The δ13C value is regarded as an important indicator for tolerance to drought stress (DS), which is a severe abiotic stress that influences rice productivity. However, exploration of drought-responsive genes (DRGs) related to δ13C regulation is less reported. In this study, we investigated the natural variation in δ13C values in 102 japonica rice accessions. Among them, two rice accessions with contrasting δ13C values, Longdao 10 (LD10, DS-tolerant) and Binxu (BX, DS-sensitive), were used for further analysis. LD10 possesses better drought resistance with 2% lower δ13C values, 35% lower stomatal length and density, 33% lower water loss, and 11% lower stomatal conductance in comparison to BX. Transcriptome analysis shows that there are 2325 and 1378 differentially expressed genes (DEGs) induced by DS in LD10 and BX at the tillering stage, respectively, while there are 1076 and 492 DEGs in LD10 and BX at the graining stage, respectively. In total, 21 overlapped DEGs (defined as DRGs) were identified due to DS effects across two rice accessions over two stages. Among them, the expression levels of six genes, including chloride transporter (CLT1) and photosystem II polypeptide (PSBP), were further tested using qRT-PCR. Furthermore, we found that four methyltransferase genes were upregulated in BX compared to LD10 under DS. Consistently, the methylation levels of CLT1 and PSBP were higher along both promoter and CDS regions for CG, CHG, and CHH types. This study highlights the importance of the expression of these DRGs in response to DS and provides deep insights into DNA methylation-driven gene expression conferring different drought responses in rice.
Rice has been reported to be highly sensitive to salt stress at the seedling stage. However, the lack of target genes that can be used for improving salt tolerance has resulted in several saline soils unsuitable for cultivation and planting. To characterize new salt-tolerant genes, we used 1,002 F2:3 populations derived from Teng-Xi144 and Long-Dao19 crosses as the phenotypic source to systematically characterize seedlings’ survival days and ion concentration under salt stress. Utilizing QTL-seq resequencing technology and a high-density linkage map based on 4,326 SNP markers, we identified qSTS4 as a major QTL influencing seedling salt tolerance, which accounted for 33.14% of the phenotypic variation. Through functional annotation, variation detection and qRT-PCR analysis of genes within 46.9 Kb of qSTS4, it was revealed that there was one SNP in the promoter region of OsBBX11, which resulted in a significant response difference between the two parents to salt stress. Transgenic plants using knockout-based technology and demonstrated that Na+ and K+ in the roots of the functional-loss-type OsBBX11 were translocated largely to the leaves under 120 mmol/L NaCl compared with the wild-type, causing osbbx11 leaves to die after 12 days of salt stress due to an imbalance in osmotic pressure. In conclusion, this study identified OsBBX11 as a salt-tolerance gene, and one SNPs in the OsBBX11 promoter region can be used to identify its interacting transcription factors. This provides a theoretical basis for finding the molecular mechanism of OsBBX11 upstream and downstream regulation of salt tolerance and molecular design breeding in the future.
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