Abstract
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.
Highlights
Low temperature is a natural disaster that is often encountered in the entire process of rice growth and development, which is one of the main environmental factors limiting its growth and development, geographical distribution, yield, and quality formation [1,2]
EVM0001397 (SNAC2) and EVM0031981 (OsSPX1) were in MCqtl1-4 and MCqtl6-3, respectively. This result indicated that differentially expressed genes (DEGs) analysis combined with Meta-QTLs mapping can effectively reduce the number of candidate genes and accurately locate the key genes of cold stress
The obtained DEGs were systematically classified by various enrichment methods such as Gene Ontology (GO), COG, KEGG, and Mapman, which can fully analyze the cold stress regulation mechanism in rice roots
Summary
Low temperature is a natural disaster that is often encountered in the entire process of rice growth and development, which is one of the main environmental factors limiting its growth and development, geographical distribution, yield, and quality formation [1,2]. Comparative transcriptome analysis of rice LTH (cold tolerant) and IR29 (cold sensitive) identified many stress-inducible genes and emphasized that CBF and MYBS3 regulons are involved in cold tolerance in rice [23]. Many rice varieties have been transcriptome analyzed and identified many DEGs. As established, different varieties/genotypes of the same species can exhibit a high degree of genetic variability in cold tolerance [23,27,28]. The roots of a cold-tolerant rice genotype (RPY geng) seedlings were selected for RNA-seq to analyze the cold stress mechanism. The study of gene expression profiles in response to cold stress will inspire the regulation network of cold tolerance and provide many candidate genes for agronomic plant manipulation
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
