This study investigates the role of alternative splicing in cold stress responses in rice. The researchers constructed a pan-transcriptome of 11 rice cultivars using Iso-Seq and RNA-Seq, analyzing their transcriptional regulatory landscape under cold stress. They found that alternative splicing plays a significant role in the cold stress response, with a large-scale AS response triggered by cold exposure. The study identified candidate genes, OsCATC and Os03g0701200, that could be targeted for genetic engineering to enhance cold tolerance. Additionally, the researchers identified two key serine-arginine-rich proteins, OsRS33 and OsRS2Z38, which are crucial for cold tolerance. The analysis of cold tolerance and resequencing data from 165 rice cultivars suggested that the splicing factor gene OsRS2Z38 may have been a key selection gene in the domestication of japonica rice for cold adaptation. The study provides a comprehensive understanding of the genetic basis of cold response mechanisms in plants and highlights the importance of alternative splicing in this process.This study investigates the role of alternative splicing in cold stress responses in rice. The researchers constructed a pan-transcriptome of 11 rice cultivars using Iso-Seq and RNA-Seq, analyzing their transcriptional regulatory landscape under cold stress. They found that alternative splicing plays a significant role in the cold stress response, with a large-scale AS response triggered by cold exposure. The study identified candidate genes, OsCATC and Os03g0701200, that could be targeted for genetic engineering to enhance cold tolerance. Additionally, the researchers identified two key serine-arginine-rich proteins, OsRS33 and OsRS2Z38, which are crucial for cold tolerance. The analysis of cold tolerance and resequencing data from 165 rice cultivars suggested that the splicing factor gene OsRS2Z38 may have been a key selection gene in the domestication of japonica rice for cold adaptation. The study provides a comprehensive understanding of the genetic basis of cold response mechanisms in plants and highlights the importance of alternative splicing in this process.