Transcriptome Analysis of Salt Stress Response of Wild Rice (Oryza sativa) Salt Tolerant Introgression Line IL363 at Seedling Stage
WANG Chun-Xue1,*, QIU Dong-Feng1,2,*, JIAO Ya-Ru1, WANG Ting-Bao1, HE Yong1, ZHANG Zai-Jun2, LIU Gang2,**, TIAN Zhi-Hong1,**
1 College of Life Science / Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education / Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Jingzhou 434025, China; 2 Institute of Food Crops / Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement / Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
Abstract：Exploring salt tolerant genes in rice (Oryza sativa), analyzing their molecular regulatory mechanisms, and breeding new salt tolerant rice varieties are one of the most economical and effective ways to cope with salt stress. This study used rice cultivar '9311' and the salt-tolerant introgression line IL363 of O. longistaminata, which was created with '9311' as there current parent, as materials. RNA-seq was used to perform whole genome transcriptome analysis on plants treated with salt stress (0.75% NaCl) for 3 and 5 d during the seedling stage. The results showed that, compared with untreated plants, 2 090 and 6 219 differentially expressed genes (DEGs) were identified in '9311' after 3 and 5 d of salt stress, and 169 and 2 535 genes were detected in IL363, respectively. This indicated that IL363 exhibited fewer DEGs during the early stage of salt stress. GO enrichment analysis revealed that the DEGs were primarily enriched in functional categories such as binding, catalytic activity, metabolic processes, and cellular processes. KEGG enrichment analysis showed that DEGs were mainly enriched in MAPK signaling and metabolic pathways, while DEGs in the treatment group were predominantly concentrated in pathways such as plant hormone signal transduction and the biosynthesis of secondary metabolites. Based on whole-genome chip detection results and functional annotations, 19 key candidate genes were selected for structural variation analysis from 53 screened genes potentially related to the differential salt tolerance between the 2 materials. Among these, 15 genes were located within the introgressed chromosomal segments, and 4 genes were important functional genes directly associated with salt stress. The structural variation analysis revealed that out of the 19 genes, 10 genes harbored variations in their exon regions, while 9 genes exhibited variations exclusively in non-coding regions. This study provides a theoretical basis for further unraveling the salt tolerance mechanisms of rice and supplies valuable candidate genes for salt-resistant rice breeding.
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