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.
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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
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
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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
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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
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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
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