Integrated RNA-seq Analysis and Meta-QTLs Mapping Provide Insights into Cold Stress Response in Rice Seedling Roots

Abstract

<jats:p>Rice (Oryza sativa L.) is a widely cultivated food crop around the world, especially in Asia. However, rice seedlings often suffer from cold stress, which affects their growth and yield. Here, RNA-seq analysis and Meta-QTLs mapping were performed to understand the molecular mechanisms underlying cold tolerance in the roots of 14-day-old seedlings of rice (RPY geng, cold-tolerant genotype). A total of 4779 of the differentially expressed genes (DEGs) were identified, including 2457 up-regulated and 2322 down-regulated DEGs. The GO, COG, KEEG, and Mapman enrichment results of DEGs revealed that DEGs are mainly involved in carbohydrate transport and metabolism, signal transduction mechanisms (plant hormone signal transduction), biosynthesis, transport and catabolism of secondary metabolites (phenylpropanoid biosynthesis), defense mechanisms, and large enzyme families mechanisms. Notably, the AP2/ERF-ERF, NAC, WRKY, MYB, C2H2, and bHLH transcription factors participated in rice’s cold–stress response and tolerance. On the other hand, we mapped the identified DEGs to 44 published cold–stress-related genes and 41 cold-tolerant Meta-QTLs regions. Of them, 12 DEGs were the published cold–stress-related genes and 418 DEGs fell into the cold-tolerant Meta-QTLs regions. In this study, the identified DEGs and the putative molecular regulatory network can provide insights for understanding the mechanism of cold stress tolerance in rice. In addition, DEGs in KEGG term-enriched terms or cold-tolerant Meta-QTLs will help to secure key candidate genes for further functional studies on the molecular mechanism of cold stress response in rice.</jats:p>

Comparative Transcriptome Analysis Reveals the Mechanisms Underlying Differences in Salt Tolerance Between indica and japonica Rice at Seedling Stage

“…Rice seedlings were grown in 96-well PCR plates with Yoshida solution (Coolaber, Beijing, China) replaced every 2 days, 26 • C, and a 16/8 h light/dark photoperiod, 60% relative humidity in plant growth incubators (ZSX1500GS, Jingshen Instrument, Shanghai, China) for 14 days (Kong et al, 2020). Fourteen-day-old seedlings of RPY geng and Chao 2R were changed into 100 mM NaCl Yoshida solution for salt stress treatment (Supplementary Figure 1).…”

“…Candidate genes in most QTLs reported so far are unknown due to the too large mapping interval. Meta-QTLs analysis can effectively narrow the mapping interval of QTLs to achieve reliable prediction of candidate genes by integrating the QTLs results from a large number of studies (Kong et al, 2020). 11 salt stress-related Meta-QTLs were reported via integrating QTL information from 12 studies (Islam et al, 2019).…”

Full-length Transcriptome Reconstruction Reveals Genetic Differences in Hybrids of Oryza Sativa and Oryza Punctata With Different Ploidy and Genome Compositions

“…Therefore, the mechanisms underlying the polyploid characteristics are being revealed gradually [41]. Previous studies have focused mainly on the response of rice to the environment through up-or down-regulation of the transcriptome [42][43][44]. For example, Chen et al showed that environmental tolerance could be enhanced in rice by promoting energy consumption and the biosynthesis of sugar and amino acids using transcriptomics [45].…”

CRISPR/Cas9-Mediated Knockout of HOS1 Reveals Its Role in the Regulation of Secondary Metabolism in Arabidopsis thaliana

“…When plants are exposed to low-temperature stress, CBF expression is rapidly induced, followed by subsequent upregulation of downstream genes responsible for cold adaptation [26]. Members of the MYC (basic helix-loop-helix, bHLH), WRKY, MYB and NAC transcription factor families are also known to be involved in cold stress response, emphasizing the importance of transcriptional control [23,27].…”