Transcriptomic profiling of the cold stress and recovery responsiveness of two contrasting Guizhou HE rice genotypes

At the seed germination stage, rice is sensitive to cold stress, which adversely affects its growth and development. Guizhou HE rice comprises several different landraces, most of which are cold tolerant.

To identify differentially expressed genes and molecular mechanism underlying the cold tolerance of Guizhou HE.

Two Guizhou HE genotypes, AC44 (cold-sensitive) and AC96 (cold-tolerant), which exhibit opposite phenotypes in response to cold treatment at the seed germination stage were used. Comprehensive gene expressions of AC44 and AC96 under 4 °C cold treatment and subsequent recovery conditions were comparatively analyzed by RNA sequencing.

Overall, 11,082 and 7749 differentially expressed genes were detected in AC44 and AC96, respectively. Comparative transcriptome analysis demonstrated that, compared with AC44, AC96 presented fewer upregulated and downregulated genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses demonstrated that AC96 presented more upregulated GO terms, especially terms associated with biological processes. However, AC44 presented more terms related to cellular components, mainly chloroplasts. Moreover, DEGs related to the auxin signaling pathway (including ARF and IAA family members) and transcription factors (including members of the F-box, bZIP, basic helix-loop-helix [bHLH], and MYB-like transcription factor families) were found to be expressed specifically in AC96; thus, these DEGs may be responsible for the cold tolerance of AC96.

These findings present information about the cold tolerance mechanism of Guizhou HE rice at the germination stage, providing valuable resources and candidate genes for breeding cold-tolerant rice genotypes.