Comparative transcriptome profiling of chilling tolerant rice chromosome segment substitution line in response to early chilling stress

Rice (Oryza sativa L.) is thermophilic crop and all of its growth stages are affected by low temperature stress. However, some populations of common wild rice in Guangxi Province (China) (GXWR) can tolerate low temperature stress. To understand the molecular mechanisms underlying chilling tolerance in these wild rice resources, transcriptome sequencing was performed to study the differentially expressed genes (hereafter referred to as DEGs) between GXWR-derived chilling-tolerant chromosome segment substitution line (hereafter referred to as CSSL), DC90, and its chilling-sensitive recurrent parent 9311 under early chilling stress. Comparative transcriptomic analysis revealed 659 DEGs exclusively identified in DC90 in response to early chilling stress. Functional clustering by CARMO (comprehensive annotation platform for functional exploration of rice multi-omics data) showed that majority of the DEGs were enriched in chloroplasts, suggesting a connection between chilling stress tolerance and photosynthesis regulation exists in rice. KEGG analysis of these DEGs presented a complicated chilling responsive regulatory network, including 'phytohormone signaling', 'photosynthesis pathway', 'ribosome translation machinery', 'phenylpropanoid biosynthesis', which is coordinately involved in early chilling response. Here, the identified DEGs and unveiled molecular regulatory network sheds light on deep understanding the mechanisms underlying rice chilling stress tolerance. As well, KEGG term-enriched DEGs, chilling tolerant QTLs (quantitative trait loci), and co-localized DEGs in introgression interval, will be focused for further functional investigation of the molecular mechanisms of chilling stress response in rice.