Rice最新文献

Direct-seeded rice offers multiple advantages, including lower labour costs and a reduced CO₂ footprint. However, the risk of flooding during germination and at the early seedling and vegetative stages is high. Therefore, the capacity for anaerobic germination in waterlogged soils, as well as tolerance to partial and complete submergence, are both essential. It remains unclear whether anaerobic germination and flood tolerance are linked or if they act independently in the environment. Therefore, it is timely to investigate the relationship between these two traits in the context of progressing climate change. We investigated the submergence tolerance of 4-week-old plants of three African landraces, which had previously been shown to possess anaerobic germination capacity. Additionally, we included one submergence-sensitive check and two tolerant checks. These six genotypes were evaluated at three time points: initially (prior to submergence), after three days of submergence, and at the time of desubmergence following 29 days of submergence. We measured survival, key photosynthetic traits (leaf gas films, underwater net photosynthesis, chlorophyll concentration), and carbohydrate reserves. We found that the African landraces tolerant to anaerobic germination all outlived the submergence-sensitive check, 'IR42,' during 29 days of complete submergence. Moreover, all tested genotypes exhibited significant declines over the 29 days of submergence in gas film thickness, underwater net photosynthesis, leaf chlorophyll concentration, and leaf water-soluble carbohydrates and starch. However, no significant differences were observed among the genotypes. The underlying mechanisms of anaerobic germination tolerance in the three African landraces remain unknown, as they do not possess the gene Anaerobic Germination 1 (AG1). Furthermore, it is unclear whether the three genotypes contain the gene Submergence 1 (SUB1); however, SUB1 confers submergence tolerance only and does not provide tolerance to anaerobic germination. Based on the present study, we cannot rule out the possibility that the novel anaerobic germination tolerance observed in the three African landraces is somehow linked to submergence tolerance as well. A thorough bioinformatic analysis is therefore needed to further characterize these landraces.

Efficient callus induction is essential for the genetic transformation of rice (Oryza sativa), yet its regulatory mechanisms remain elusive. Previously, through a genome-wide association study (GWAS), we identified a significant associated locus on chromosome 8. In this study, we characterized this locus and demonstrated that OsSDG715, encoding a histone H3K9 methyltransferase, is the causal gene that positively regulates callus formation in rice. Results revealed that OsSDG715 is highly expressed during callus induction and exhibits natural variations associated with callus induction rate (CIR). Knockout of OsSDG715 via CRISPR/Cas9 led to a significant decrease in CIR and impaired callus morphology, indicating its positive regulation of callus formation. RNA-seq analyses revealed that 326 and 705 differentially expressed genes (DEGs) were upregulated and downregulated in sdg715 mutants, including auxin-responsive genes (OsIAA14, OsYUCCA6), cytokinin-related genes (OsCKX4, ARR10), and stress-responsive factors. Further analysis showed reduced endogenous indole-3-acetic acid (IAA) levels and increased zeatin levels in sdg715 mutants. These findings advance our understanding of the molecular mechanisms underlying rice callus formation, and offering valuable insights for optimizing tissue culture in molecular breeding.

Background: Hybrid sterility is a common phenomenon in hybrids between the Asian cultivated rice (Oryza sativa L.) and its relatives with AA genome, which limits the utilization of interspecific heterosis and favorable gene introgression. Numerous loci for hybrid sterility have been identified between O. sativa and its relatives. However, it remains elusive whether hybrid sterility between different species is controlled by a set of conserved loci, and whether there are variations in the genetic mode of these loci.

Results: In this study, six novel hybrid sterility loci for pollen sterility were identified from different cross combinations between O. sativa and its three wild relatives. S59 caused hybrid pollen sterility in hybrids between O. sativa and O. rufipogon. S60 and S61 controlled the hybrid pollen sterility between O. sativa and O. glumaepatula. S62, S63 and S64 governed the hybrid pollen sterility between O. sativa and O. barthii. Genetic and linkage analysis showed that S59, S60, and S62 were located in near the same region on the short arm of chromosome 5. S61 and S63 were mapped near RM27460 on the short arm of chromosome 12. S64 was restricted into the 60.27 kb region between RM4853 and RM3372 on the short arm of chromosome 3. The genetic behavior of six novel hybrid sterility loci follows one-locus allelic interaction model, the male gametes carrying the alleles of O. sativa in the heterozygotes were selectively aborted except for S62.

Conclusions: The findings from this research would provide a better understanding for the genetic nature of interspecific hybrid sterility in rice.

Grain chalkiness is an undesirable agronomic trait that negatively affects both the yield and quality of rice (Oryza sativa). The molecular mechanisms underlying chalky grain phenotype have remained largely unclear. In this study, we selected the rice variety HK300 with a high chalkiness, and ZR24D with a low chalkiness, as experimental materials and systematically characterized the reasons of grain chalkiness formation at molecular level by means of RNA-seq analysis. Analysis results revealed that the differentially expressed genes (DEGs) in these two rice varieties were significantly enriched in transcriptional regulation, sucrose and starch metabolism, and phytohormone signal transduction. Moreover, we found the expression of 13 genes related to trehalose pathway (4 out of 14 TPS genes and 9 out of 13 TPP genes in rice genome) were significantly different between the two varieties, indicating trehalose synthesis pathways may contribute to the increased chalkiness formation. Notably, the number of DEGs associated with the signal transduction pathway for indole-3-acetic acid (IAA), which has been rarely studied for its involvement in chalkiness formation, was the highest among those associated with plant hormone signal transduction. Among them, the expression of two IAA receptor genes, OsAFB3 and OsAFB5, were significantly lower in HK300 than that in ZR24D through RNA-seq and qRT-PCR. Furthermore, we newly validated the two genes negatively regulated the formation of chalkiness through gene knockout. Our findings provided the theoretical basis and novel gene resources for molecular breeding aimed at improving rice quality.

The perennial life cycle involves the reiterative development of sexual and asexual organs. Asexual structures such as rhizomes are found in various plant species, fostering extensive growth and competitive advantages. In the African wild rice Oryza longistaminata, we investigated the formation of rhizomes from axillary buds, which notably bend diagonally downward of the main stem, as the factors determining whether axillary buds become rhizomes or tillers are unclear. Our study revealed that rhizome buds initiate between the third and fifth nodes of seedlings beyond the 6-leaf stage, while the buds above the sixth node develop into tillers. We propose that precise regulation of gibberellin (GA) biosynthesis plays a pivotal role in optimal rhizome bud development, as demonstrated by a comparative transcriptome analysis between tiller buds and rhizome buds and quantification of phytohormones. Furthermore, GA₄ treatment upregulated the expression of genes associated with flowering repression and cell wall modification. These findings highlight the integration of GA biosynthesis and flowering repression genes as crucial in asexual organ development, shedding new light on the molecular mechanisms governing rhizome bud development in O. longistaminata and deepening our understanding of asexual reproduction regulation in perennial plants.

Improving grain quality is second only to enhancing grain yield in breeding hybrid rice. Yet, rice grain quality, especially milling and appearance quality, is facing increasing threats from global warming due to climate change, leading to a relatively slow progress in high-quality rice breeding. Identifying additional grain quality genes is an effective way to combat against the threats on rice grain quality. In the present study, we used the germplasm from 3,000 Rice Genomes Project for genome-wide association study, and identified GL7/GW7/SLG7 as a major QTL besides GS3 and GW5 for grain shape. Among nine haplotypes of GL7 (H1-9), H1-H4, which harbored an 11-bp deletion, were designated as the functional GL7 allele and were primarily present in Geng/Japonica (GJ) rice. We developed KASP markers for GL7 major haplotypes (H1 and H2), and established a breeding system assisted by the markers to effectively improve Xian/Indica (XI) hybrids for grain quality. Yuehesimiao (YHSM) and Yixiang 1 A (YX1A) are widely applicated XI restorer line and sterile line in three-line hybrids. The improved hybrid YX1A^GL7/YHSM^GL7 exhibited longer grain, higher ratio of grain length-to-width and larger rate of head rice, but lower chalkiness rate and degree than that of any other hybrids and both parents. Furthermore, the improved hybrid with GL7 had statistically same yield of grains with all other hybrids, indicating no penalty of grain yield while improving grain quality. The GL7 haplotype along with its marker KASP-S2 and breeding strategy resulted from this study could be valuable sources for developing XI hybrids with high quality and high yield of grains in rice.

Plant architecture and grain size are critical traits for rice breeding. Brassinosteroid (BR), a class of plant hormones, regulates these traits by modulating cell elongation, division, and differentiation. Therefore, exploring BR-related genes to leverage their pleiotropic effects is crucial for crop improvement. We identify a novel gene, Large Grain 2 (LG2), which encodes a Golgi-localized protein containing an NHL domain. This gene plays a crucial role in regulating both plant architecture and grain size in rice. Mechanistically, FUWA, a paralog of LG2, directly interacts with LG2 and enhances its protein stability. Furthermore, our findings indicate that LG2 is involved in BR signaling. Collectively, these results suggest that the LG2-FUWA module synergistically regulate plant architecture and grain size through the BR pathway in rice. Our study provides new insights into the function of NHL domain-containing proteins in plants and introduces a novel BR component for crop improvement. The LG2-FUWA module regulates plant architecture and grain size through the BR pathway in rice.

Rice, as the largest consumer of global freshwater resources, faces significant challenges due to increasing drought conditions exacerbated by climate change. In this study, we explore the critical role of FKBP12, a molecular chaperone protein, in modulating drought tolerance in rice. Utilizing a T-DNA insertional mutant (fkbp12) and FKBP12-overexpressing lines, we investigated the gene's influence on rice under various drought conditions. Our results revealed that the fkbp12 mutant exhibited significantly enhanced drought tolerance compared to the wild type, evidenced by improved water retention, reduced cellular damage, and an upregulated expression of key drought-responsive genes such as OsNCED3, OsSNAC1, and OsDREB2A. This suggests a compensatory upregulation of abscisic acid (ABA)-mediated pathways, enhancing the plant's ability to cope with water deficit. Conversely, overexpression of FKBP12 resulted in increased sensitivity to drought, likely due to disruption in stress signaling and reactive oxygen species (ROS) scavenging mechanisms. Additionally, we observed an impact on seed development, where the fkbp12 mutant presented smaller seed sizes, indicating a potential trade-off between growth and stress tolerance. This comprehensive analysis not only highlights the diverse roles of FKBP12 in drought stress response but also its implications for rice yield and seed development, providing valuable insights for breeding more resilient rice varieties in the face of escalating climate challenges.

Empirical breeding efforts targeting cold tolerance and ideal plant architecture have significantly improved yield and facilitated the geographic expansion of japonica rice cultivation. However, the genetic drivers and underlying molecular mechanisms of these traits remain insufficiently understood. Here, we identify Plant Height 8 (PH8) as a key gene regulating both plant stature and cold stress response in rice. Genome wide association analysis (GWAS), supported by functional validation, shows that loss of PH8 reduces plant height without affecting other agronomic traits. Notably, we found that PH8 also negatively regulates cold tolerance. A prevalent haplotype, PH8^Hap.0, exhibits reduced PH8 expression due to natural variation in its promoter region, resulting in shorter plants and enhanced cold tolerance. Selective sweep and geographic distribution analyses indicate that PH8^Hap.0 originated in high-latitude regions and underwent strong directional selection during modern japonica improvement. Functional assays demonstrate that PH8 enhances cold tolerance via improved reactive oxygen species (ROS) scavenging by repressing APX2, an antioxidant gene involved in ROS detoxification. Our findings reveal PH8 as a dual regulator of plant architecture and cold stress adaptation, and highlight PH8^Hap.0 as a historically selected allele that contributed to the climatic adaptation and geographical expansion of japonica rice.