Deep RNAseq indicates protective mechanisms of cold-tolerant indica rice plants during early vegetative stage

Low temperature exposure during early vegetative stages limits rice plant's growth and development. Most genes previously related to cold tolerance in rice are from the japonica subspecies. To help clarify the mechanisms that regulate cold tolerance in young indica rice plants, comparative transcriptome analysis of 6 h cold-treated leaves from two genotypes, cold-tolerant and cold-sensitive, was performed. The cold-tolerant and cold-sensitive genotypes were previously characterized, and are sister lines (derived from the same crossing). Overall design: To identify and characterize novel genes and metabolic pathways involved in rice cold tolerance, we used two indica rice genotypes (previously identified as cold-tolerant and cold-sensitive by Adamski et al. 2016) in parallel transcriptomic analyses under cold treatment (10 °C for 6 h). Plants were in the three-leaf stage when cold treatment was applyed. RNA was extracted from leaves.