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

Rice cultivation in Bangladesh’s 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.