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.

Cold stress (CS) significantly impacts rice (Oryza sativa L.) growth during seedling and heading stages. Based on two-year field observations, this study identified two rice lines, L9 (cold stress-sensitive) and LD18 (cold stress-tolerant), showing contrasting CS responses. L9 exhibited a 38% reduction in photosynthetic efficiency, whereas LD18 remained unchanged, correlating with seed rates. Transcriptome analysis identified differentially expressed genes (DEGs) with LD18 showing enriched pathways (carbon fixation, starch/sucrose metabolism, and glutathione metabolism). LD18 displayed dramatically enhanced expression of MAPK-related genes (LOC4342017, LOC9267741, and LOC4342267) and increased ABA signaling genes (LOC4333690, LOC4345611, and LOC4335640) compared with L9 exposed to CS. Results from qPCR confirmed the enhanced expression of the three MAPK-related genes in LD18 with a dramatic reduction in L9 under CS relative to that under CK. We also observed up to 66% reduction in expression levels of the three genes related to the ABA signaling pathway in L9 relative to LD18 under CS. Consistent with the results of photosynthetic efficiency, metabolic analysis suggests pyruvate metabolism, TCA cycle, and carbon metabolism enrichment in LD18 under CS. The study reveals reprogramming of the carbon assimilation metabolic pathways, emphasizing the critical roles of the key DEGs involved in ABA and MAPK signaling pathways in positive regulation of LD18 response to CS, offering the foundation toward cold tolerance breeding through targeted gene editing.

Background/Objectives: Low-temperature stress during the grain-filling stage negatively affects rice grain quality and yield. Understanding the physiological and molecular mechanisms underlying cold tolerance is critical for breeding rice varieties with improved resilience. Methods: In this study, eight rice varieties with differential cold tolerance—LD1603, 13108, LD18, and 4-1021 (cold-tolerant) and LD3, LD4, LD121, and LD1604 (cold-sensitive)—were subjected to 17.5 °C low-temperature stress during grain filling in a naturally illuminated phytotron. Amylose and protein content, as well as taste quality, were analyzed. RNA sequencing was performed to identify differentially expressed genes and transcription factors associated with cold response. Results: Under low-temperature stress, amylose and protein content significantly increased in all eight varieties. The taste quality of cold-sensitive varieties declined markedly, whereas cold-tolerant varieties maintained higher and more stable taste quality values. Transcriptomic analysis revealed that key enzyme genes (INV, SUS, HXK, FRK, amyA, and TPP) in the starch and sucrose metabolism pathway were significantly upregulated in cold-tolerant varieties (LD18 and 4-1021), but suppressed in cold-sensitive varieties. Several cold-responsive transcription factors from the NAC, WRKY, AP2/ERF, MYB, and bZIP families were also identified. Weighted gene co-expression network analysis (WGCNA) further revealed hub TFs (OsWRKY1, OsWRKY24, OsWRKY53, and OsMYB4) and structural genes (OsPAL04 and OsCDPK7) potentially involved in cold tolerance during grain filling. Conclusions: This study enhanced our understanding of the molecular response to low temperature during rice grain filling and provided candidate genes for developing cold-tolerant rice varieties through molecular breeding.

The purpose of this research is to clarify the genetic groups associated with high-quality germplasms with different genotypes and investigate the responses of their yield and quality traits to varied fertilization regimes, thereby providing references for premium breeding and cultivation practices. A total of 29 samples, including 15 newly developed lines and 14 elite cultivars, were analyzed as to their genetic structure. A split-plot field experiment was conducted to evaluate the responses of yield, quality, and agronomic traits to different fertilization treatments. The 29 samples were classified into three genetic groups. Line 1, developed by our team, formed a unique group, while Lines 3 and 8 constituted another distinct group. In the 2022 trial, the protein content ranged from 6.8% to 9.0%, amylose content from 17.9% to 20.1%, and taste value from 73.8 to 85.7. The top five samples in yield were Line 4, Line 2, Line 5, Line 6, and Line 1, with significant differences among them (p < 0.05) and markedly higher yields compared to other samples. For taste value, Longdao 17029, Line 2, Line 4, Line 5, and Line 6 ranked highest, with Longdao 17029 exhibiting significantly superior taste scores (p < 0.05). Fertilizer treatments ranked by yield were as follows: Treatment 1 (N₁₂₀P₁₀₀K₁₀₀) > Treatment 4 (Longfutianxia slow-release fertilizer) > Treatment 2 (N₉₆P₁₀₀K₁₀₀ + bio-organic fertilizer) > Treatment 3 (N₀P₀K₀), with significant differences (p < 0.05). Treatment 2 achieved a significantly higher taste value than the others (p < 0.05). In the 2023 trial, Longdao 17029 demonstrated higher leaf color index and net photosynthetic rate during the grain-filling stage, compared to Longdao 18 and Longdao 21. Lines 1, 3, and 8 are valuable for broadening the genetic diversity of rice in cold regions. Line 4 and Longdao 17029 show potential as novel germplasms for improving yield and taste quality. Moderate nitrogen reduction, combined with bio-organic fertilizer application, enhances rice taste value.

Grain protein content (GPC) is an important determinant of rice nutritional and eating quality. In this study, 624 cold-region japonica rice accessions were evaluated for GPC and taste value at Harbin Minzhu, Ulanhot, and a saline–alkali site in the Songnen Plain, and 495 accessions with complete phenotypic and genotypic data were used for genome-wide association analysis. GPC showed significant positive correlations across sites and an entry-mean broad-sense heritability of 0.663. Using 1,527,603 high-quality SNPs, GLM-Q identified 56 significant GPC-associated SNPs, mainly on chromosomes 11 and 7, with site-specific patterns. Annotation of GLM-Q significant SNPs yielded 28 non-redundant positional candidate genes. In GEMMA, chromosome 11 signals did not remain genome-wide significant, whereas chromosome 7 associations remained significant. Haplotypes of Os11g0239500, Os11g0239900, Os07g0264100, and Os03g0244200 differed in GPC and taste value. Joint haplotype analysis of Os11g0239500 and Os07g0264100 classified 319 accessions into four types. Type IV had the lowest mean GPC (7.84%) and the highest mean taste value (81.14), whereas Type I had a mean GPC of 8.78% and a mean taste value of 77.45. The identified candidate genes and haplotypes may be useful for screening cold-region japonica rice with low GPC and high eating quality.

Salinity–alkalinity stress is one of the major abiotic stresses that limit rice production in the world. The salinity–alkalinity tolerance of rice at the germination stage has a direct effect on the survival and final yield of seedlings in direct sowing. However, there are few reports of quantitative trait locus (QTL) mapping and mapping-based cloning of alkaline tolerance at the bud burst stage. Here, new alkaline tolerance loci were constructed for F_2:3 and BC₃F₄ by using IR36 and Long-Dao124 (LD124) rice varieties with significant differences in alkaline tolerance. Through linkage analysis and a fine-mapping strategy, qAT3 was identified as the major QTL for alkaline tolerance at the bud burst stage, which could explain 14.79% of the phenotypic variation on average. Then the interval was fine-mapped to 110.265 kb, and the candidate gene LOC_Os03g03150 was predicted by quantitative real-time polymerase chain reaction (qRT-PCR) analysis and sequencing analysis. This provides a key theory for the molecular breeding of alkali-tolerant genes and the study of the molecular mechanism of alkali tolerance in LD124.