Rice最新文献

Rice serves as a fundamental staple crop, supporting the dietary needs of nearly one-third of the global population. This critical role necessitates immediate and strategic efforts to develop multi-attribute genotypes to ensure sustainable food and nutritional security for the burgeoning population. The augmentation of rice production is not only vital for addressing immediate food demands but also crucial for fostering long-term sustainability, thereby supporting livelihoods and driving economic development. Achieving this transformation necessitates a holistic and systems-level understanding of the molecular and regulatory networks that govern phenotypic plasticity and agronomic performance. While coding regions are pivotal for expression, non-coding elements play an even more prominent role in regulating transcriptional activity and orchestrating essential biological processes. Natural allelic variation within these non-coding elements serves as an evolutionary substrate for regulatory rewiring, contributing to adaptive plasticity, domestication traits, and intraspecific diversification. Therefore, the precise modulation of desirable agronomic traits could be facilitated by targeted engineering of such elements, which often allows for the fine-tuning of allelic effects in terms of the attenuation and partial restoration of alleles to impact desirable traits over coding components, which often results in complete exclusion or lethality. Therefore, we attempted to provide a comprehensive synthesis of functionally characterized non-coding elements exclusively for rice, highlight their functional roles, and emphasize how natural variation within these elements is critical for selecting traits associated with domestication and the breeding of elite genotypes. Notably, the potential of engineered non-coding RNA elements for the enhancement of agronomically advantageous traits is critically discussed. The future roadmap of non-coding element editing in rice is expected to be significantly shaped by continuous technological innovations in the editing toolbox, coupled with breakthrough discoveries for non-coding elements influencing agronomical traits. These advances have the potential to revolutionize the development of superior rice genotypes, ultimately contributing to the global effort to ensure food and nutritional security.

The intersubspecific rice hybrid Xieyou9308 exhibits striking hybrid vigor and serves as a valuable resource for dissecting the genetic basis of yield heterosis in indica-japonica crosses. However, the molecular mechanisms underlying this hybrid vigor remain poorly understood. Leveraging a set of recombinant inbred lines (RILs) and an immortalized F2 (IMF₂) population derived from Xieyou9308, 1,300,425 genomic variants were identified, which were consolidated into 3818 BIN markers. Genomic regions inherited from Zhonghui9308 were positively associated with traits including plant height, heading date, panicle length, and grain number per panicle. In contrast, regions derived from XieqingzaoB, particularly those located on chromosome 3, positively associated with grain length and 1000-grain weight. In the RIL population, 43 additive QTLs and 3 pairs of epistatic QTLs were identified for 10 agronomic traits, with the majority mapped to chromosomes 3 and 10, which harbor candidate genes including Ehd1, GS3, and OsTB1. In the IMF₂ population, 118 significant QTLs exhibiting partial dominance and 11 epistatic interactions were identified, underscoring the contributions of both partial dominance and epistasis to trait expression. Transcriptomic analysis further corroborated these findings, showing that alleles predominantly from Zhonghui9308 contributed to a prolonged growth duration, while those from XieqingzaoB shortened the growth duration. Collectively, these findings indicate that the hybrid vigor exhibited in Xieyou9308 is attributable to the synergistic effects of superior parental alleles and their epistatic interactions. These insights offer a valuable foundation for molecular breeding strategies aimed at improving yield in indica-japonica hybrid rice.

Soil salinization seriously impacts the growth and development, yield, and grain quality of crops. Elucidating the molecular underlying of salt tolerance is crucial for advancing stress-resistant molecular breeding research in crops. Here, we identified a salt stress-responsive gene, SQUAMOSA-promoter binding protein like 10 (OsSPL10), and characterized its molecular function in conferring salt tolerance to rice. Firstly, we generated and characterized three distinct types of spl10 mutants using CRISPR/Cas9 mutagenesis. In spl10 mutant, the leaf withered rate was lower than that in wild type (WT), the plant height and fresh weight per plant of spl10 were higher than WT under salt stress, indicating that spl10 exhibits tolerance to salt stress. Based on biochemical and physiological assays, the OsSPL10/14 complex was identified as a key regulator of salt stress response in rice by modulating the homeostasis of reactive oxygen species (ROS). Besides, the RNA-Seq assay confirmed that OsSPL10 may be involved in plant hormone signal transduction and phenylpropanoid biosynthesis pathways under salt stress, providing valuable insights for exploring the downstream target genes of OsSPL10. These findings offer novel insights into the molecular mechanisms underlying salt tolerance mediated by the SPL transcription factor in plants.

Soil salinization is becoming a huge threat to reducing productivity of rice (Oryza sativa L.) around the world. Previous studies have found that some Domain of unknown function (DUF) proteins play an essential role in the growth and development of plants. The DUF936 family is reported to respond to abiotic stresses, but the specific molecular mechanisms of its members remain elusive. In this study, OsSSID6 (Salt-Stress Induced DUF936 protein) is found at the cell membrane and the protein's expression could be affected by several abiotic stresses. The CRISPR/Cas9 knockout lines increased salt tolerance in rice, whereas the overexpression lines showed more sensitivity. And meanwhile the similar changes of ROS-scavenging capacity were observed both in knockout and overexpression lines. Transcriptome analysis identified that the expression of genes linked to multiple metabolic pathways, including phenylpropanoid and flavonoid biosynthesis, and stress response, was significantly up-regulated in KO lines. Our findings reveal that OsSSID6 gene modulates rice salt stress tolerance by orchestrating a network of metabolic pathways, including those involved in the reactive oxygen species (ROS) scavenging system, phenylpropanoid and flavonoid biosynthesis and stress response-related mechanism. sThese results provide important information for engineering salt-tolerant crops.

Studying the salt tolerance mechanisms of rice under a single substrate has certain limitations. The salt tolerance strategies of rice may differ under different substrate conditions. This study established three substrate types by adjusting the proportions of laterite, peat moss, and river sand: S1 (high sand; low nutrient), S2 (medium sand; medium nutrient), and S3 (low sand; high nutrient). Compared with the respective fresh water control, the magnitude of dry weight reduction in each substrate gradually decreased (S1-S3), indicating that the salt stress was effectively alleviated. KEGG enrichment analysis of differentially expressed genes (DEGs) showed that Xiangliangyou900 may be more dependent on the remodeling of carbon metabolism pathway (compared to nitrogen metabolism) in S1, but the nitrogen metabolism pathway were more significant in S3. In S3, differential metabolites were significantly enriched in carbon and nitrogen metabolism pathways, but no such enrichment was found in S1, indicating that the S3 substrate, with its high nutrient and low river sand content, is more likely to trigger carbon and nitrogen metabolism remodeling. Under salt stress, the methylation level of C bases in the CHH type increased in S1 and decreased in S3. The methylation level of CHH-type C bases in the whole genome was more strongly correlated with the physicochemical parameters of the substrate (compared to CG and CHG types).This study speculated that rice may optimize its ability to adapt to salt stress by specifically regulating the methylation of CHH-type C bases to mediate gene expression. The results of this study help enrich the theoretical system of the rice salt stress response mechanism.