OsSPL9 Regulates Grain Number and Grain Yield in Rice

OsSPL9 promotes Cu uptake and translocation in rice grown in high-Fe red soil

Most rice varieties are able to grow in red high-Fe soil, but the underlying mechanism remains elusive. Through forward genetic screening, we identified a red soil-sensitive-1 (rss1) mutant that exhibited severely retarded growth when grown in red soil but showed no evident phenotype in cinnamon soil. Under the red soil/high-Fe conditions, rss1 exhibited increased Fe but decreased copper (Cu) concentrations in both roots and shoots, and the rss1 phenotype was partially rescued by Cu supplement. RSS1 encodes an OsSPL9 transcription factor that is expressed in pericycle cells and parenchyma cells surrounding xylem in roots. Under high-Fe conditions, OsSPL9 activated expression of Cu transporters, including OsYSL16, OsCOPT1, and OsCOPT5 by binding to their promoters, and OsYSL16 overexpression partially rescued rss1 defects. We thus propose that OsSPL9 overcomes high-Fe imposed Cu deficiency by activating the expressions of Cu transporter genes, allowing rice to adapt to red soil.

Genome-Wide Mapping, Allelic Fingerprinting, and Haplotypes Validation Provide Insights Into the Genetic Control of Phenotypic Plasticity in Rice

Plant density significantly impacts photosynthesis, crop growth, and yield, thereby shaping the [CO2] fertilization effect and intricate physiological interactions in rice. An association panel of 171 rice genotypes was evaluated for physiological and yield-related traits, including the cumulative response index, under both normal planting density (NPD) and low planting density (LPD) conditions. LPD, serving as a proxy for elevated atmospheric [CO2], significantly increased all trait values, except for harvest index, compared to NPD. A genome-wide association study identified 172 QTNs, including 12 associated with multiple traits under NPD or LPD conditions. Candidate gene mining and network analysis within QTN regions identified potential candidates such as OsHAK1, RGA1, OsalphaCA3, OsalphaCA4, OsalphaCA5, OsCYP38, and OsPIN1, influencing various physiological and yield-related traits under LPD conditions. A significant relationship between the percentage of favorable alleles in genotypes and their performance under different conditions was observed. Potential haplotypes were validated using genotypes identified with contrasting [CO2] responses, grown under LPD and Free-Air [CO2] Enrichment facility. These findings can aid in selectively breeding genotypes with favorable alleles or haplotypes to enhance [CO2] responsiveness in rice. Incorporating greater phenotypic plasticity can help develop climate-smart rice varieties that increase grain yield and quality while mitigating losses from warming temperatures.

Exploring the impact of key physicochemical properties of rice on taste quality and instant rice processing

Taste quality is one of the most important indicators for assessing the quality of rice. However, there has been a lack of systematic studies investigating the impact factors of taste quality. In this study, chromosomal segment substitution lines (CSSLs) with notable differences in physicochemical properties were obtained by screening the CSSL population. A correlation analysis between the physicochemical properties and the taste qualities of rice revealed that amylose and protein content are significantly negatively correlated with the taste value of both freshly cooked and rehydrated instant rice. The alkali spreading value (ASV) had limited impact on the taste value of rice, but low-ASV rice is more resistant to cooking. Grain chalkiness played a critical role in maintaining the integrity of freshly cooked rice and instant rice grains after rehydration. In summary, our study provides crucial insights and guidance for rice breeding, with the goal of developing excellent quality and enhancing the processing of instant rice.

Methane-derived microbial biostimulant reduces greenhouse gas emissions and improves rice yield

Introduction

More than half of the world's population consumes rice as their primary food. The majority of rice production is concentrated in Asia, with the top 10 rice-growing countries accounting for 84% of the world's total rice cultivation. However, rice production is also strongly linked to environmental changes. Among all the global sources of greenhouse gas (GHG) emissions, paddy cultivation stands out as a significant contributor to global methane (CH4) and nitrous oxide (N2O) emissions. This contribution is expected to increase further with the projected increase of 28% in global rice output by 2050. Hence, modifications to rice management practices are necessary both to increase yield and mitigate GHG emissions.

Methods

We investigated the effect of seedling treatment, soil application, and foliar application of a methane-derived microbial biostimulant on grain yield and GHG emissions from rice fields over three seasons under 100% fertilizer conditions. Further, microbial biostimulant was also tested under 75% nitrogen (N) levels to demonstrate its effect on grain yield. To understand the mechanism of action of microbial biostimulant on crop physiology and yield, a series of physiological, transcript, and metabolite analyses were also performed.

Results

Our three-season open-field studies demonstrated a significant enhancement of grain yield, up to 39%, with a simultaneous reduction in CH4 (31%-60%) and N2O (34%-50%) emissions with the use of methane-derived microbial biostimulant. Under 75% N levels, a 34% increase in grain yield was observed with microbial biostimulant application. Based on the physiological, transcript, and metabolite analyses data, we were further able to outline the potential mechanisms for the diverse synergistic effects of methane-derived microbial biostimulant on paddy, including indole-3-acetic acid production, modulation of photosynthesis, tillering, and panicle development, ultimately translating to superior yield.

Conclusion

The reduction in GHG emission and enhanced yield observed under both recommended and reduced N conditions demonstrated that the methane-derived biostimulant can play a unique and necessary role in the paddy ecosystem. The consistent improvements seen across different field trials established that the methane-derived microbial biostimulant could be a scalable solution to intensify rice productivity with a lower GHG footprint, thus creating a win-win-win solution for farmers, customers, and the environment.

OsSPL11 positively regulates grain size by activating the expression of GW5L in rice

KEY MESSAGE

Rice OsSPL11 activates the expression of GW5L through binding to its promoter and positively regulates grain size. Grain size (GS) is an important determinant of grain weight and yield potential in cereal. Here, we report the functional analysis of OsSPL11 in grain length (GL), grain width (GW), and 1000-grain weight (TGW). OsSPL11 mutant plants, osspl11 lines, exhibited a decrease in GL, GW, and TGW, and OsSPL11-OE lines showed an increase in GL and TGW. Expression analysis revealed that OsSPL11 was located in the nucleus and highly expressed in spikelet hull and young development grains, consistent with its function in determining GS. Further analysis confirmed that OsSPL11 directly activates the expression of GW5L to regulate GS, meanwhile OsSPL11 expression is negatively regulated by OsGBP3. Taken together, our findings demonstrate that OsSPL11 could be a key regulator of affecting GS during the spikelet hull development and facilitate the process of improving grain yield by GS modification in rice.

Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits

Unraveling the regulatory mechanisms that govern complex traits is pivotal for advancing crop improvement. Here we present a comprehensive regulome atlas for rice (Oryza sativa), charting the chromatin accessibility across 23 distinct tissues from three representative varieties. Our study uncovers 117,176 unique open chromatin regions (OCRs), accounting for ~15% of the rice genome, a notably higher proportion compared to previous reports in plants. Integrating RNA-seq data from matched tissues, we confidently predict 59,075 OCR-to-gene links, with enhancers constituting 69.54% of these associations, including many known enhancer-to-gene links. Leveraging this resource, we re-evaluate genome-wide association study results and discover a previously unknown function of OsbZIP06 in seed germination, which we subsequently confirm through experimental validation. We optimize deep learning models to decode regulatory grammar, achieving robust modeling of tissue-specific chromatin accessibility. This approach allows to predict cross-variety regulatory dynamics from genomic sequences, shedding light on the genetic underpinnings of cis-regulatory divergence and morphological disparities between varieties. Overall, our study establishes a foundational resource for rice functional genomics and precision molecular breeding, providing valuable insights into regulatory mechanisms governing complex traits.

Environmental control of rice flowering time

Correct measurement of environmental parameters is fundamental for plant fitness and survival, as well as for timing developmental transitions, including the switch from vegetative to reproductive growth. Important parameters that affect flowering time include day length (photoperiod) and temperature. Their response pathways have been best described in Arabidopsis, which currently offers a detailed conceptual framework and serves as a comparison for other species. Rice, the focus of this review, also possesses a photoperiodic flowering pathway, but 150 million years of divergent evolution in very different environments have diversified its molecular architecture. The ambient temperature perception pathway is strongly intertwined with the photoperiod pathway and essentially converges on the same genes to modify flowering time. When observing network topologies, it is evident that the rice flowering network is centered on EARLY HEADING DATE 1, a rice-specific transcriptional regulator. Here, we summarize the most important features of the rice photoperiodic flowering network, with an emphasis on its uniqueness, and discuss its connections with hormonal, temperature perception, and stress pathways.

OsαCA1 Affects Photosynthesis, Yield Potential, and Water Use Efficiency in Rice

Plant growth and crop yield are essentially determined by photosynthesis when considering carbon dioxide (CO2) availability. CO2 diffusion inside a leaf is one of the factors that dictate the CO2 concentrations in chloroplasts. Carbonic anhydrases (CAs) are zinc-containing enzymes that interconvert CO2 and bicarbonate ions (HCO3−), which, consequently, affect CO2 diffusion and thus play a fundamental role in all photosynthetic organisms. Recently, the great progress in the research in this field has immensely contributed to our understanding of the function of the β-type CAs; however, the analysis of α-type CAs in plants is still in its infancy. In this study, we identified and characterized the OsαCA1 gene in rice via the analysis of OsαCAs expression in flag leaves and the subcellular localization of its encoding protein. OsαCA1 encodes an α-type CA, whose protein is located in chloroplasts with a high abundance in photosynthetic tissues, including flag leaves, mature leaves, and panicles. OsαCA1 deficiency caused a significant reduction in assimilation rate, biomass accumulation, and grain yield. The growth and photosynthetic defects of the OsαCA1 mutant were attributable to the restricted CO2 supply at the chloroplast carboxylation sites, which could be partially rescued by the application of an elevated concentration of CO2 but not that of HCO3−. Furthermore, we have provided evidence that OsαCA1 positively regulates water use efficiency (WUE) in rice. In summary, our results reveal that the function of OsαCA1 is integral to rice photosynthesis and yield potential, underscoring the importance of α-type CAs in determining plant physiology and crop yield and providing genetic resources and new ideas for breeding high-yielding rice varieties.

Validation of a high-confidence regulatory network for gene-to-NUE phenotype in field-grown rice

Nitrogen (N) and Water (W) - two resources critical for crop productivity - are becoming increasingly limited in soils globally. To address this issue, we aim to uncover the gene regulatory networks (GRNs) that regulate nitrogen use efficiency (NUE) - as a function of water availability - in Oryza sativa, a staple for 3.5 billion people. In this study, we infer and validate GRNs that correlate with rice NUE phenotypes affected by N-by-W availability in the field. We did this by exploiting RNA-seq and crop phenotype data from 19 rice varieties grown in a 2x2 N-by-W matrix in the field. First, to identify gene-to-NUE field phenotypes, we analyzed these datasets using weighted gene co-expression network analysis (WGCNA). This identified two network modules ("skyblue" & "grey60") highly correlated with NUE grain yield (NUEg). Next, we focused on 90 TFs contained in these two NUEg modules and predicted their genome-wide targets using the N-and/or-W response datasets using a random forest network inference approach (GENIE3). Next, to validate the GENIE3 TF→target gene predictions, we performed Precision/Recall Analysis (AUPR) using nine datasets for three TFs validated in planta. This analysis sets a precision threshold of 0.31, used to "prune" the GENIE3 network for high-confidence TF→target gene edges, comprising 88 TFs and 5,716 N-and/or-W response genes. Next, we ranked these 88 TFs based on their significant influence on NUEg target genes responsive to N and/or W signaling. This resulted in a list of 18 prioritized TFs that regulate 551 NUEg target genes responsive to N and/or W signals. We validated the direct regulated targets of two of these candidate NUEg TFs in a plant cell-based TF assay called TARGET, for which we also had in planta data for comparison. Gene ontology analysis revealed that 6/18 NUEg TFs - OsbZIP23 (LOC_Os02g52780), Oshox22 (LOC_Os04g45810), LOB39 (LOC_Os03g41330), Oshox13 (LOC_Os03g08960), LOC_Os11g38870, and LOC_Os06g14670 - regulate genes annotated for N and/or W signaling. Our results show that OsbZIP23 and Oshox22, known regulators of drought tolerance, also coordinate W-responses with NUEg. This validated network can aid in developing/breeding rice with improved yield on marginal, low N-input, drought-prone soils.

Genome-Wide Analysis of SQUAMOSA-Promoter-Binding Protein-like Family in Flowering Pleioblastus pygmaeus

SQUAMOSA Promoter-Binding Protein-Like (SPL) family is well-known for playing an important role in plant growth and development, specifically in the reproductive process. Bamboo plants have special reproductive characteristics with a prolonged vegetative phase and uncertain flowering time. However, the underlying functions of SPL genes in reproductive growth are undisclosed in bamboo plants. In the study, a total of 28 SPLs were screened from an ornamental dwarf bamboo species, Pleioblastus pygmaeus. Phylogenetic analysis indicates that 183 SPLs from eight plant species can be classified into nine subfamilies, and the 28 PpSPLs are distributed among eight subfamilies. Homologous analysis shows that as many as 32 pairs of homologous genes were found between P. pygmaeus and rice, and 83 pairs were found between P. pygmaeus and Moso bamboo, whose Ka/Ks values are all <1. MiRNA target prediction reveals that 13 out of the 28 PpSPLs have recognition sites complementary to miRNA156. To screen the SPLs involved in the reproductive growth of bamboo plants, the mRNA abundance of the 28 PpSPLs was profiled in the different tissues of flowering P. pygmaeus and non-flowering plants by RNA-Seq. Moreover, the relative expression level of eight PpSPLs is significantly higher in flowering P. pygmaeus than that in non-flowering plants, which was also validated by RT-qPCR. Combined with phylogenetic analysis and homologous analysis, the eight significant, differentially expressed PpSPLs were identified to be associated with the reproductive process and flower organ development. Among them, there are four potential miRNA156-targeting PpSPLs involved in the flowering process. Of significant interest in the study is the identification of 28 SPLs and the exploration of four key flowering-related SPLs from P. pygmaeus, which provides a theoretic basis for revealing the underlying functions of SPLs in the reproductive growth of bamboo plants.

Genetic and molecular pathways controlling rice inflorescence architecture

Rice inflorescence is one of the major organs in determining grain yield. The genetic and molecular regulation on rice inflorescence architecture has been well investigated over the past years. In the present review, we described genes regulating rice inflorescence architecture based on their roles in meristem activity maintenance, meristem identity conversion and branch elongation. We also introduced the emerging regulatory pathways of phytohormones involved in rice inflorescence development. These studies show the intricacies and challenges of manipulating inflorescence architecture for rice yield improvement.

Genetic control of branching patterns in grass inflorescences

Inflorescence branching in the grasses controls the number of florets and hence the number of seeds. Recent data on the underlying genetics come primarily from rice and maize, although new data are accumulating in other systems as well. This review focuses on a window in developmental time from the production of primary branches by the inflorescence meristem through to the production of glumes, which indicate the transition to producing a spikelet. Several major developmental regulatory modules appear to be conserved among most or all grasses. Placement and development of primary branches are controlled by conserved auxin regulatory genes. Subtending bracts are repressed by a network including TASSELSHEATH4, and axillary branch meristems are regulated largely by signaling centers that are adjacent to but not within the meristems themselves. Gradients of SQUAMOSA-PROMOTER BINDING-like and APETALA2-like proteins and their microRNA regulators extend along the inflorescence axis and the branches, governing the transition from production of branches to production of spikelets. The relative speed of this transition determines the extent of secondary and higher order branching. This inflorescence regulatory network is modified within individual species, particularly as regards formation of secondary branches. Differences between species are caused both by modifications of gene expression and regulators and by presence or absence of critical genes. The unified networks described here may provide tools for investigating orphan crops and grasses other than the well-studied maize and rice.

The CRISPR/Cas9-Mediated Modulation of SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE 8 in Alfalfa Leads to Distinct Phenotypic Outcomes

Alfalfa (Medicago sativa L.) is the most widely grown perennial leguminous forage and is an essential component of the livestock industry. Previously, the RNAi-mediated down-regulation of alfalfa SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE 8 (MsSPL8) was found to lead to increased branching, regrowth and biomass, as well as enhanced drought tolerance. In this study, we aimed to further characterize the function of MsSPL8 in alfalfa using CRISPR/Cas9-induced mutations in this gene. We successfully generated alfalfa genotypes with small insertions/deletions (indels) at the target site in up to three of four MsSPL8 alleles in the first generation. The efficiency of editing appeared to be tightly linked to the particular gRNA used. The resulting genotypes displayed consistent morphological alterations, even with the presence of up to two wild-type MsSPL8 alleles, including reduced leaf size and early flowering. Other phenotypic effects appeared to be dependent upon mutational dosage, with those plants with the highest number of mutated MsSPL8 alleles also exhibiting significant decreases in internode length, plant height, shoot and root biomass, and root length. Furthermore, MsSPL8 mutants displayed improvements in their ability to withstand water-deficit compared to empty vector control genotypes. Taken together, our findings suggest that allelic mutational dosage can elicit phenotypic gradients in alfalfa, and discrepancies may exist in terms of MsSPL8 function between alfalfa genotypes, growth conditions, or specific alleles. In addition, our results provide the foundation for further research exploring drought tolerance mechanisms in a forage crop.