Transcriptome sequencing of 36 rice samples was used to identify the cold tolerance mechanism of rice

Purpose: In this study, RNA-seq was used to analyzed the molecular mechanism of cold tolerance in rice Methods: Rice 9311 (cold intolerant) and DC907 (cold tolerant) were used as experimental materials for transcriptome sequencing on Illumina HIseq platform. Fastq is used to evaluate the quality of the original data, and NGS QC Toolkit is used to filter the original data to obtain clean reads. Clean reads were compared to the rice 9311 reference genome using HISAT2 software. Put the genome mapping results of all sequenced reads data together, assemble them with cufflinks, and then compare them with known gene models with cuffcompare. The gene expression level of each sample was analyzed by HTSeq software. All treatments were analyzed for differential expression using DEseq. Results: A total of 36 samples were used for RNA sequencing analysis, with three biological replicates per treatment. Each sample generates at least 2G data. The genes regulated by cold stress treatment (1,3 days) and recovery treatment (1,3 days) were determined by comparative analysis. There were 12 treatments, 3 biological replicates per treatment, a total of 36 samples. Near-isogenic lines DC907 and 931 were used as test materials.