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

ABSTRACT: Screening and breeding more salt-tolerant varieties is an effective way to deal with the global reduction in rice (Oryza sativa L.) yield caused by salt stress. However, the molecular mechanism underlying differences in salt tolerance between varieties, especially between the subspecies, is still unclear. We herein performed a comparative transcriptomic analysis under salt stress in contrasting two rice genotypes, namely RPY geng (japonica, tolerant variety) and Luohui 9 (named as Chao 2R in this study, indica, susceptible variety). 7208 and 3874 differentially expressed genes (DEGs) were identified under salt stress in Chao 2R and RPY geng, separately. Of them, 2714 DEGs were co-expressed in both genotypes, while 4494 and 1190 DEGs were specifically up/down-regulated in Chao 2R and RPY geng, respectively. Gene ontology (GO) analysis results provided a more reasonable explanation for the salt tolerance difference between the two genotypes. The expression of normal life process genes in Chao 2R were severely affected under salt stress, but RPY geng regulated the expression of multiple stress-related genes to adapt to the same intensity of salt stress, such as secondary metabolic process (GO:0019748), oxidation-reduction process (GO:0009067), etc. Furthermore, we highlighted important pathways and transcription factors (TFs) related to salt tolerance in RPY geng specific DEGs sets based on MapMan annotation and TF identification. Through Meta-QTLs mapping and homologous analysis, we screened out 18 salt stress-related candidate genes (RPY geng specific DEGs) in 15 Meta-QTLs. Our findings not only offer new insights into the difference in salt stress tolerance between the rice subspecies but also provide critical target genes to facilitate gene editing to enhance salt stress tolerance in rice.

SUBMITTER: Kong W

PROVIDER: S-EPMC8578091 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Rice in tropical and sub-tropical areas is often subjected to cold stress at the seedling stage, resulting in poor growth and yield loss. Although japonica rice is generally more cold tolerant (CT) than indica rice, there are several favorable alleles for CT exist in indica that can be used to enhance CT in rice with a japonica background. Genome-wide gene expression profiling is an efficient way to decipher the molecular genetic mechanisms of CT enhancement and to provide valuable information for CT improvement in rice molecular breeding. In this study, the transcriptome of the CT introgression line (IL) K354 and its recurrent parent C418 under cold stress were comparatively analyzed to explore the possible CT enhancement mechanisms of K354.A total of 3184 differentially expressed genes (DEGs), including 195 transcription factors, were identified in both lines under cold stress. About half of these DEGs were commonly regulated and involved in major cold responsive pathways associated with OsDREB1 and OsMyb4 regulons. K354-specific cold-induced genes were functionally related to stimulus response, cellular cell wall organization, and microtubule-based movement processes that may contribute to increase CT. A set of genes encoding membrane fluidity and defensive proteins were highly enriched only in K354, suggesting that they contribute to the inherent CT of K354. Candidate gene prediction based on introgressed regions in K354 revealed genotype-dependent CT enhancement mechanisms, associated with Sir2, OsFAD7, OsWAK112d, and programmed cell death (PCD) related genes, present in CT IL K354 but absent in its recurrent parent C418. In K354, a number of DEGs were co-localized onto introgressed segments associated with CT QTLs, providing a basis for gene cloning and elucidation of molecular mechanisms responsible for CT in rice.Genome-wide gene expression analysis revealed that genotype-specific cold induced genes and genes with higher basal expression in the CT genotype contribute jointly to CT improvement. The molecular genetic pathways of cold stress tolerance uncovered in this study, as well as the DEGs co-localized with CT-related QTLs, will serve as useful resources for further functional dissection of the molecular mechanisms of cold stress response in rice.

Project description:Excessive amounts of metal are toxic and severely affect plant growth and development. Understanding the genetic control of metal tolerance is crucial to improve rice resistance to Fe, Zn, and Al toxicity. The multi-parent advanced generation inter-cross (MAGIC) populations were genotyped using a 55 K rice SNP array and screened at the seedling stage for Fe, Zn, and Al toxicity using a hydroponics system. Association analysis was conducted by implementing a mixed linear model (MLM) for each of the five MAGIC populations double cross DC1 (founders were SAGC-08, HHZ5-SAL9-Y3-Y1, BP1976B-2-3-7-TB-1-1, PR33282-B-8-1-1-1-1-1), double cross DC2 (founders of double cross were FFZ1, CT 16658-5-2-2SR-2-3-6MP, IR 68, IR 02A127), eight parents population 8way (founders were SAGC-08, HHZ5-SAL9-Y3-Y1, BP1976B-2-3-7-TB-1-1, PR33282-B-8-1-1-1-1-1, FFZ1, CT 16658-5-2-2SR-2-3-6MP, IR 68, IR 02A127), DC12 (DC1+DC2) and rice multi-parent recombinant inbred line population RMPRIL (DC1+DC2+8way). A total of 21, 30, and 21 QTL were identified for Fe, Zn, and Al toxicity tolerance, respectively. For multi tolerance (MT) as Fe, Zn, and Al tolerance-related traits, three genomic regions, MT1.1 (chr.1: 35.4-36.3 Mb), MT1.2 (chr.1: 35.4-36.3 Mb), and MT3.2 (chr.3: 35.4-36.2 Mb) harbored QTL. The chromosomal regions MT2.1 (chr.2: 2.4-2.8 Mb), MT2.2 (chr.2: 24.5-25.8 Mb), MT4 (chr.4: 1.2 Mb Mb), MT8.1 (chr.8: 0.7-0.9 Mb), and MT8.2 (chr.8: 2.2-2.4 Mb) harbored QTL for Fe and Zn tolerance, while MT2.3 (chr.2: 30.5-31.6 Mb), MT3.1 (chr.3: 12.5-12.8 Mb), and MT6 (chr.6: 2.0-3.0 Mb) possessed QTL for Al and Zn tolerance. The chromosomal region MT9.1 (chr.9: 14.2-14.7 Mb) possessed QTL for Fe and Al tolerance. A total of 11 QTL were detected across different MAGIC populations and 12 clustered regions were detected under different metal conditions, suggesting that these genomic regions might constitute valuable regions for further marker-assisted selection (MAS) in breeding programs.

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

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