Future flooding tolerant rice germplasm: Resilience afforded beyond <i>Sub1A</i> gene

Developing high-yielding, flood-tolerant rice (Oryza sativa L.) varieties is essential for enhancing productivity and livelihoods in flood-prone ecologies. We explored genetic avenues beyond the well-known SUB1A gene to improve flood resilience in rice. We screened a collection of 6274 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 37 exhibited high submergence tolerance, surpassing the survival rate of SUB1A introgression 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 quantitative trait loci (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.

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Publication Details

Journal
The Plant Genome
Published
2025-05-08
DOI
https://doi.org/10.1002/tpg2.70040
Citations
3
Primary Topic
Plant responses to water stress
Type
article
Field-Weighted Citation Impact
5.25

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article

Future flooding tolerant rice germplasm: Resilience afforded beyond Sub1A gene

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3 citations
The Plant Genome
Plant responses to water stress
5.25
article

Future flooding tolerant rice germplasm: Resilience afforded beyond Sub1A gene

Monoranjan Jana, Waseem Hussain, Vikas Kumar Singh, Farzana Islam Rume, Sharmistha Ghosal, Joie Ramos, P. Nath, Anisar Rahman, Sushanta Kumar Dash, Navin Pradhan, Apurva Khanna, Sharat Kumar Pradhan, Pallavi Sinha, Hans Bhardwaj, Challa Venkateshwarlu, Suman Debnath, Janardan Das, Girija Rani Merugumala, Sanjay Kumar Chetia, Yater Das, I Made Dana, Dhiren Chowdhury, Sankalp Bhosale, Mir Mohammad Ali, Jauhar Ali, Anumalla Mahender, Margaret Catolos, Ajay Kohli, Md. Nurul Islam, Muhammad Rakib Hasan, S. P. Singh, Bidhan Roy, Alok Nath, Muhiuddin Faruquee, Sakina Khanam, K. M. Iftekharuddaula, Ma Teresa Sta. Cruz, Hosna Jannat Tonny, Jaswanth Konijerla
article en
3 citations

Abstract

Developing high-yielding, flood-tolerant rice (Oryza sativa L.) varieties is essential for enhancing productivity and livelihoods in flood-prone ecologies. We explored genetic avenues beyond the well-known SUB1A gene to improve flood resilience in rice. We screened a collection of 6274 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 37 exhibited high submergence tolerance, surpassing the survival rate of SUB1A introgression 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 quantitative trait loci (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.

The Plant GenomeVol. 18(2)
Acharya N. G. Ranga Agricultural University (IN), Indian Institute of Rice Research (IN), International Rice Research Institute (PH), Bangladesh Agricultural University (BD), Bihar Agricultural University (IN), Government of West Bengal (IN), Assam Agricultural University (IN), North Bengal Agricultural University (IN), International Crops Research Institute for the Semi-Arid Tropics (IN), Bangladesh Rice Research Institute (BD), Central Rice Research Institute (IN)
Bill and Melinda Gates Foundation
Openalex Percentile: Top 6%
Plant responses to water stress
5.25
DOIOpen Access PDFOpenAlex
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