A pan-transcriptomic analysis reveals that alternative splicing regulates cold tolerance in rice. Researchers analyzed 11 rice cultivars under cold stress using Iso-Seq and RNA-Seq to identify genes and splicing factors involved in cold tolerance. They found that alternative splicing plays a significant role in the cold stress response, with two key splicing factors, OsRS33 and OsRS2Z38, playing central roles in cold tolerance. OsRS2Z38 was identified as a key gene in the domestication of japonica rice for cold adaptation. The study also identified candidate genes, such as CATALASE C (OsCATC) and Os03g0701200, for enhancing cold tolerance through genetic engineering. The analysis of 165 rice cultivars suggested that OsRS2Z38 may have been selected during japonica domestication for cold adaptation. The study provides a comprehensive resource for understanding the genetic basis of cold response mechanisms in plants. The findings highlight the importance of alternative splicing in regulating cold stress responses and suggest that splicing factors like OsRS33 and OsRS2Z38 are critical for cold tolerance in rice. The study also shows that cold stress induces significant changes in alternative splicing events, increasing transcript diversity and enabling the regulation of gene expression in response to cold stress. The results suggest that OsRS2Z38 is a key splicing factor that contributes to cold tolerance in rice, with different haplotypes of OsRS2Z38 associated with varying levels of cold tolerance in indica and japonica rice. The study provides insights into the genetic mechanisms underlying cold tolerance in rice and highlights the importance of alternative splicing in plant responses to abiotic stress.A pan-transcriptomic analysis reveals that alternative splicing regulates cold tolerance in rice. Researchers analyzed 11 rice cultivars under cold stress using Iso-Seq and RNA-Seq to identify genes and splicing factors involved in cold tolerance. They found that alternative splicing plays a significant role in the cold stress response, with two key splicing factors, OsRS33 and OsRS2Z38, playing central roles in cold tolerance. OsRS2Z38 was identified as a key gene in the domestication of japonica rice for cold adaptation. The study also identified candidate genes, such as CATALASE C (OsCATC) and Os03g0701200, for enhancing cold tolerance through genetic engineering. The analysis of 165 rice cultivars suggested that OsRS2Z38 may have been selected during japonica domestication for cold adaptation. The study provides a comprehensive resource for understanding the genetic basis of cold response mechanisms in plants. The findings highlight the importance of alternative splicing in regulating cold stress responses and suggest that splicing factors like OsRS33 and OsRS2Z38 are critical for cold tolerance in rice. The study also shows that cold stress induces significant changes in alternative splicing events, increasing transcript diversity and enabling the regulation of gene expression in response to cold stress. The results suggest that OsRS2Z38 is a key splicing factor that contributes to cold tolerance in rice, with different haplotypes of OsRS2Z38 associated with varying levels of cold tolerance in indica and japonica rice. The study provides insights into the genetic mechanisms underlying cold tolerance in rice and highlights the importance of alternative splicing in plant responses to abiotic stress.