Fig 1.
Phenotype of 33S and Nipponbare after exposed to cold treatment.
A. Seedling of 33S and Nipponbare. B. Shoot length of 33S and Nipponbare seedlings after cold treatment. C. Root length of 33S and Nipponbare seedlings after cold treatment. Different letters above the box indicate a significant difference at P < 0.05. Error bar was statistic by standard deviation.
Fig 2.
Number of DEGs after low temperature treatment in 33S and Nipponbare.
A. Significantly up- or down-regulated genes in 33S-Cold vs. 33S-CK. B. Significantly up- or down-regulated genes in N-Cold vs. N-CK. C. Venn diagram indicating the number of DEGs common to 33S and Nipponbare. N indicates the variety of Nipponbare, CK indicates the control seedling not treated by cold temperature. DEGs were screened using a threshold of P <0.05 and |log2FoldChange| > = 1.
Fig 3.
Functional analysis of cold responsive genes.
A. GO enrichment analysis of the DEGs in 33S rice seedlings after seven days of low-temperature treatment. B. GO enrichment analysis of the DEGs in Nipponbare rice seedlings after seven days of low-temperature treatment. The DEGs were classified into three main GO categories (biological processes, molecular functions and cellular components). C. KEGG pathway enrichment analysis of DEGs in 33S rice seedlings after seven days of low-temperature treatment. D. KEGG pathway enrichment analysis of DEGs in Nipponbare rice seedlings after seven days of low-temperature treatment. The P-value to determine the enrichment significance was calculated through hypergeometric distribution.
Fig 4.
RT-qPCR verification of expression profiles obtained through RNA-seq.
Data are mean ± SD of three biological replicates. Asterisks indicate significant difference compared to control samples (*P < 0.05; **P < 0.01). The actin 1 gene was used as an internal standard gene was used as an internal reference.
Table 1.
List of DEGs enriched in plant hormone signal transduction.
Table 2.
List of DEGs enriched in protein processing in endoplasmic reticulum pathway.
Table 3.
Transcription factors response to low temperature treatment in 33S and Nipponbare.
Fig 5.
Functional analysis and metabolism overview of specific DEGs in 33S in response to cold stress.
A. Overview of metbolism. B. Response activities.