Future flooding tolerant rice germplasm: resilience afforded beyondSub1Agene
Authors: Anumalla Mahender , Khanna Apurva , Catolos Margaret , Ramos Joie , Sta. Cruz Ma Teresa , Venkateshwarlu Challa , Konijerla Jaswanth , Pradhan Sharat Kumar , Dash Sushanta Kumar , Das Yater , Chowdhury Dhiren , Chetia Sanjay Kumar , das Janardan , Nath Phuleswar , Merugumala Girija Rani , Roy Bidhan , Pradhan Navin , Jana Monoranjan , Dana Indrani , Debnath Suman , Nath Anirban , Singh Suresh Prasad , Iftekharuddaula Khandakar Md , Ghosal Sharmistha , Ali Mohammad , Khanam Sakina , Ul Islam Md Mizan , Faruquee Muhiuddin , Tonny Hosna Jannat , Hasan Md Rokebul , Rahman Anisar , Ali Jauhar , Sinha Pallavi , Singh Vikas Kumar , Islam Mohammad Rafiqul , Bhosale Sankalp , Kohli Ajay , Bhardwaj Hans , Hussain Waseem 
Published: February 2025

Developing high-yielding, flood-tolerant rice varieties is essential for enhancing productivity and livelihoods in flood-prone ecologies. We explored genetic avenues beyond the well-knownSUB1Agene to improve flood resilience in rice. We screened a collection of 6,274 elite genotypes from IRRI’s germplasm repository for submergence and stagnant flooding tolerance over multiple seasons and years. This rigorous screening identified 89 outstanding elite genotypes, among which thirty-seven exhibited high submergence tolerance, surpassing the survival rate ofSUB1Aintrogression genotypes by 40-50%. Thirty-five genotypes showed significant tolerance to stagnant flooding, and 17 demonstrated dual tolerance capabilities, highlighting their adaptability to varying flood conditions. The genotypes identified have a broader genetic diversity and harbor 86 key QTLs and genes related to traits such as grain quality, grain yield, herbicide resistance, and various biotic and abiotic traits, highlighting the richness of the identified elite collection. Besides germplasm, we introduce an innovative breeding approach called ‘Transition from Trait to Environment’ (TTE). TTE leverages a parental pool of high-performing genotypes with complete submergence tolerance to drive population improvement and enable genomic selection in the flood breeding program. Our approach of TTE achieved a remarkable 65% increase in genetic gain for submergence tolerance, with the resulting fixed breeding genotypes demonstrating exceptional performance in flood-prone environments of India and Bangladesh. The elite genotypes identified herein represent invaluable genetic resources for the global rice research community. By adopting the TTE approach, which is trait agonistic, we establish a robust framework for developing more resilient genotypes using advanced breeding tools.

Plain Language Summary

To address climate challenges, an urgent focus is necessary to identify and develop flood-tolerant rice varieties, particularly for flood-prone ecosystems across Asia and Africa. We screened 6,274 elite genotypes from IRRI’s germplasm and identified 89 promising lines with improved tolerance to submergence and stagnant flooding. Among these, 37 demonstrated 40-50% greater submergence tolerance thanSUB1Aintrogression lines, 35 exhibited stagnant flooding tolerance, and 17 showed dual tolerance. These genotypes contain 86 key QTLs and genes associated with yield, grain quality, and biotic and abiotic tolerance traits. A new breeding strategy, the ‘Transition from Trait to Environment’ (TTE) approach, was developed. We achieved a genetic gain of 65% for submergence tolerance in rice using this method. The newly identified germplasm provides invaluable genetic resources for the global rice research community to develop flood-tolerant rice genotypes.

Core ideas

⍰ TheSUB1Agene, enabling rice to survive underwater for 14 days, marked a significant breakthrough.

⍰ We have identified elite genotypes with submergence tolerance significantly surpassing theSUB1Agene-mediated tolerance.

⍰ The diverse elite genotypes identified harbor 86 key genes and QTLs that affect various traits positively.

⍰ Developed a unique breeding strategy for implementing population improvement in challenging environments.

⍰ The new breeding strategy demonstrated a genetic gain of 65% for submergence tolerance.