Salinity stress is one of the major abiotic stresses affecting crop growth and production. Rice is an important food crop in the world, but also a salt-sensitive crop, and the rice seedling stage is the most sensitive to salt stress, which directly affects the final yield formation. In this study, two RIL populations derived from the crosses of CD (salt-sensitive)/WD (salt-tolerant) and KY131 (salt-sensitive)/XBJZ (salt-tolerant) were used as experimental materials, and the score of salinity toxicity (SST), the relative shoot length (RSL), the relative shoot fresh weight (RSFW), and the relative shoot dry weight (RSDW) were used for evaluating the degree of tolerance under salt stress in different lines. The genetic linkage map containing 978 and 527 bin markers were constructed in two RIL populations. A total of 14 QTLs were detected on chromosomes 1, 2, 3, 4, 7, 9, 10, 11, and 12. Among them, qSST12-1, qSST12-2, and qRSL12 were co-localized in a 140-kb overlap interval on chromosome 12, which containing 16 candidate genes. Furthermore, transcriptome sequencing and qRT-PCR were analyzed in CD and WD under normal and 120 mM NaCl stress. LOC_Os12g29330, LOC_Os12g29350, LOC_Os12g29390, and LOC_Os12g29400 were significantly induced by salt stress in both CD and WD. Sequence analysis showed that LOC_Os12g29400 in the salt-sensitive parents CD and KY131 was consistent with the reference sequence (Nipponbare), whereas the salt-tolerant parents WD and XBJZ differed significantly from the reference sequence both in the promoter and exon regions. The salt-tolerant phenotype was identified by using two T₃ homozygous mutant plants of LOC_Os12g29400; the results showed that the score of salinity toxicity (SST) of the mutant plants (CR-3 and CR-5) was significantly lower than that of the wild type, and the seedling survival rate (SSR) was significantly higher than that of the wild type, which indicated that LOC_Os12g29400 could negatively regulate the salinity tolerance of rice at the seedling stage. The results lay a foundation for the analysis of the molecular mechanism of rice salinity tolerance and the cultivation of new rice varieties.

Drought stress poses a significant threat to rice production, necessitating the identification of genes associated with drought tolerance. This study employed a combination of genome-wide association study (GWAS) and linkage mapping to pinpoint seedling drought tolerance genes in Japonica rice. Using the leaf rolling scale (LRS) as the phenotypic index, we assessed rice drought tolerance under polyethylene glycol-induced drought during the seedling stage. A lead SNP C8_28933410 by GWAS was identified, which was located within qLRS-8-1 identified by linkage mapping on chromosome 8. Combing the LD block analyses and QTL interval, a 138.6 kb overlap interval was considered as the candidate region. Haplotype analysis, qRT-PCR, sequence analysis, and mutant phenotype verification led to the speculation that LOC_Os08g05520 is a candidate gene associated with drought tolerance. Our findings provide a valuable reference for breeders aiming to enhance rice drought tolerance.

Background: As key members of the plant receptor-like kinase family, rice CrRLK1Ls play diverse roles in plant growth, development, and stress responses. Although rice CrRLK1Ls have been initially characterized, our understanding of their functions remains limited. Methods: We identified OsCrRLK1L genes via Hidden Markov Model (HMM) searches against the rice genome. Subsequent analyses encompassed their physicochemical properties, chromosomal distribution, gene structure, phylogenetic relationships, conserved domains, and cis-acting elements.Salt-responsive candidates were screened using a GEO dataset, and their expression profiles were validated under salt stress using quantitative real-time PCR. Result: A total of 36 OsCrRLK1L genes, all containing both Malectin and tyrosine kinase domains, were identified in the rice genome and showed an uneven chromosomal distribution. Phylogenetic analysis classified them into three subclades, with Group II and Group III being specific to rice and Arabidopsis thaliana, respectively. Promoter analysis revealed that the promoter regions of these genes contained an abundance of cis-acting elements related to hormone and stress responses. RNA-Seq and enrichment analysis indicated that OsCrRLK1L genes exhibit tissue specificity and participate in salt stress responses. Furthermore, CrRLK1L2 and CrRLK1L10 showed tissue-specific differential expression under salt stress. Conclusions: In summary, our study lays the groundwork for future research into the biological roles of OsCrRLK1L genes during salt stress.

Alkaline stress is one of the most critical limiting factors affecting high and stable rice yields. Therefore, analyzing the impact of alkaline stress on rice productivity and identifying salt- and alkali-tolerant genes are crucial for breeding rice varieties with strong stress resistance. In this study, the alkali-sensitive variety QJ74 and the alkali-tolerant variety QJ22 were used as parental lines. Under alkaline conditions (pH 9.0), 30 alkali-sensitive and 30 alkali-tolerant F₂ individuals from the segregating population were selected for BSA-Seq. Transcriptomic analysis was performed on the parental lines under the same alkaline treatment. The results showed that under alkali stress, QJ22 exhibited significantly greater plant height and chlorophyll content, but significantly lower relative electrical conductivity and malondialdehyde content than QJ74, indicating less severe cell membrane damage. Meanwhile, QJ22 showed significantly higher proline content and superoxide dismutase and peroxidase activities, together with significantly lower Na⁺ and higher K⁺ contents compared with QJ74. Overall, QJ22 outperformed QJ74 in cell membrane stability, photosynthetic pigment maintenance, antioxidant enzyme activity, and osmotic regulation, demonstrating strong alkali tolerance. Based on these findings, under alkali stress (pH 9.0), 30 alkali-sensitive and 30 alkali-tolerant F₂ individuals from the cross between the two parents were selected for BSA-Seq, and transcriptomic sequencing was performed on the parental lines under the same conditions. A combined BSA-Seq and RNA-Seq analysis identified five candidate genes (Os10g0376200, Os10g0389000, Os10g0389500, Os10g0390500 and Os10g0401000). Subsequent cis-acting element analysis, phylogenetic analysis, and qRT-PCR validation revealed that Os10g0389000 is a promising alkali stress-responsive candidate gene potentially contributing to the differential alkali tolerance between QJ74 and QJ22. This study integrated BSA-Seq and RNA-Seq to systematically identify candidate genes involved in the alkali stress response in rice, providing key genetic targets and a molecular basis for developing new alkali-tolerant varieties.

Background: Cold stress is a major abiotic factor limiting rice growth and yield. Elucidating the molecular mechanisms underlying cold tolerance is therefore of great significance for variety improvement. This study focused on the cold-tolerant variety QJ10 and the cold-sensitive variety DHX2, systematically comparing their physiological and transcriptomic differences under cold stress and identifying genes and modules associated with the cold stress response. Methods: After 0, 3, 5, and 7 days of treatment at 4 °C, we measured leaf MDA and Pro contents, as well as SOD and POD activities. We performed multi-time-point transcriptome sequencing using RNA-seq, and conducted data mining and validation through differential expression analysis, Mfuzz trend clustering, WGCNA co-expression network analysis, GENIE3 regulatory network prediction, and qRT-PCR. Results: Compared with DHX2, QJ10 exhibited lower MDA levels and higher levels of Pro, SOD, and POD under cold stress. Transcriptome analysis identified a total of 13,599 differentially expressed genes. Trend clustering revealed that QJ10 primarily maintained genes associated with growth, development, and basal metabolism, whereas DHX2 tended to activate defense responses. WGCNA identified the MEturquoise module, which showed significant positive correlations with both cold treatment duration and the activities of SOD and POD. Genes in this module were significantly enriched in pathways such as carbon metabolism, photosynthesis, and ion transport. Twelve key transcription factors were identified, nine of which were highly expressed at the late stage of cold stress in QJ10. GENIE3 further predicted seven key regulatory factors centered on OsNAC2, OsLBD, and OsARF19; the expression patterns of these factors were validated by qRT-PCR and were consistent with the transcriptomic results. Conclusions: This study revealed that the cold tolerance of QJ10 is associated with enhanced antioxidant capacity, upregulation of genes related to carbon metabolism, and the induced expression of specific transcription factors. The key transcription factors identified here provide candidate genes for studying the molecular mechanisms of cold tolerance in rice. However, their regulatory functions require further experimental validation.