for polymorphism. Highly polymorphic markers based on polymorphic information content (PIC) values were identified, which will be useful for molecular breeding. Data was used to identify an “indica genotyping set” based on high level of polymorphism, chromosome position and marker quality which will provide kits of markers for marker assisted selection (MAS). Genetic diversity analysis using SSR data was more consistent with pedigrees compared to analysis with SNP data indicating that more than 384 SNPs are required when elite indica breeding material is used. The results also indicated that there were polymorphic “blind spots” for the fixed SNP set suggesting that SSRs could still be used to complement fixed-SNP genotyping platforms for some molecular breeding applications.

Citations

Citations to this article as recorded by  

• Establishment and Polymorphism Analysis of SNP Markers in the Gynogenic Blunt Snout Bream
  Ping Wu, Yuhuan Wei, Siyao Weng, Mingguang Hu, Jiaxing Li, Wenxuan Tang, Lei Zhang, Qinbo Qin, Ting Yi, Wuhui Li, Min Tao, Chun Zhang, Qizhi Liu, Shaojun Liu
  Biology.2026; 15(2): 188.     CrossRef
• Marker-assisted backcross breeding for introgression of white rust resistance in Indian mustard (Brassica juncea) cultivar
  Monika, Vijay Veer Singh, Anjana Goel, Ibandalin Mawlong, Bishal Gurung
  Physiological and Molecular Plant Pathology.2026; 145: 103314.     CrossRef
• Whole-genome simple sequence repeat development and genetic diversity analysis of sponge gourd (Luffa cylindrica)
  Rongjing Cui, Zhu Wang, Li Jia, Yongmei Miao, Congsheng Yan, Ming Qian, Yingjie Shu, Kaijing Zhang
  PeerJ.2026; 14: e20934.     CrossRef
• Genotyping of Commercial European Cannabis Seeds Based on Multiple Mapped Marker Loci: A Comparative Study of Drug and Hemp Varieties
  Marcello Borin, Francesco Scariolo, Maddalena Cappello Fusaro, Irene Lucchetta, Gio Batta Sacilotto, Marco Gazzola, Stefano Bona, Gianni Barcaccia
  Plants.2025; 14(19): 3050.     CrossRef
• Genetic diversity and population structure of regional rice genotypes from Colombia’s Caribbean and pacific regions: differentiation and ancestry in relation to the 3000 Rice genomes project
  Jhon A. Berdugo-Cely, Jazmín V. Pérez-Pazos, Shirley P. Perez-Cantero, Jose G. Morales-Angulo, Jorge L. Romero-Ferrer
  Genetic Resources and Crop Evolution.2025; 72(8): 10001.     CrossRef
• Construction of near-isogenic lines for studying the resistance mechanism of durable blast resistant variety
  K Y Nasution, N Mustaqimah, P Melati, A K Dewi, M Y Maryono, I Dwimahyani, Sobrizal
  IOP Conference Series: Earth and Environmental Science.2025; 1478(1): 012001.     CrossRef
• Genetic factors underlying anaerobic germination in rice: Genome‐wide association study and transcriptomic analysis
  Ranjita Thapa, Rodante E. Tabien, Michael J. Thomson, Endang M. Septiningsih
  The Plant Genome.2024;[Epub]     CrossRef
• SNP loci identification and KASP marker development system for genetic diversity, population structure, and fingerprinting in sweetpotato (Ipomoea batatas L.)
  Feiyang Yang, Tao Lang, Jingyu Wu, Cong Zhang, Huijuan Qu, Zhigang Pu, Fan Yang, Ma Yu, Junyan Feng
  BMC Genomics.2024;[Epub]     CrossRef
• Comparative Genetic Diversity Assessment and Marker–Trait Association Using Two DNA Marker Systems in Rice (Oryza sativa L.)
  Mohammed I. Al-daej, Adel A. Rezk, Mohamed M. El-Malky, Tarek A. Shalaby, Mohamed Ismail
  Agronomy.2023; 13(2): 329.     CrossRef
• Genetic Evaluation of In Vitro Micropropagated and Regenerated Plants of Cannabis sativa L. Using SSR Molecular Markers
  Kostas Ioannidis, Ioanna Tomprou, Vangelis Mitsis, Polyxeni Koropouli
  Plants.2022; 11(19): 2569.     CrossRef
• GENETIC VARIABILITY AND DIVERSITY OF UPLAND RICE LANDRACES
  Suwansa CHUCHERT, Charassri NUALSRİ, Watcharin SOONSUWON
  Turkish Journal Of Field Crops.2022; 27(2): 175.     CrossRef
• Developing and Testing Molecular Markers in Cannabis sativa (Hemp) for Their Use in Variety and Dioecy Assessments
  Marcello Borin, Fabio Palumbo, Alessandro Vannozzi, Francesco Scariolo, Gio Batta Sacilotto, Marco Gazzola, Gianni Barcaccia
  Plants.2021; 10(10): 2174.     CrossRef
• Identification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers
  Debjani Roy Choudhury, Ramesh Kumar, Vimala Devi S, Kuldeep Singh, N. K. Singh, Rakesh Singh
  Frontiers in Genetics.2021;[Epub]     CrossRef
• Molecular genetic diversity and population structure analyses of rutabaga accessions from Nordic countries as revealed by single nucleotide polymorphism markers
  Zhiyu Yu, Rudolph Fredua-Agyeman, Sheau-Fang Hwang, Stephen E. Strelkov
  BMC Genomics.2021;[Epub]     CrossRef
• Genetic diversity of selected pigmented traditional rice (Oryza sativa L.) varieties from Mindanao, Philippines using agromorphological traits and simple sequence repeats markers
  Mary Valerie G. Embate, Mark Ian C. Calayugan, Renerio P. Gentallan, Pompe C. Sta Cruz, Jose E. Hernandez, Teresita H. Borromeo
  Journal of Crop Science and Biotechnology.2021; 24(3): 259.     CrossRef
• Development and application of microsatellite markers within transcription factors in flare tree peony (Paeonia rockii) based on next-generation and single-molecule long-read RNA-seq
  Na LIU, Fang-yun CHENG, Xin GUO, Yuan ZHONG
  Journal of Integrative Agriculture.2021; 20(7): 1832.     CrossRef
• Genetic diversity, SNP-trait associations and genomic selection accuracy in a west African collection of Kersting’s groundnut [Macrotyloma geocarpum(Harms) Maréchal & Baudet]
  Félicien Akohoue, Enoch Gbenato Achigan-Dako, Clay Sneller, Allen Van Deynze, Julia Sibiya, Lewis Lukens
  PLOS ONE.2020; 15(6): e0234769.     CrossRef
• Association mapping for yield traits in Paeonia rockii based on SSR markers within transcription factors of comparative transcriptome
  Na Liu, Fangyun Cheng
  BMC Plant Biology.2020;[Epub]     CrossRef
• Identification of polymorphic SSR markers in elite genotypes of pearl millet and diversity analysis
  Sushil Kumar, Charles T. Hash, Govind Singh, Ramana Kumari Basava, Rakesh K. Srivastava
  Ecological Genetics and Genomics.2020; 14: 100051.     CrossRef
• Detection of QTL for panicle architecture in $$hbox {F}_{2}$$ population of rice
  Rohini Bhat, Anil Kumar Singh, Romesh Kumar Salgotra, Manmohan Sharma, Muntazir Mushtaq, Sreshti Bagati, Sharmishta Hangloo, Amrinder Singh
  Journal of Genetics.2019;[Epub]     CrossRef
• Genetic diversity of maize genotypes with variable resistance toStriga asiaticabased on SSR markers
  A.I.T. Shayanowako, H. Shimelis, M.D. Laing, L. Mwadzingeni
  Cereal Research Communications.2018; 46(4): 668.     CrossRef
• A High-Density EST-SSR-Based Genetic Map and QTL Analysis of Dwarf Trait in Cucurbita pepo L.
  Chenggang Xiang, Ying Duan, Hongbo Li, Wei Ma, Sanwen Huang, Xiaolei Sui, Zhonghua Zhang, Changlin Wang
  International Journal of Molecular Sciences.2018; 19(10): 3140.     CrossRef
• New Hypervariable SSR Markers for Diversity Analysis, Hybrid Purity Testing and Trait Mapping in Pigeonpea [Cajanus cajan (L.) Millspaugh]
  Abhishek Bohra, Rintu Jha, Gaurav Pandey, Prakash G. Patil, Rachit K. Saxena, Indra P. Singh, D. Singh, R. K. Mishra, Ankita Mishra, F. Singh, Rajeev K. Varshney, N. P. Singh
  Frontiers in Plant Science.2017;[Epub]     CrossRef
• Comparison of transcriptome-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers for genetic fingerprinting, diversity evaluation, and establishment of relationships in eggplants
  Pietro Gramazio, Jaime Prohens, Dionís Borràs, Mariola Plazas, Francisco Javier Herraiz, Santiago Vilanova
  Euphytica.2017;[Epub]     CrossRef
• Rice molecular markers and genetic mapping: Current status and prospects
  Ghulam Shabir, Kashif Aslam, Abdul Rehman Khan, Muhammad Shahid, Hamid Manzoor, Sibgha Noreen, Mueen Alam Khan, Muhammad Baber, Muhammad Sabar, Shahid Masood Shah, Muhammad Arif
  Journal of Integrative Agriculture.2017; 16(9): 1879.     CrossRef
• A method for genotyping elite breeding stocks of leaf chicory (Cichorium intybus L.) by assaying mapped microsatellite marker loci
  Andrea Ghedina, Giulio Galla, Thierry Cadalen, Jean-Louis Hilbert, Silvano Tiozzo Caenazzo, Gianni Barcaccia
  BMC Research Notes.2015;[Epub]     CrossRef

DNA barcoding is the use of short DNA sequences of the genome for large scale species identification. The Consortium for the Barcode of Life (CBOL) plant-working group recommended a 2-locus combination as the standard plant barcode. The evolutions of the chloroplast regions combined with nuclear gens are sufficiently rapid to allow discrimination between closely related species. We evaluated the efficacy of the proposed plant barcoding loci, matK, along with ITS2 for barcoding the Vigna species. To assess the discriminatory ability of barcoding loci for identifying the Vigna species, we sampled 52 of the taxonomically best known groups in the genus. Topologies of the phylogenetic trees based on ITS2 and matK analyses were similar but a few accessions were placed into distant phylogenetic groups. Neither ITS2 nor matK analyses were able to discriminate some closely related Vigna species. Thus, we used concatenated data to increase the resolving power of ITS2 and used matK as an additional tool for phylogenetic analysis in Vigna because characterization of the nucleotide sequences of the matK region was easier and more cost-effective than that of the ITS region.

Citations

Citations to this article as recorded by  

• Genetic Diversity of Asian Vigna Species (Subgenus Ceratotropis; Genus Vigna) in India Based on ITS2 Sequences Data
  Suraj D. Umdale, Nikhil B. Gaikwad, Shaila Kadam, Mahendra L. Ahire, Pankaj S. Mundada, Kangila V. Bhat
  Plant Molecular Biology Reporter.2023; 41(3): 454.     CrossRef
• Identification of Apiaceae using ITS, ITS2 and psba-trnH barcodes
  Zhehui Jiang, Meiqi Zhang, Lingyang Kong, Yihong Bao, Weichao Ren, Hongyuan Li, Xiubo Liu, Zhen Wang, Wei Ma
  Molecular Biology Reports.2023; 50(1): 245.     CrossRef
• Molecular characterization and phylogenetic relationships in Asiatic Vigna using ITS and cpDNA loci
  Ruchi Vir, Tabassum Jehan, K. V. Bhat, Suman Lakhanpaul
  Vegetos.2022; 36(4): 1397.     CrossRef
• Comparative Genetic Analysis between the Jeju ‘Inchangkyool’ and Chinese ‘Ichangensis’ (Citrus ichangensis) using Internal Chloroplast trnL-trnF Intergenic Spacers and Transcribed Spacer Sequence Regions
  Min Ju Kim, Mi Sun Kim, Kihye Shin, Sukman Park, Cheolwoo Choi, Su Hyun Yun, Seong Beom Jin
  Korean Journal of Breeding Science.2021; 53(1): 16.     CrossRef
• Novel Genetic Resources in the Genus Vigna Unveiled from Gene Bank Accessions
  Yu Takahashi, Prakit Somta, Chiaki Muto, Kohtaro Iseki, Ken Naito, Muthaiyan Pandiyan, Senthil Natesan, Norihiko Tomooka, Vijai Gupta
  PLOS ONE.2016; 11(1): e0147568.     CrossRef

This study examined the genetic variation of cyanidin 3-glucoside (C3G) contents in blackish-purple rice. F₂ populations were established from crosses between blackish purple rice and normal white rice. The blackish rice cultivars used were Jilinheimi, Heidao38, LK1A-2-12-1-1, Heugjinju, and No2, and the common white rice cultivars used were Hwachung super giant embryo and Heugbal. The purple pericarp color is known to be controlled by a set of dominant alleles, Pb(Prp-b) and Pp(Prp-a). In this study, the segregation of the black purple:brown:white pericarp in the F₂ population was 9:3:4, demonstrating that the purple pericarp color was controlled by two dominant complementary genes. The F₂ distribution of C3G showed continuous variation, with a tendency toward a lower level in all the crosses. However, some F₂ crosses, such as Jilinheimi/Heidao38 and Jilinheimi/LK1A-2-12-1-1, showed transgressive segregation of the C3G content. C3G content of Jilinheimi linked on 84% level in C3G content of F₂ population between Jilinheimi/Heidao38, and 41.3% level in Jilinheimi/LK1A-2-12-1-1. The results of the color difference meter and C3G content analysed by HPLC revealed highly significant correlations between the seed coat color of the colored rice germplasm and that of the segregated populations. There was a significant positive correlation between the C3G content with L* (lightness) and b* (yellowness). The a* (redness) was different in each cross, but there was a significant positive correlation between the C3G content with L* and b*.

Citations

Citations to this article as recorded by  

• The effect of processing duration and pressure on the physicochemical characteristics and development of puffed rice
  Madalina O. Marincaș, Romina A. Marc, Andreea Pușcaș, Andruța Mureșan, Rodica Sima, Mihaela C. Vlassa, Vlad Mureșan, Crina C. Mureșan
  Applied Food Research.2026; 6(1): 101629.     CrossRef
• Unraveling grain quality in cereals: development, heat stress, and molecular mechanisms
  Ping Li, Zheng Li, Jiangyue Su, Yanjie Lv, Shuhua Liao, Pu Wang, Shoubing Huang
  Food Chemistry.2026; 512: 148900.     CrossRef
• Comprehensive genetic diversity revealed in the pre-breeding RILs (O. sativa × O. rufipogon) with enhanced yield and pigmented grain quality
  Subhas Chandra Roy, Pankaj Shil
  Frontiers in Genetics.2025;[Epub]     CrossRef
• Genome-Wide Association Study of Agricultural and Biochemical Traits in Radiation-Induced Colored Wheat
  Min Jeong Hong, Chan Seop Ko, Dae Yeon Kim
  Agronomy.2025; 15(8): 1933.     CrossRef
• Advances and Future Prospects of Pigment Deposition in Pigmented Rice
  Hong Lang, Xingtian Jia, Bing He, Xiaoming Yu
  Plants.2025; 14(6): 963.     CrossRef
• Anatomical and Digital Image Analysis of Flavonoid-Mediated Grain Coloration in Rye (Secale cereale L.)
  Pavel A. Zykin, Elena A. Andreeva, Natalia V. Tsvetkova, Andrey N. Bulanov, Anatoly V. Voylokov
  Plants.2025; 14(16): 2557.     CrossRef
• Genome-wide association mapping of genes for anthocyanin and flavonoid contents in Vietnamese landraces of black rice
  Cuong Hung Pham, Tuyen Duc Do, Hoa Thi Lan Nguyen, Nga Thi Hoang, Trung Duc Tran, Mi Thi Thao Vu, Hanh Hong Doi, Thu-Giang Thi Bui, Robert James Henry
  Euphytica.2024;[Epub]     CrossRef
• Morphoagronomical Evaluation of Several Indonesian Pigmented Rice (Oryza sativa L.) Accessions from East Java and Central Java, Indonesia
  Yeni Avidhatul Husnah, Turhadi Turhadi, Anna Safitri, Fatchiyah Fatchiyah
  Plant Breeding and Biotechnology.2024;[Epub]     CrossRef
• Explicating genetic architecture governing nutritional quality in pigmented rice
  Jebi Sudan, Uneeb Urwat, Asmat Farooq, Mohammad Maqbool Pakhtoon, Aaqif Zaffar, Zafir Ahmad Naik, Aneesa Batool, Saika Bashir, Madeeha Mansoor, Parvaze A. Sofi, Najeebul Ul Rehman Sofi, Asif B. Shikari, Mohd. Kamran Khan, Mohammad Anwar Hossain, Robert J.
  PeerJ.2023; 11: e15901.     CrossRef
• Deciphering the Genetic Architecture of Color Variation in Whole Grain Rice by Genome-Wide Association
  Wenjun Wang, Xianjin Qiu, Ziqi Wang, Tianyi Xie, Wenqiang Sun, Jianlong Xu, Fan Zhang, Sibin Yu
  Plants.2023; 12(4): 927.     CrossRef
• Recent Insights into Anthocyanin Pigmentation, Synthesis, Trafficking, and Regulatory Mechanisms in Rice (Oryza sativa L.) Caryopsis
  Enerand Mackon, Guibeline Charlie Jeazet Dongho Epse Mackon, Yafei Ma, Muhammad Haneef Kashif, Niyaz Ali, Babar Usman, Piqing Liu
  Biomolecules.2021; 11(3): 394.     CrossRef
• The Genetic Basis and Nutritional Benefits of Pigmented Rice Grain
  Edwige Gaby Nkouaya Mbanjo, Tobias Kretzschmar, Huw Jones, Nelzo Ereful, Christopher Blanchard, Lesley Ann Boyd, Nese Sreenivasulu
  Frontiers in Genetics.2020;[Epub]     CrossRef

The genetic variability and yield stability are complex traits with large environmental components that are utilized for breeding of improved plant performance under drought conditions. In order to better understand the relationship among genotype, trait components, and environment, marker-trait associations in 20 wheat varieties using phenotypic and ISSR (Inter-Simple Sequence Repeat) markers under drought conditions were examined. The combined analysis of variance results showed that the tested traits were significantly influenced by years, irrigation treatments, and the varieties. The drought stress conditions resulted in a substantial reduction in grain yield by 33.70%. The varieties viz., Shakha-93, Sahel-1, Giza-160, Giza-168, Sids-1, Sids-4 and Nilen were relatively drought resistant (DSI, Drought Susceptibility Index values< 1) and gave high grain yield when compared with the average of all varieties under drought stress. The stability analysis revealed that the cultivar named ‘Sids-1’ showed high and stable yield (b_i=1 and S²d_i = 0), so it could be selected to be grown under drought stress conditions. On the other hand, Shakha-92 and Bacanora-88 showed below-average stability (b_i = 1.35 & 1.42), indicating that these genotypes perform well under normal conditions. The percent of polymorphism (%P) among varieties ranged from 25 to 80% with an average of 52.08%. Polymorphism information content (PIC) values varied from 0.08 to 0.28. Plant height and 1000-kernel weight showed significant regressions (23.83 and 27.54) under normal irrigation conditions, respectively. Moreover, under drought stress conditions, plant height, 1000-kernel weight and no. of spikes/m² showed significant regressions of 40.38, 20.95 and 24.95, respectively.

Citations

Citations to this article as recorded by  

• Molecular Characterization of Some Wheat Varıeties and Genotypes Grown in Syrıa and Türkiye Using ISSR Marker Technique
  Mhammed Anwr Jatal, Civan Çelik, Yaşar Karakurt, Emre Sevindik
  Biology Bulletin.2026;[Epub]     CrossRef
• Genetic association analysis of grain yield-related traits in Aegilops tauschii under drought and non-stress conditions
  Mehran Falaknaz, Ali Aalami, Ali Ashraf Mehrabi, Danial Kahrizi, Atefeh Sabouri
  Scientific Reports.2025;[Epub]     CrossRef
• ISSRs profiles and protein patterns related to yield and yield compositions in several bread wheat genotypes growing under thermal stress
  Esam M. Mohamedahmed, Adil A. El Hussein, Marmar A. El Siddig
  Journal of King Saud University - Science.2024; 36(4): 103139.     CrossRef
• Breeding for silicon-use efficiency, protein content and drought tolerance in bread wheat ( Triticum aestivum L.): a review
  Marylyn M. Christian, Hussein Shimelis, Mark D. Laing, Toi J. Tsilo, Isack Mathew
  Acta Agriculturae Scandinavica, Section B — Soil & Plant Science.2022; 72(1): 17.     CrossRef
• Integrated farming systems for prosperity of marginal farmers and sustainable agriculture: a roadmap for India
  U K BEHERA
  The Indian Journal of Agricultural Sciences.2019; 89(11): 1755.     CrossRef
• Association Analysis for Stability Parameters in Bread Wheat Using ISSR Markers
  anita Yaghotipoor, Ezatollah Farshadfar, Mohsen Saeidi
  Journal of Crop Breeding.2018; 10(26): 153.     CrossRef