Iftekharuddaula, K. M. | Search bioRxiv

bioRxiv2025

Stage-specific screening reveals complex resilience pathways to cold stress in rice

Rice cultivation in Bangladeshs northern and northeastern regions face a critical challenge - cold stress during the seedling and reproductive stages, which can drastically reduce yield. As a precursor to generate improved elite lines, a diverse panel of rice germplasm was screened to identify genotypes with resilience to low temperature at both key developmental phases. Seedling-stage tolerance was assessed using an artificial cold-water tank, while reproductive-stage tolerance was evaluated under both natural field conditions and controlled cold screening facilities. Performance was measured through a combination of quantitative traits (plant height, days to heading, panicle length) and qualitative indicators (panicle degeneration, panicle exsertion, spikelet fertility). Two breeding lines - BR8907-B-1-2-CS1-4-CS2-P3-4 and BR8909-B-12-2-CS1-4-CS2-P2-3-2, demonstrated seedling-stage cold tolerance with minimum leaf discoloration and the highest survival rate across three experimental batches. Five genotypes (Bhutan, IR83222-F11-173, Rata Boro, BRRI dhan74, BR11712-4R-227) showed tolerance during the reproductive stage. Three lines (Bhutan, BR11712-4R-227, and BR12266-44-11-32-5-1-1-HR10-B) showed moderately tolerant to tolerant across both stages. Six genotypes, including BR10317-5R-25, IR18A1859, and BRRI dhan28 were consistently vulnerable to cold stress at both stages. Principal Component Analysis (PCA) revealed that under field conditions, both seedling and reproductive traits contributed to shared components - suggesting overlapping physiological mechanisms. However, under controlled environments, the traits separated distinctly, pointing to stage-specific genetic control. These results are consistent with reports of distinct QTLs contributing to cold tolerance at different stages, highlighting the complex nature of cold tolerance and informing breeding strategies for enhanced cold resilience in rice.

plant biology↗

bioRxiv2025

Future flooding tolerant rice germplasm: resilience afforded beyond Sub1A gene

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-known SUB1A gene to improve flood resilience in rice. We screened a collection of 6,274 elite genotypes from IRRIs 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 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 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 SummaryTo 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 IRRIs germplasm and identified 89 promising lines with improved tolerance to submergence and stagnant flooding. Among these, 37 demonstrated 40-50% greater submergence tolerance than SUB1A introgression 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 The SUB1A gene, enabling rice to survive underwater for 14 days, marked a significant breakthrough. We have identified elite genotypes with submergence tolerance significantly surpassing the SUB1A gene-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.

plant biology↗