Comparative transcriptome analysis of the mechanism difference in heat stress response between indica rice cultivar "IR64" and japonica cultivar "Koshihikari" at the seedling stage

Yingfeng Wang; Yubo Wang; Wenjuan Chen; Yating Dong; Guilian Zhang; Huabing Deng; Xiong Liu; Xuedan Lu; Feng Wang; Guihua Chen; Yunhua Xiao; Wenbang Tang

doi:10.3389/fgene.2023.1135577

Comparative transcriptome analysis of the mechanism difference in heat stress response between indica rice cultivar "IR64" and japonica cultivar "Koshihikari" at the seedling stage

Front Genet. 2023 Apr 21:14:1135577. doi: 10.3389/fgene.2023.1135577. eCollection 2023.

Authors

Yingfeng Wang¹, Yubo Wang¹, Wenjuan Chen¹, Yating Dong¹, Guilian Zhang¹, Huabing Deng¹, Xiong Liu¹, Xuedan Lu¹, Feng Wang¹, Guihua Chen¹, Yunhua Xiao¹, Wenbang Tang^{1

2}

Affiliations

¹ Hunan Provincial Key Laboratory of Rice and Rapeseed Breeding for Disease Resistance, College of Agronomy, Hunan Agricultural University, Changsha, China.
² State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China.

Abstract

Heat stress (HS) has become a major abiotic stress in rice, considering the frequency and intensity of extreme hot weather. There is an urgent need to explore the differences in molecular mechanisms of HS tolerance in different cultivars, especially in indica and japonica. In this study, we investigated the transcriptome information of IR64 (indica, IR) and Koshihikari (japonica, Kos) in response to HS at the seedling stage. From the differentially expressed genes (DEGs) consistently expressed at six time points, 599 DEGs were identified that were co-expressed in both cultivars, as well as 945 and 1,180 DEGs that were specifically expressed in IR and Kos, respectively. The results of GO and KEGG analysis showed two different HS response pathways for IR and Kos. IR specifically expressed DEGs were mainly enriched in chloroplast-related pathways, whereas Kos specifically expressed DEGs were mainly enriched in endoplasmic reticulum and mitochondria-related pathways. Meanwhile, we highlighted the importance of NO biosynthesis genes, especially nitrate reductase genes, in the HS response of IR based on protein-protein interaction networks. In addition, we found that heat shock proteins and heat shock factors play very important roles in both cultivars. This study not only provides new insights into the differences in HS responses between different subspecies of rice, but also lays the foundation for future research on molecular mechanisms and breeding of heat-tolerant cultivars.

Keywords: DEGs; RNA-seq; heat stress; indica; japonica; rice (Oryza sativa L.).

Grants and funding

This research was funded by the National Natural Science Foundation of China (No. 31901528, 31871599, and 32172078), the Major Project of Agricultural Biological Breeding (2022ZD0400402), and the Science and Technology Innovation Program of Hunan Province (No. 2022RC1147, 2021NK1001, 2022JJ30285, and 2021JC0007).