Genetic Regulation of Shoot Architecture

Multi-omics analysis reveals the regulatory mechanism of branching development in Quercus fabri

The ability of axillary meristems to form axillary buds and subsequently develop into branches is influenced by phytohormones, environmental conditions, and genetic factors. The main trunk of Quercus fabri is prone to branching, which not only impacts the appearance and density of the wood and significantly reduces the yield rate. This study conducted transcriptomic, proteomic, and metabolomic analyses on three stages of axillary bud development in Q. fabri. A total of 12,888 differentially expressed genes (DEGs), 8193 differentially accumulated proteins (DAPs), and 1788 differentially accumulated metabolites (DAMs) were identified through comparisons among the stages and subjected to multi-omics joint analysis. Conduct interaction network analysis on DEGs and DAPs to identify the significant transcription factor family (AP2/ERF) involved in the regulation of axillary bud development. Furthermore, KEGG enrichment analysis of DEGs, DAPs and DAMs indicated significant enrichment in plant hormone signaling pathways. The analysis of endogenous hormone levels and qRT-PCR results for pathway genes demonstrated that the expression levels of IAA and tZ significantly increased during late developmental stages, whereas the expression levels of ABA, ACC and JA significantly decreased. In summary, these findings contribute to a comprehensive understanding of the regulatory networks underlying the branching development of Q. fabri. SIGNIFICANCE: Q. fabri exhibits robust vegetative growth, and its primary trunk is prone to branching, significantly influencing the wood yield rate. Through a joint analysis of transcriptomics, proteomics, and metabolomics, we comprehensively examined the regulatory network governing the axillary bud development of Q. fabri. Our findings revealed the crucial roles of the AP2/ERF transcription factor family and plant hormone signal transduction pathways in branch development. These insights contribute to a deeper understanding of the mechanisms regulating branch development.

Crucial Roles of Brassinosteroids in Cell Wall Composition and Structure Across Species: New Insights and Biotechnological Applications

Brassinosteroids (BR) are steroidal phytohormones essential for plant growth, development, and stress resistance. They fulfil this role partially by modulating cell wall structure and composition through the control of gene expression involved in primary and secondary cell wall biosynthesis and metabolism. This affects the deposition of cellulose, lignin, and other components, and modifies the inner architecture of the wall, allowing it to adapt to the developmental status and environmental conditions. This review focuses on the effects that BR exerts on the main components of the cell wall, cellulose, hemicellulose, pectin and lignin, in multiple and relevant plant species. We summarize the outcomes that result from modifying cell wall components by altering BR gene expression, applying exogenous BR and utilizing natural variability in BR content and describing new roles of BR in cell wall structure. Additionally, we discuss the potential use of BR to address pressing needs, such as increasing crop yield and quality, enhancing stress resistance and improving wood production through cell wall modulation.

Transcriptomics and Plant Hormone Analysis Reveal the Mechanism of Branching Angle Formation in Tea Plants (Camellia sinensis)

The branching angle of tea plants is a key factor in determining their branching structure, which significantly affects yield, suitability for mechanical harvesting, and overall plant architecture. However, the mechanisms underlying branching angle formation in tea plants remain unclear. In this study, we explored the mechanism of branching angle formation in tea plants by analysing the transcriptome and plant hormone levels of tea plant cultivars with different branching angles. The results indicated that gibberellin positively regulates the branching angle of tea plants, cytokinins, auxin, and abscisic acid involved in the formation of branching angles in tea plants. The transcriptome analysis revealed that candidate regulatory factors, including plant-hormone-related genes (the gibberellin synthesis gene GA3ox1 and metabolism gene GA2ox1; the cytokinin metabolism genes CKX and UGT; the auxin signal transduction-related gene LAX3; and the abscisic acid signal transduction gene PYL4), genes regulating cell division and growth (LAZY1, TAC1, and MAX1), and transcription factors (MYBs, WRKYs, TCPs, AP2/ERFs, and MADS-box), are involved in the formation of branching angles in tea plants. These results offer insights into the mechanism of branching angle formation in tea plants, providing important theoretical reference for the selection and breeding of tea cultivars suitable for mechanical harvesting, thereby improving agricultural efficiency and sustainability.

Gene silencing in broomrapes and other parasitic plants of the Orobanchaceae family: mechanisms, considerations, and future directions

Holoparasites of the Orobanchaceae family are devastating pests causing severe damage to many crop species, and are nearly impossible to control with conventional methods. During the past few decades, RNAi has been seen as a promising approach to control various crop pests. The exchange of small RNAs (sRNAs) between crops and parasitic plants has been documented, indicating potential for the development of methods to protect them via the delivery of the sRNAs to parasites, a method called host-induced gene silencing (HIGS). Here we describe various approaches used for gene silencing in plants and suggest solutions to improve the long-distance movement of the silencing triggers to increase the efficiency of HIGS in parasitic plants. We also investigate the important biological processes during the life cycle of the parasites, with a focus on broomrape species, providing several appropriate target genes that can be used, in particular, in multiplex gene silencing experiments. We also touch on how the application of nanoparticles can improve the stability and delivery of the silencing triggers, highlighting its potential for control of parasitic plants. Finally, suggestions for further research and possible directions for RNAi in parasitic plants are provided.

A favorable natural variation in CCD7 from orchardgrass confers enhanced tiller number

Tiller number is a crucial determinant that significantly influences the productivity and reproductive capacity of forage. The regeneration potential, biomass production, and seed yield of perennial forage species are highly reliant on the development of tillering. Strigolactones (SLs) are recently discovered carotenoid-derived phytohormones that play a crucial role in the regulation of tillering in annual crops. However, the modulation of tiller growth in perennial forage by SLs remains insufficiently investigated. In this study, we identified two alleles of the SLs biosynthesis gene, DgCCD7A and DgCCD7D, which encode CAROTENOID CLEAVAGE DIOXYGENASE 7 (CCD7), from two distinct subspecies of orchardgrass (Dactylis glomerata) exhibiting contrasting tillering phenotype and SLs content. The functionality of the DgCCD7A allele derived from high-tillering phenotypic orchardgrass was found to be diminished compared to that of DgCCD7D from the low-tillering type in rescuing the increased branching phenotype of CCD7-defective mutants in Arabidopsis and rice (Oryza sativa). Notably, the introduction of DgCCD7A in rice resulted in an increase in tiller number without significantly compromising grain yield. Moreover, we demonstrated that the L309P variation in DgCCD7A is a rare natural variant exclusively found in orchardgrass. Our findings revealed that DgCCD7A, a rare favorable natural variation of CCD7 in orchardgrass, holds significant potential for breeding application in improving the plant architecture of perennial forage and crops.

Boron controls apical dominance in Pea (Pisum sativum) via promoting polar auxin transport

Plant architecture and subsequent productivity are determined by the shoot apical dominance, which is disturbed by the deficiency of boron, one of the essential trace elements for plant growth and reproduction. However, the mechanism by which B controls shoot apical dominance or axillary bud outgrows under B deficiency is still unclear. This work aimed to investigate the mechanistic basis of this process, with focus on the interaction between B and polar auxin transport. Adopting an all-buds phenotyping methodology and employing several complementary approaches, we found that boron deficiency inhibited plant growth and changed the shoot architecture, resulting in the outgrowth of axillary buds at nodes 1-3. This was related to the auxin accumulation in shoot apical parts buds under B deficiency. Applying N-1-naphthylphthalamic acid to inhibit auxin transport from the shoot apex promoted the outgrowth of axillary buds in boron-sufficient (+B) plants. In decapitated plants, the application of exogenous auxin to the shoot apex only inhibited the outgrowth of axillary buds in +B plants. At higher auxin doses, the toxic effect of IAA was observed in the lower part of the shoot, which was more severe in +B plants than in B-deprived (-B) plants. Furthermore, the expression of PsPIN3 was significantly downregulated under -B conditions. These results indicate that B deficiency inhibits PAT from the apical bud through the main stem to the lower parts, leading to an increase of auxin level in the apical bud, which inhibits the growth of apical buds while stimulating the outgrowth of axillary buds.

Leaf angle regulation toward a maize smart canopy

Dense planting of single-cross hybrids contributes to maize yield increase over the past decades. Leaf angle, an important agronomic trait relevant to planting density, plays a fundamental role in light penetration into the canopy and photosynthetic efficiency. Leaf angle is a key parameter of plant architecture in the concept of smart canopy. Maize smart-canopy-like plant architecture exhibits optimal leaf angle, resulting in erect upper leaves and intermediate or horizontal lower leaves. Leaf angle regulation is a promising way forward in the breeding of varieties with canopy ideotypes. In this review, we first describe the relationship between maize polarity axes and leaf angle formation. Then, we revisit advances in the mutant and quantitative genetics research of maize leaf angle, highlighting the biological implications of transcription factors for maize leaf angle regulation. We underscore that KNOX family is essential for the blade-sheath boundary establishment and brassinosteroid pathway components as well as regulator ZmRAVL1 serve as key hubs of the transcriptional hierarchy governing maize leaf angle formation. We also suggest potential avenues for manipulating maize leaf angles across canopy layers.

The mutation of ent-kaurenoic acid oxidase, a key enzyme involved in gibberellin biosynthesis, confers a dwarf phenotype to cucumber

KEY MESSAGE

A dwarf mutant with short branches (csdf) was identified from EMS-induced mutagenesis. Bulked segregant analysis sequencing and map-based cloning revealed CsKAO encoding ent-kaurenoic acid oxidase as the causal gene. Plant architecture is the primary target of artificial selection during domestication and improvement based on the determinate function for fruit yield. Plant architecture is regulated by complicated genetic networks, more underlying mechanism remains to be elucidated. Here, we identified a dwarf mutant (csdf) in an EMS-induced cucumber population, and genetic analysis revealed the mutated phenotype is controlled by a single recessive gene. Optical microanalysis showed the decrease in cell length is mainly contribute to the dwarf phenotype. By strategy of BSA-seq combined with map-based cloning, CsaV3_6G006520 (CsKAO) on chromosome 6 was identified as the candidate gene for csdf. Gene cloning and sequence alignment revealed a G to A mutation in the sixth exon, which causes the premature stop codon in CsKAO of csdf. Expression analysis revealed CsKAO was expressed in various tissues with abundant transcripts, and has significant differences between WT and csdf. Gene annotation indicated CsKAO encodes a cytochrome P450 family ent-kaurenoic acid oxidase which functioned in GA biosynthesis. GA-relevant analysis showed that endogenous GA contents were significantly decreased and the dwarfism phenotype could be restored by exogenous GA3 treatment; while, some of the representative enzyme genes involved in the GA pathway were up-regulated in csdf. Besides, IAA content is decreased in the terminal bud and increased in the lateral bud in csdf as well as several IAA-related genes are differentially expressed. Overall, those findings suggest that CsKAO regulated plant height via the influence on GAs pathways, and IAA might interact with GAs on plant architecture morphogenesis in cucumber.

The OsNL1-OsTOPLESS2-OsMOC1/3 pathway regulates high-order tiller outgrowth in rice

Tiller is an important factor in determining rice yield. Currently, researches mainly focus on the outgrowth of low-order tiller (LOT), while the regulation mechanism of high-order tiller (HOT) outgrowth has remained unknown. In this study, we detected one OsNL1 mutant, nl1, exhibiting HOT numbers increase, and found that OsNL1 interacts with OsTOPLESS2, which was mediated by the core motif of nine amino acids VDCTLSLGT within the HAN domain of OsNL1. The topless2 mutant exhibits similar HOT number increase as in the nl1. Through ChIP-seq analysis, we revealed that OsNL1 recruits OsTOPLESS2 to conduct histone deacetylation in the promoters of OsMOC1 and OsMOC3 to regulate HOT outgrowth. Moreover, we showed that the HAN domain is essential for OsNL1 function as a repressor. In summary, our study reveals partial mechanism of HOT outgrowth in rice and deciphers the molecular biology function of the HAN domain. This will contribute to the comprehensive understanding of tiller outgrowth and the role of HAN-domain-containing genes.

The chloroplast pentatricopeptide repeat protein RCN22 regulates tiller number in rice by affecting sugar levels via the TB1-RCN22-RbcL module

As an important yield component, rice tiller number controls panicle number and determines grain yield. Regulation of rice tiller number by chloroplast pentatricopeptide repeat (PPR) proteins has not been reported previously. Here, we report the rice reduced culm number22 (rcn22) mutant, which produces few tillers owing to suppressed tiller bud elongation. Map-based cloning revealed that RCN22 encodes a chloroplast-localized P-type PPR protein. We found that RCN22 specifically binds to the 5' UTR of RbcL mRNA (encoding the large subunit of Rubisco) and enhances its stability. The reduced abundance of RbcL mRNA in rcn22 leads to a lower photosynthetic rate and decreased sugar levels. Consequently, transcript levels of DWARF3 (D3) and TEOSINTE BRANCHED1 (TB1) (which encode negative regulators of tiller bud elongation) are increased, whereas protein levels of the positive regulator DWARF53 (D53) are decreased. Furthermore, high concentrations of sucrose can rescue the tiller bud growth defect of the rcn22 mutant. On the other hand, TB1 directly binds to the RCN22 promoter and downregulates its expression. The tb1/rcn22 double mutant shows a tillering phenotype similar to that of rcn22. Our results suggest that the TB1-RCN22-RbcL module plays a vital role in rice tiller bud elongation by affecting sugar levels.

Arabidopsis histone acetyltransferase complex coordinates cytoplasmic histone acetylation and nuclear chromatin accessibility

Conserved type B histone acetyltransferases are recognized for their role in acetylating newly synthesized histones in the cytoplasm of eukaryotes. However, their involvement in regulating chromatin within the nucleus remains unclear. Our study shows that the Arabidopsis thaliana type B histone acetyltransferase HAG2 interacts with the histone chaperones MSI2, MSI3, and NASP, as well as the histones H3 and H4, forming a complex in both the cytoplasm and the nucleus. Within this complex, HAG2 and MSI2/3 constitute a histone acetylation module essential for acetylating histone H4 in the cytoplasm. Furthermore, this module works together with NASP to regulate histone acetylation, chromatin accessibility, and gene transcription in the nucleus. This complex enhances chromatin accessibility near transcription start sites while reducing accessibility near transcription termination sites. Our findings reveal a distinct role for the Arabidopsis type B histone acetyltransferase in the nucleus, shedding light on the coordination between cytoplasmic histone acetylation and nuclear chromatin regulation in plants.

FINE CULM1 Encoding a TEOSINTE BRANCHED1-like TCP Transcription Factor Negatively Regulates Axillary Meristem Formation in Rice

Shoot branching is a critical determinant of plant architecture and a key factor affecting crop yield. The shoot branching involves two main processes: axillary meristem formation and subsequent bud outgrowth. While considerable progress has been made in elucidating the genetic mechanisms underlying the latter process, our understanding of the former process remains limited. Rice FINE CULM1 (FC1), which is an ortholog of teosinte branched1 in maize (Zea mays) and BRANCHED1/2 in Arabidopsis (Arabidopsis thaliana), is known to act in the latter process by repressing bud outgrowth. In this study, we found that FC1 also plays a role in the former process, i.e. axillary meristem formation, in rice. This study was triggered by our unexpected observation that fc1 mutation suppresses the loss of axillary meristems in the loss-of-function mutant of the rice WUSCHEL gene TILLERS ABSENT1 (TAB1). In tab1 fc1, unlike in tab1, both stem cells and undifferentiated cells were maintained during axillary meristem formation, similar to the wild type. Morphological analysis showed that axillary meristem formation was accelerated in fc1, compared to the wild type. Consistent with this, cell proliferation was more active in the region containing stem cells and undifferentiated cells during axillary meristem formation in fc1 than in the wild type. Taken altogether, these findings suggest that FC1 negatively regulates axillary meristem formation by mildly repressing cell proliferation during this process.

The SLR1-OsMADS23-D14 module mediates the crosstalk between strigolactone and gibberellin signaling to control rice tillering

Strigolactones (SLs) and gibberellins (GAs) have been found to inhibit plant branching or tillering, but molecular mechanisms underlying the interplay between SL and GA signaling to modulate tillering remain elusive. We found that the transcription factor OsMADS23 plays a crucial role in the crosslink between SL and GA signaling in rice tillering. Loss-of-function mutant osmads23 shows normal axillary bud formation but defective bud outgrowth, thus reducing the tiller number in rice, whereas overexpression of OsMADS23 significantly increases tillering by promoting tiller bud outgrowth. OsMADS23 physically interacts with DELLA protein SLENDER RICE1 (SLR1), and the interaction reciprocally stabilizes each other. Genetic evidence showed that SLR1 is required for OsMADS23 to control rice tillering. OsMADS23 acts as an upstream transcriptional repressor to inhibit the expression of SL receptor gene DWARF14 (D14), and addition of SLR1 further enhances OsMADS23-mediated transcriptional repression of D14, indicating that D14 is the downstream target gene of OsMADS23-SLR1 complex. Moreover, application of exogenous SL and GA reduces the protein stability of OsMADS23-SLR1 complex and promotes D14 expression. Our results revealed that SLs and GAs synergistically inhibit rice tillering by destabilizing OsMADS23-SLR1 complex, which provides important insights into the molecular networks of SL-GA synergistic interaction during rice tillering.

Combining two main NAL1 functional alleles can increase rice yield

NARROW LEAF1 (NAL1) is one of the key genes in regulating photosynthesis and plant architecture. As the antagonistic effects of NAL1 have concurrent impacts on photosynthesis and yield component traits, how we can effectively utilize the NAL1 gene to further increase rice yield is not clear. In this study, we used two different main functional NAL1 alleles, each of which has previously been proven to have specifically advantageous traits, and tested whether the combined NAL1 alleles have a higher yield than the homozygous alleles. Our results exhibited that the combined NAL1 alleles had better parent heterosis (BPH) for panicle number and the total filled grain number per plant, and had middle parent heterosis (MPH) for spikelet number per panicle without affecting thousand-grain weight when compared with the homozygous alleles. In consequence, the NAL1 hybrid plants displayed highly increased grain yield compared with both homozygous parents. The hybrid plants also had better plant architecture and higher canopy photosynthesis. Western blot and proteomics results showed the hybrid plants had a middle abundant NAL1 protein level, and the upregulated proteins were mainly involved in the nucleus and DNA binding process but the downregulated proteins were mainly involved in the oxidation-reduction process, single-organism metabolic process, and fatty acid biosynthetic process. Furthermore, the hybrid vigor effect of NAL1 was confirmed by substituting the mutual male parent 9311 with 9311-NIL in two super hybrid rice varieties (LYP9 and YLY1). This study demonstrates that we can achieve a higher level of grain production in hybrid rice by using the heterosis of NAL1.

Natural variation in the Tn1a promoter regulates tillering in rice

Rice tillering is an important agronomic trait that influences plant architecture and ultimately affects yield. This can be genetically improved by mining favourable variations in genes associated with tillering. Based on a previous study on dynamic tiller number, we cloned the gene Tiller number 1a (Tn1a), which encodes a membrane-localised protein containing the C2 domain that negatively regulates tillering in rice. A 272 bp insertion/deletion at 387 bp upstream of the start codon in the Tn1a promoter confers a differential transcriptional response and results in a change in tiller number. Moreover, the TCP family transcription factors Tb2 and TCP21 repress the Tn1a promoter activity by binding to the TCP recognition site within the 272 bp indel. In addition, we identified that Tn1a may affect the intracellular K+ content by interacting with a cation-chloride cotransporter (OsCCC1), thereby affecting the expression of downstream tillering-related genes. The Tn1a+272 bp allele, associated with high tillering, might have been preferably preserved in rice varieties in potassium-poor regions during domestication. The discovery of Tn1a is of great significance for further elucidating the genetic basis of tillering characteristics in rice and provides a new and favourable allele for promoting the geographic adaptation of rice to soil potassium.

A MYB transcription factor underlying plant height in sorghum qHT7.1 and maize Brachytic 1 loci

Manipulating plant height is an essential component of crop improvement. Plant height was generally reduced through breeding in wheat, rice, and sorghum to resist lodging and increase grain yield but kept high for bioenergy crops. Here, we positionally cloned a plant height quantitative trait locus (QTL) qHT7.1 as a MYB transcription factor controlling internode elongation, cell proliferation, and cell morphology in sorghum. A 740 bp transposable element insertion in the intronic region caused a partial mis-splicing event, generating a novel transcript that included an additional exon and a premature stop codon, leading to short plant height. The dominant allele had an overall higher expression than the recessive allele across development and internode position, while both alleles' expressions peaked at 46 days after planting and progressively decreased from the top to lower internodes. The orthologue of qHT7.1 was identified to underlie the brachytic1 (br1) locus in maize. A large insertion in exon 3 and a 160 bp insertion at the promoter region were identified in the br1 mutant, while an 18 bp promoter insertion was found to be associated with reduced plant height in a natural recessive allele. CRISPR/Cas9-induced gene knockout of br1 in two maize inbred lines showed significant plant height reduction. These findings revealed functional connections across natural, mutant, and edited alleles of this MYB transcription factor in sorghum and maize. This enriched our understanding of plant height regulation and enhanced our toolbox for fine-tuning plant height for crop improvement.

Genetic Basis of Tillering Angle from Other Plants to Wheat: Current Progress and Future Perspectives

Plant architecture is an important agronomic trait that impacts crop yield. The tiller angle is a critical aspect of the plant's structural organization, which is influenced by both internal and external factors. The genetic mechanisms underlying the tiller angle have been extensively investigated in other plants. However, research on wheat is relatively limited. Additionally, mechanics has emerged as a connection between biochemical signaling and the development of three-dimensional biological forms. It not only reveals how physical interactions at the cellular level influence overall morphogenesis but also elucidates the interplay between these mechanical processes and molecular signaling pathways that collectively determine plant morphology. This review examines the recent advancements in the study of tillering angle in wheat and other plants. It discusses progress in research ranging from observable characteristics to the regulation of genes, as well as the physiological and biochemical aspects, and the adaptability to environmental factors. In addition, this review also discusses the effects of mechanical on plant growth and development, and provides ideas for the study of mechanical regulation mechanism of tillering angle in wheat. Consequently, based on the research of other plants and combined with the genetic and mechanical principles, this approach offers novel insights and methodologies for studying tillering in wheat. This interdisciplinary research framework not only enhances our understanding of the mechanisms underlying wheat growth and development but may also uncover the critical factors that regulate tillering angle, thereby providing a scientific foundation for improving wheat yield and adaptability.

Functions and Mechanisms of Brassinosteroids in Regulating Crop Agronomic Traits

Brassinosteroids (BRs) perform crucial functions controlling plant growth and developmental processes, encompassing many agronomic traits in crops. Studies of BR-related genes involved in agronomic traits have suggested that BRs could serve as a potential target for crop breeding. Given the pleiotropic effect of BRs, a systematic understanding of their functions and molecular mechanisms is conducive for application in crop improvement. Here, we summarize the functions and underlying mechanisms by which BRs regulate the several major crop agronomic traits, including plant architecture, grain size, as well as the specific trait of symbiotic nitrogen fixation in legume crops. For plant architecture, we discuss the roles of BRs in plant height, branching number and leaf erectness, and propose how progress in these fields may contribute to designing crops with optimal agronomic traits and improved grain yield by accurately modifying BR levels and signaling pathways.

Genome-wide association study reveals novel QTLs and candidate genes for panicle number in rice

Introduction

Panicle number (PN) is one of the three key yield components in rice, maintaining stable tiller and PN is a crucial characteristic of an ideal plant architecture. Understanding the molecular mechanisms underlying PN is essential for breeders aiming to improve rice yield.

Methods

To dissect the genetic architecture of panicle number, a genome-wide association study (GWAS) was conducted in 411 japonica rice varieties. GWAS analysis was carried out with the mixed linear model using 743,678 high-quality SNPs.

Results

Over two experimental years, we detected a total of seven quantitative trait loci (QTLs), located on chromosomes 1, 4, 6, 8, 11, and 12; notably, qPN1.1 and qPN8 were detected consistently in both years. By combining haplotype and expression analyses, OsCKX11 was identified as the candidate gene for qPN8, while LOC_Os01g07870 and LOC_Os01g07950 were identified as candidate genes for qPN1.1. Significant differences were observed among the haplotypes of these candidate genes. Additionally, qRT-PCR results showed that LOC_Os01g07870 expression levels were significantly lower in accessions with high panicle numbers compared to those with low panicle numbers.

Discussion

To understand the natural biological function of these candidate genes, further research involving overexpression or silencing in rice is needed. Despite these challenges, our results will lay the foundation for further study of panicle development and provide valuable genetic resources for developing high-panicle-number rice cultivars using genetic engineering and molecular breeding.

The rice R2R3 MYB transcription factor FOUR LIPS connects brassinosteroid signaling to lignin deposition and leaf angle

Leaf angle is an important agronomic trait for crop architecture and yield. In rice (Oryza sativa), the lamina joint is a unique structure connecting the leaf blade and sheath that determines leaf angle. Brassinosteroid (BR) signaling involving GLYCOGEN SYNTHASE KINASE-3 (GSK3)/SHAGGY-like kinases and BRASSINAZOLE-RESISTANT1 (BZR1) has a central role in regulating leaf angle in rice. In this study, we identified the atypical R2R3-MYB transcription factor FOUR LIPS (OsFLP), the rice homolog of Arabidopsis (Arabidopsis thaliana) AtFLP, as a participant in BR-regulated leaf angle formation. The spatiotemporal specificity of OsFLP expression in the lamina joint was closely associated with lignin deposition in vascular bundles and sclerenchyma cells. OsFLP mutation caused loose plant architecture with droopy flag leaves and hypersensitivity to BRs. OsBZR1 directly targeted OsFLP, and OsFLP transduced BR signals to lignin deposition in the lamina joint. Moreover, OsFLP promoted the transcription of the phenylalanine ammonia-lyase family genes OsPAL4 and OsPAL6. Intriguingly, OsFLP feedback regulated OsGSK1 transcription and OsBZR1 phosphorylation status. In addition, an Ala-to-Thr substitution within the OsFLP R3 helix-turn-helix domain, an equivalent mutation to that in Osflp-1, affected the DNA-binding ability and transcriptional activity of OsFLP. Our results reveal that OsFLP functions with OsGSK1 and OsBZR1 in BR signaling to maintain optimal leaf angle by modulating the lignin deposition in mechanical tissues of the lamina joint.

The WOX9-WUS modules are indispensable for the maintenance of stem cell homeostasis in Arabidopsis thaliana

The dynamic balance between the self-renewal and differentiation of stem cells in plants is precisely regulated by a series of developmental regulated genes that exhibit spatiotemporal-specific expression patterns. Several studies have demonstrated that the WOX family transcription factors play critical roles in maintaining the identity of stem cells in Arabidopsis thaliana. In this study, we obtained amiR-WOX9 transgenic plants, which displayed terminating prematurely of shoot apical meristem (SAM) development, along with alterations in inflorescence meristem and flower development. The phenotype of amiR-WOX9 plants exhibited similarities to that of wus-101 mutant, characterized by a stop-and-go growth pattern. It was also found that the expression of WUS in amiR-WOX9 lines was decreased significantly, while in UBQ10::WOX9-GFP transgenic plants, the WUS expression was increased significantly despite no substantial alteration in meristem size compared to Col. Therefore, these data substantiated the indispensable role of WOX9 in maintaining the proper expression of WUS. Further investigations unveiled the direct binding of WOX9 to the WUS promoter via the TAAT motif, thereby activating its expression. It was also found that WUS recognized identical the same TAAT motif cis-elements in its own promoter, thereby repress self-expression. Next, we successfully identified a physical interaction between WOX9 and WUS, and verified that it was harmful to the expression of WUS. Finally, our experimental findings demonstrate that WOX9 was responsible for the direct activating of WUS, which however was interfered by the ways of WUS binding its own promoter and the interaction of WUS and WOX9, thereby ensuring the appropriate expression pattern of WUS and then the stem cell stability. This study contributes to an enhanced comprehension of the regulatory network of the WOX9-WUS module in maintaining the equilibrium of the SAM.

Cotton BOP1 mediates SUMOylation of GhBES1 to regulate fibre development and plant architecture

The Arabidopsis BLADE-ON-PETIOLE (BOP) genes are primarily known for their roles in regulating leaf and floral patterning. However, the broader functions of BOPs in regulating plant traits remain largely unexplored. In this study, we investigated the role of the Gossypium hirsutum BOP1 gene in the regulation of fibre length and plant height through the brassinosteroid (BR) signalling pathway. Transgenic cotton plants overexpressing GhBOP1 display shorter fibre lengths and reduced plant height compared to the wild type. Conversely, GhBOP1 knockdown led to increased plant height and longer fibre, indicating a connection with phenotypes influenced by the BR pathway. Our genetic evidence supports the notion that GhBOP1 regulates fibre length and plant height in a GhBES1-dependent manner, with GhBES1 being a major transcription factor in the BR signalling pathway. Yeast two-hybrid, luciferase complementation assay and pull-down assay results demonstrated a direct interaction between GhBOP1 and GhSUMO1, potentially forming protein complexes with GhBES1. In vitro and in vivo SUMOylation analyses revealed that GhBOP1 functions in an E3 ligase-like manner to mediate GhBES1 SUMOylation and subsequent degradation. Therefore, our study not only uncovers a novel mechanism of GhBES1 SUMOylation but also provides significant insights into how GhBOP1 regulates fibre length and plant height by controlling GhBES1 accumulation.

Altered expression of amino acid permease OsAAP11 mediates bud outgrowth and tillering by regulating transport and accumulation of amino acids in rice

Kam sweet rice is a cultural treasure in Qiandongnan, Guizhou Province. However, the situation with low yield and economic value in Kam sweet rice urgently requires improved mechanistic understanding of tillering to increase its yield. In this study, we found that the rate of axillary bud elongation differed significantly among Kam sweet rice varieties, which was positively correlated with tiller number. Transcriptome analysis suggests that genes involved in nitrogen metabolism and plant hormone signaling pathways could be the main reasons for the differences in tillering among these varieties. The amino acid transporter OsAAP11 in the transcriptome was essential for bud outgrowth and rice tillering based on the phenotypic performance of its transgenic plants. Further results found that OsAAP11 was able to transport amino acids such as proline, glycine, and alanine in rice. Natural variations were found in the promoter region of this gene in different Kam sweet rice varieties, which may lead to differences in the transcription levels of OsAAP11. Overall, the results suggest that the natural variations of OsAAP11 in rice might lead to variations in its expression levels, further affecting bud outgrowth and tillering through regulating the transport and accumulation of amino acids.

Cell wall remodeling confers plant architecture with distinct wall structure in Nelumbo nucifera

Lotus (Nelumbo nucifera G.) is a perennial aquatic horticultural plant with diverse architectures. Distinct plant architecture (PA) has certain attractive and practical qualities, but its genetic morphogenesis in lotus remains elusive. In this study, we employ genome-wide association analysis (GWAS) for the seven traits of petiole length (PLL), leaf length (LL), leaf width (LW), peduncle length (PLF), flower diameter (FD), petal length (PeL), and petal width (PeW) in 301 lotus accessions. A total of 90 loci are identified to associate with these traits across 4 years of trials. Meanwhile, we perform RNA sequencing (RNA-seq) to analyze the differential expression of the gene (DEG) transcripts between large and small PA (LPA and SPA) of lotus stems (peduncles and petioles). As a result, eight key candidate genes are identified that are all primarily involved in plant cell wall remodeling significantly associated with PA traits by integrating the results of DEGs and GWAS. To verify this result, we compare the cell wall compositions and structures of LPA versus SPA in representative lotus germplasms. Intriguingly, compared with the SPA lotus, the LPA varieties have higher content of cellulose and hemicellulose, but less filling substrates of pectin and lignin. Additionally, we verified longer cellulose chains and higher cellulose crystallinity with less interference in LPA varieties. Taken together, our study illustrates how plant cell wall remodeling affects PA in lotus, shedding light on the genetic architecture of this significant ornamental trait and offering a priceless genetic resource for future genomic-enabled breeding.

Genome-wide association analysis reveals novel candidate loci and a gene regulating tiller number in orchardgrass

Tillers are specialized lateral shoots arising from axillary buds at basal nodes, and are also an important agronomic trait that determines the aboveground biomass and grain yield of various gramineous crops. So far, few genes have been reported to control tiller formation and most have been in the annual crop rice (Oryza sativa). Orchardgrass (Dactylis glomerata) is an important perennial forage crop with great economic and ecological value, but its genes regulating tillering have remained largely unknown. In the present study, we used a natural population of 264 global orchardgrass germplasms to determine genes associated with quantitative variation in tiller number through genome-wide association study analysis. A total of 19 putative loci and 55 genes associated with tiller number were thus identified. Additionally, 26 putative differentially expressed genes with tiller number, including DgCYC-C1, were identified by RNA-seq and genome-wide association study analysis. DgCYC-C1 which is involved in cell division, was overexpressed, revealing that DgCYC-C1 positively regulates tiller number. These results provide some new candidate genes or loci for the improvement of tiller number in crops, which might advance new sustainable strategies to meet global crop production challenges.

Mining Candidate Genes for Maize Tassel Spindle Length Based on a Genome-Wide Association Analysis

Maize tassel spindle length is closely related to the number of pollen grains and the duration of the flowering stage, ultimately affecting maize yield and adaptations to stress conditions. In this study, 182 maize inbred lines were included in an association population. A genome-wide association study was conducted on maize tassel spindle length using the Q + K model. With p ≤ 1.0 × 10-4 applied as the significance threshold, 240 SNPs significantly associated with tassel spindle length were detected, which were associated with 99 quantitative trait loci (QTLs), with 21 QTLs detected in two or more environments. Moreover, 51 candidate genes were detected in 21 co-localized QTLs. A KEGG enrichment analysis and candidate gene expression analysis indicated that Zm00001d042312 affects plant hormone signal transduction and is highly expressed in maize tassels. A haplotype analysis of Zm00001d042312 revealed three main haplotypes, with significant differences between Hap1 and Hap2. In conclusion, we propose that Zm00001d042312 is a gene that regulates maize tassel spindle length. This study has further elucidated the genetic basis of maize tassel spindle length, while also providing excellent genetic targets and germplasm resources for the genetic improvement of maize tassel spindle length and yield.

Sugar transporter modulates nitrogen-determined tillering and yield formation in rice

Nitrogen (N) fertilizer application ensures crop production and food security worldwide. N-controlled boosting of shoot branching that is also referred as tillering can improve planting density for increasing grain yield of cereals. Here, we report that Sugar Transporter Protein 28 (OsSTP28) as a key regulator of N-responsive tillering and yield formation in rice. N supply inhibits the expression of OsSTP28, resulting in glucose accumulation in the apoplast of tiller buds, which in turn suppresses the expression of a transcriptional inhibitor ORYZA SATIVA HOMEOBOX 15 (OSH15) via an epigenetic mechanism to activate gibberellin 2-oxidases (GA2oxs)-facilitated gibberellin catabolism in shoot base. Thereby, OsSTP28-OSH15-GA2oxs module reduces the level of bioactive gibberellin in shoot base upon increased N supply, and consequently promotes tillering and grain yield. Moreover, we identify an elite allele of OsSTP28 that can effectively promote N-responsive tillering and yield formation, thus representing a valuable breeding target of N use efficiency improvement for agricultural sustainability.

Analysis of characteristics of rice tillering dynamics influenced by sowing dates based on DTM

To quantitatively analyze the regularity and characteristics of tillering dynamics of rice at different sowing dates. In this paper, the whole process of rice tillering was decomposed into two aspects: tiller occurrence and tiller extinction, and two Logistic functions were used to describe them respectively, so as to establish a dynamic tillering model in rice based on double Logistic function (Dynamic Tillering Model, DTM). Then, according to DTM, dynamic tillering indexes (DTIs) were defined and their calculation formulas were derived. Finally, the characteristics and laws of rice tillering dynamic response to sowing dates were analyzed using DTM and DTIs with the observed tillering data of three rice varieties, (Hui-Liangyou 898 (HLY898), Y-Liangyou 900 (YLY900) and Y-Liangyou 911 (YLY911)), in six sowing dates (March 15, March 20, March 25, March 30, April 5, April 10). The results show that: 1. The model fits well. The normalized RMSE (RMSEn) of the DTM fitted to the observed tillering data of different rice varieties sown at different times were all less than 10 %, and their mean values were less than 5 %. 2.The variation degree of DTIs under the influence of sowing dates had certain consistency among the three rice varieties. the inherent rate of tillering (R it ), the maximum tillering rate (R mt ), the maximum tillers extinction rate (R me ) and the duration of tillering (D t ) varied greatly, while the total number of grow tillers (N g ), the peak time of tillering (T pt ), the peak time of tillers extinction (T pe ) and the end time of tillering (T et ) had smaller variation. 3. The eight DTIs, the inherent rate of tillering (R it ), the duration of tillering (D t ), the maximum tillering rate (R mt ), the number of retained tillers (N r ), the peak time of tillering (T pt ), the end time of tillering (T et ), the start time of tillers extinction (T se ) and duration of tillers extinction (D e ), had a consistent linear response to the sowing dates among the three rice varieties. 4. Under different sowing dates, the dynamic characteristics of tillering of YLY900 and YLY911 were relatively close, while HLY898 had great differences from YLY900 and YLY911. In this paper, the evolution process of the number of tillers of rice was accurately described by the DTM, and the regularity and characteristics of tillering dynamics of rice were deeply revealed using the DTIs, with agronomic experiment of three varieties with six sowing dates. Therefore, it has important theoretical value to deeply understand the law of the tillering dynamic of rice affected by sowing dates and has important practical significance for guiding accurate planting and fine management of rice production from the perspective of grasping tillering dynamics.

Strigolactone-gibberellin crosstalk mediated by a distant silencer fine-tunes plant height in upland cotton

Optimal plant height is crucial in modern agriculture, influencing lodging resistance and facilitating mechanized crop production. Upland cotton (Gossypium hirsutum) is the most important fiber crop globally; however, the genetic basis underlying plant height remains largely unexplored. In this study, we conducted a genome-wide association study to identify a major locus controlling plant height (PH1) in upland cotton. This locus encodes gibberellin 2-oxidase 1A (GhPH1) and features a 1133-bp structural variation (PAVPH1) located approximately 16 kb upstream. The presence or absence of PAVPH1 influences the expression of GhPH1, thereby affecting plant height. Further analysis revealed that a gibberellin-regulating transcription factor (GhGARF) recognizes and binds to a specific CATTTG motif in both the GhPH1 promoter and PAVPH1. This interaction downregulates GhPH1, indicating that PAVPH1 functions as a distant upstream silencer. Intriguingly, we found that DWARF53 (D53), a key repressor of the strigolactone (SL) signaling pathway, directly interacts with GhGARF to inhibit its binding to targets. Moreover, we identified a previously unrecognized gibberellin-SL crosstalk mechanism mediated by the GhD53-GhGARF-GhPH1/PAVPH1 module, which is crucial for regulating plant height in upland cotton. These findings shed light on the genetic basis and gene interaction network underlying plant height, providing valuable insights for the development of semi-dwarf cotton varieties through precise modulation of GhPH1 expression.

Heading Date 3a Stimulates Tiller Bud Outgrowth in Oryza sativa L. through Strigolactone Signaling Pathway

Heading date 3a (Hd3a, a FLOWERING LOCUS T (FT) ortholog from rice) is well known for its important role in rice (Oryza sativa L.), controlling floral transition under short-day (SD) conditions. Although the effect of Hd3a on promoting branching has been found, the underlying mechanism remains largely unknown. In this report, we overexpressed an Hd3a and BirAG (encoding a biotin ligase) fusion gene in rice, and found that early flowering and tiller bud outgrowth was promoted in BHd3aOE transgenic plants. On the contrary, knockout of Hd3a delayed flowering and tiller bud outgrowth. By using the BioID method, we identified multiple Hd3a proximal proteins. Among them, D14, D53, TPR1, TPR2, and TPRs are central components of the strigolactone signaling pathway, which has an inhibitory effect on rice tillering. The interaction between Hd3a, on the one hand, and D14 and D53 was further confirmed by the bimolecular fluorescence complementation (BiFC), yeast two-hybrid (Y2H), and co-immunoprecipitation (Co-IP) methods. We also found that Hd3a prevented the degradation of D53 induced by rac-GR24 (a strigolactone analog) in rice protoplasts. RT-qPCR assay showed that the expression levels of genes involved in strigolactone biosynthesis and signal transduction were altered significantly between WT and Hd3a overexpression (Hd3aOE) or mutant (hd3a) plants. OsFC1, a downstream target of the strigolactone signaling transduction pathway in controlling rice tillering, was downregulated significantly in Hd3aOE plants, whereas it was upregulated in hd3a lines. Collectively, these results indicate that Hd3a promotes tiller bud outgrowth in rice by attenuating the negative effect of strigolactone signaling on tillering and highlight a novel molecular network regulating rice tiller outgrowth by Hd3a.

Fine-mapping of a QTL and identification of candidate genes associated with the lateral branch angle of peanuts (Arachis hypogaea L.) on chromosome B05

Peanuts play a crucial role as an oil crop, serving not only as a primary source of edible oil but also offering ample protein and vitamins for human consumption. The lateral branch angle of peanuts is the angle between the main stem and the first pair of lateral branches, which is an important agronomic trait of peanuts, significantly impacts the peg penetration into the soil, plant growth, and pod yield. It is closely intertwined with planting density, cultivation techniques, and mechanized harvesting methods. Therefore, the lateral branch angle holds substantial importance in enhancing peanut yield and facilitating mechanization. In order to conduct in-depth research on the lateral branch angle of peanuts, this research is grounded in the QTL mapping findings, specifically focusing on the QTL qGH associated with the lateral branch angle of peanuts located on chromosome B05 (142610834-146688220). By using Jihua 5 and PZ42 for backcrossing, a BC1F2 population comprising 8000 individual plants was established. Molecular markers were then developed to screen the offspring plants, recombine individual plants, conduct fine mapping. he results showed that using the phenotype and genotype of 464 recombinant individual plants selected from 8000 offspring, narrow down the localization interval to 48kb, and designate it as qLBA. The gene Arahy.C4FM6Y, responsible for the F-Box protein, was identified within qLBA through screening. Real-time quantitative detection of Arahy.C4FM6Y was carried out using M130 and Jihua 5, revealing that the expression level of Arahy.C4FM6Y at the junction of the main stem and the first lateral branch of peanuts was lower in M130 compared to Jihua 5 during the growth period of the first lateral branch from 1 to 10 centimeters. Consequently, Arahy.C4FM6Y emerges as a gene that restrains the increase in the angle of the first lateral branch in peanuts. This investigation offers novel genetic reservoirs for peanut plant type breeding and furnishes a theoretical foundation for molecular marker-assisted peanut breeding.

Cytokinin catabolism and transport are involved in strigolactone-modulated rice tiller bud elongation fueled by phosphate and nitrogen supply

Phosphate (P) and nitrogen (N) fertilization affect rice tillering, indicating that P- and N-regulated tiller growth has a crucial effect on grain yield. Cytokinins and strigolactones (SLs) promote and inhibit tiller bud outgrowth, respectively; however, the underlying mechanisms are unclear. In this study, tiller bud outgrowth and cytokinin fractions were evaluated in rice plants fertilized at different levels of P and N. Low phosphate or nitrogen (LP or LN) reduced rice tiller numbers and bud elongation, in line with low cytokinin levels in tiller buds and xylem sap as well as low TCSn:GUS expression, a sensitive cytokinin signal reporter, in the stem base. Furthermore, exogenous cytokinin (6-benzylaminopurin, 6-BA) administration restored bud length and TCSn:GUS activity in LP- and LN-treated plants to similar levels as control plants. The TCSn:GUS activity and tiller bud outgrowth were less affected by LP and LN supplies in SL-synthetic and SL-signaling mutants (d17 and d53) compared to LP- and LN-treated wild-type (WT) plants, indicating that SL modulate tiller bud elongation under LP and LN supplies by reducing the cytokinin levels in tiller buds. OsCKX9 (a cytokinin catabolism gene) transcription in buds and roots was induced by LP, LN supplies and by adding the SL analog GR24. A reduced response of cytokinin fractions to LP and LN supplies was observed in tiller buds and xylem sap of the d53 mutant compared to WT plants. These results suggest that cytokinin catabolism and transport are involved in SL-modulated rice tillering fueled by P and N fertilization.

The BnaBPs gene regulates flowering time and leaf angle in Brassica napus

The flowering time and plant architecture of Brassica napus were significantly associated with yield. In this study, we found that the BREVIPEDICELLUS/KNAT1(BP) gene regulated the flowering time and plant architecture of B. napus. However, the precise regulatory mechanism remains unclear. We cloned two homologous BP genes, BnaBPA03 and BnaBPC03, from B. napus Xiaoyun. The protein sequence analysis showed two proteins containing conserved domains KNOX I, KNOX II, ELK, and HOX of the KONX protein family. The CRISPR/Cas9 knockout lines exhibited early budding and flowering time, coupled with floral organ abscission earlier and a larger leaf angle. On the contrary, overexpression plants displayed a phenotype that was the inverse of these characteristics. Furthermore, we observed upregulation of gibberellin and ethylene biosynthesis genes, as well as floral integrator genes in knocked-out plants. The results revealed that BnaBPs play a role in flowering time, floral organ abscission, and leaf angle as well as germination processes mediated. Additionally, BnaBPs exerted an impact on the biosynthesis pathways of ethylene and GA.

PagKNAT2/6b promotes shoot branching by attenuating auxin-strigolactone signalling in poplar

Shoot branching from axillary bud (AB) directly determines plant architecture. However, the mechanism through which AB remains dormant or emerges to form branches as plants grow remains largely unknown. Here, the auxin-strigolactone (IAA-SL) pathway was first shown to regulate shoot branching in poplar, and we found that PagKNAT2/6b could modulate this pathway. PagKNAT2/6b was expressed mainly in the shoot apical meristem and AB and was induced by shoot apex damage. PagKNAT2/6b overexpressing poplar plants (PagKNAT2/6b OE) exhibited multiple branches that mimicked the branching phenotype of nontransgenic plants after decapitation treatment, while compared with nontransgenic controls, PagKNAT2/6b antisense transgenic poplar and Pagknat2/6b mutant lines exhibited a significantly decreased number of branches after shoot apex damage treatment. In addition, we found that PagKNAT2/6b directly inhibits the expression of the key IAA synthesis gene PagYUC6a, which is specifically expressed in the shoot apex. Moreover, overexpression of PagYUC6a in the PagKNAT2/6b OE background reduced the number of branches after shoot apex damage treatment. Overall, we conclude that PagKNAT2/6b responds to shoot apical injury and regulates shoot branching through the IAA-SL pathway. These findings may provide a theoretical basis and candidate genes for genetic engineering to create new forest tree species with different crown types.

Harnessing Multi-Omics Strategies and Bioinformatics Innovations for Advancing Soybean Improvement: A Comprehensive Review

Soybean improvement has entered a new era with the advent of multi-omics strategies and bioinformatics innovations, enabling more precise and efficient breeding practices. This comprehensive review examines the application of multi-omics approaches in soybean-encompassing genomics, transcriptomics, proteomics, metabolomics, epigenomics, and phenomics. We first explore pre-breeding and genomic selection as tools that have laid the groundwork for advanced trait improvement. Subsequently, we dig into the specific contributions of each -omics field, highlighting how bioinformatics tools and resources have facilitated the generation and integration of multifaceted data. The review emphasizes the power of integrating multi-omics datasets to elucidate complex traits and drive the development of superior soybean cultivars. Emerging trends, including novel computational techniques and high-throughput technologies, are discussed in the context of their potential to revolutionize soybean breeding. Finally, we address the challenges associated with multi-omics integration and propose future directions to overcome these hurdles, aiming to accelerate the pace of soybean improvement. This review serves as a crucial resource for researchers and breeders seeking to leverage multi-omics strategies for enhanced soybean productivity and resilience.

Plant developmental oddities

MAIN CONCLUSION

Plants lacking shoot apical meristem develop with unique body shapes, suggesting rewiring of developmental genes. This loss of the meristem is likely influenced by a combination of environmental factors and evolutionary pressures. This study explores the development of plant bodies in three families (Podostemaceae, Lemnaceae, and Gesneriaceae) where the shoot apical meristem (SAM), a key structure for growth, is absent or altered. The review highlights alternative developmental strategies these plants employ. Also, we considered alternative reproduction in those species, namely through structures like turions, fronds, or modified leaves, bypassing the need for a SAM. Further, we report on studies based on the expression patterns of genes known to be involved in SAM formation and function. Interestingly, these genes are still present but expressed in atypical locations, suggesting a rewiring of developmental networks. Our view on the current literature and knowledge indicates that the loss or reduction of the SAM is driven by a combination of environmental pressures and evolutionary constraints, leading to these unique morphologies. Further research, also building on Next-Generation Sequencing, will be instrumental to explore the genetic basis for these adaptations and how environmental factors influence them.

Prion-like Proteins in Plants: Key Regulators of Development and Environmental Adaptation via Phase Separation

Prion-like domains (PrLDs), a unique type of low-complexity domain (LCD) or intrinsically disordered region (IDR), have been shown to mediate protein liquid-liquid phase separation (LLPS). Recent research has increasingly focused on how prion-like proteins (PrLPs) regulate plant growth, development, and stress responses. This review provides a comprehensive overview of plant PrLPs. We analyze the structural features of PrLPs and the mechanisms by which PrLPs undergo LLPS. Through gene ontology (GO) analysis, we highlight the diverse molecular functions of PrLPs and explore how PrLPs influence plant development and stress responses via phase separation. Finally, we address unresolved questions about PrLP regulatory mechanisms, offering prospects for future research.

A dynamic regulome of shoot-apical-meristem-related homeobox transcription factors modulates plant architecture in maize

BACKGROUND

The shoot apical meristem (SAM), from which all above-ground tissues of plants are derived, is critical to plant morphology and development. In maize (Zea mays), loss-of-function mutant studies have identified several SAM-related genes, most encoding homeobox transcription factors (TFs), located upstream of hierarchical networks of hundreds of genes.

RESULTS

Here, we collect 46 transcriptome and 16 translatome datasets across 62 different tissues or stages from the maize inbred line B73. We construct a dynamic regulome for 27 members of three SAM-related homeobox subfamilies (KNOX, WOX, and ZF-HD) through machine-learning models for the detection of TF targets across different tissues and stages by combining tsCUT&Tag, ATAC-seq, and expression profiling. This dynamic regulome demonstrates the distinct binding specificity and co-factors for these homeobox subfamilies, indicative of functional divergence between and within them. Furthermore, we assemble a SAM dynamic regulome, illustrating potential functional mechanisms associated with plant architecture. Lastly, we generate a wox13a mutant that provides evidence that WOX13A directly regulates Gn1 expression to modulate plant height, validating the regulome of SAM-related homeobox genes.

CONCLUSIONS

The SAM-related homeobox transcription-factor regulome presents an unprecedented opportunity to dissect the molecular mechanisms governing SAM maintenance and development, thereby advancing our understanding of maize growth and shoot architecture.

Suprathreshold Water Spray Stimulus Enhances Plant Defenses against Biotic Stresses in Tomato

Mechanical stimuli can affect plant growth, development, and defenses. The role of water spray stimulation, as a prevalent mechanical stimulus in the environment, in crop growth and defense cannot be overlooked. In this study, the effects of water spray on tomato plant growth and defense against the chewing herbivore Helicoverpa armigera and necrotrophic fungus Botrytis cinerea were investigated. Suprathreshold water spray stimulus (LS) was found to enhance tomato plant defenses against pests and pathogens while concurrently modifying plant architecture. The results of the phytohormone and chemical metabolite analysis revealed that LS improved the plant defense response via jasmonic acid (JA) signaling. LS significantly elevated the level of a pivotal defensive metabolite, chlorogenic acid, and reduced the emissions of volatile organic compounds (VOCs) from tomato plants, thereby defending against pest and pathogen attacks. The most obvious finding to emerge from this study is that LS enhances tomato plant defenses against biotic stresses, which will pave the way for further work on the application of mechanical stimuli for pest management.

Identification of Rapeseed (Brassica napus L.) Plant Height-Associated QTL Using BSA-seq and RNA-seq

Plant height (PH) is a critical agronomic trait in Brassica napus, significantly impacting yield. Consequently, identifying genes associated with plant height is a pivotal objective in oilseed rape breeding. This study employed a combination of bulk segregant analysis sequencing (BSA-seq) and RNA sequencing (RNA-seq) for analysis. A novel quantitative trait locus (QTL), qPH_C02, was identified between 63,989,634 and 64,945,122 bp on chromosome C02, from which eight candidate genes were screened. The Gene Ontology (GO) analysis revealed enrichment in peroxisomes, while the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated enrichment in the oxidative phosphorylation (OP) pathway. It is hypothesized that the observed differences in plant height and silique length may be attributed to the regulation of peroxidase activity in the OP pathway, which in turn alters plant energy metabolism and controls nutrient uptake. Subsequently, we will further test this hypothesis. The results of this study will contribute to our understanding of the genetic basis for differences in plant height and provide a foundation for the selection and breeding of Brassica napus varieties with desired plant shapes.

Molecular Regulation of Shoot Architecture in Soybean

Soybean (Glycine max [L.] Merr.) serves as a major source of protein and oil for humans and animals. Shoot architecture, the spatial arrangement of a plant's above-ground organs, strongly affects crop yield and is therefore a critical agronomic trait. Unlike wheat and rice crops that have greatly benefitted from the Green Revolution, soybean yield has not changed significantly in the past six decades owing to its unique shoot architecture. Soybean is a pod-bearing crop with pods adhered to the nodes, and variation in shoot architecture traits, such as plant height, node number, branch number and number of seeds per pod, directly affects the number of pods and seeds per plant, thereby determining yield. In this review, we summarize the relationship between soybean yield and these major components of shoot architecture. We also describe the latest advances in identifying the genes and molecular mechanisms underlying soybean shoot architecture and discuss possible directions and approaches for breeding new soybean varieties with ideal shoot architecture and improved yield.

ScRNA-seq reveals the spatiotemporal distribution of camptothecin pathway and transposon activity in Camptotheca acuminata shoot apexes and leaves

Camptotheca acuminata Decne., a significant natural source of the anticancer drug camptothecin (CPT), synthesizes CPT through the monoterpene indole alkaloid (MIA) pathway. In this study, we used single-cell RNA sequencing (scRNA-seq) to generate datasets encompassing over 60,000 cells from C. acuminata shoot apexes and leaves. After cell clustering and annotation, we identified five major cell types in shoot apexes and four in leaves. Analysis of MIA pathway gene expression revealed that most of them exhibited heightened expression in proliferating cells (PCs) and vascular cells (VCs). In contrast to MIA biosynthesis in Catharanthus roseus, CPT biosynthesis in C. acuminata did not exhibit multicellular compartmentalization. Some putative genes encoding enzymes and transcription factors (TFs) related to the biosynthesis of CPT and its derivatives were identified through co-expression analysis. These include 19 cytochrome P450 genes, 8 O-methyltransferase (OMT) genes, and 62 TFs. Additionally, these pathway genes exhibited dynamic expression patterns during VC and EC development. Furthermore, by integrating gene and transposable element (TE) expression data, we constructed novel single-cell transcriptome atlases for C. acuminata. This approach significantly facilitated the identification of rare cell types, including peripheral zone cells (PZs). Some TE families displayed cell type specific, tissue specific, or developmental stage-specific expression patterns, suggesting crucial roles for these TEs in cell differentiation and development. Overall, this study not only provides novel insights into CPT biosynthesis and spatial-temporal TE expression characteristics in C. acuminata, but also serves as a valuable resource for further comprehensive investigations into the development and physiology of this species.

Application of CRISPR/Cas-based gene-editing for developing better banana

Banana (Musa spp.), including plantain, is one of the major staple food and cash crops grown in over 140 countries in the subtropics and tropics, with around 153 million tons annual global production, feeding about 400 million people. Despite its widespread cultivation and adaptability to diverse environments, banana production faces significant challenges from pathogens and pests that often coexist within agricultural landscapes. Recent advancements in CRISPR/Cas-based gene editing offer transformative solutions to enhance banana resilience and productivity. Researchers at IITA, Kenya, have successfully employed gene editing to confer resistance to diseases such as banana Xanthomonas wilt (BXW) by targeting susceptibility genes and banana streak virus (BSV) by disrupting viral sequences. Other breakthroughs include the development of semi-dwarf plants, and increased β-carotene content. Additionally, non-browning banana have been developed to reduce food waste, with regulatory approval in the Philippines. The future prospects of gene editing in banana looks promising with CRISPR-based gene activation (CRISPRa) and inhibition (CRISPRi) techniques offering potential for improved disease resistance. The Cas-CLOVER system provides a precise alternative to CRISPR/Cas9, demonstrating success in generating gene-edited banana mutants. Integration of precision genetics with traditional breeding, and adopting transgene-free editing strategies, will be pivotal in harnessing the full potential of gene-edited banana. The future of crop gene editing holds exciting prospects for producing banana that thrives across diverse agroecological zones and offers superior nutritional value, ultimately benefiting farmers and consumers. This article highlights the pivotal role of CRISPR/Cas technology in advancing banana resilience, yield and nutritional quality, with significant implications for global food security.

Photosynthesis regulates tillering bud elongation and nitrogen-use efficiency via sugar-induced NGR5 in rice

Rice tillering is one of the most important agronomical traits largely determining grain yield. Photosynthesis and nitrogen availability are two important factors affecting rice tiller bud elongation; however, underlying mechanism and their cross-talk is poorly understood. Here, we used map-based cloning, transcriptome profiling, phenotypic analysis, and molecular genetics to understand the roles of the Decreased Tiller Number 1 (DTN1) gene that encodes the fructose-1,6-bisphosphate aldolase and involves in photosynthesis required for light-induced axillary bud elongation in rice. Deficiency of DTN1 results in the reduced photosynthetic rate and decreased contents of sucrose and other sugars in both leaves and axillary buds, and the reduced tiller number in dtn1 mutant could be partially rescued by exogenous sucrose treatment. Furthermore, we found that the expression of nitrogen-mediated tiller growth response 5 (NGR5) was remarkably decreased in shoot base of dtn1-2, which can be activated by sucrose treatment. Overexpression of NGR5 in the dtn1-2 could partially rescue the reduced tiller number, and the tiller number of dtn1-2 was insensitive to nitrogen supply. This work demonstrated that the sugar level regulated by photosynthesis and DTN1 could positively regulate NGR5 expression, which coordinates the cross-talk between carbon and nitrate to control tiller bud outgrowth in rice.

Phyllostachys edulis argonaute genes function in the shoot architecture

Argonaute (AGO) proteins are the core components of the RNA-induced silencing complexes (RISC) in the cytoplasm and nucleus, and are necessary for the development of plant shoot meristem, which gives rise to the above-ground plant body. In this study, we identified 23 Phyllostachys edulis AGO genes (PhAGOs) that were distributed unequally on the 14 unmapped scaffolds. Gene collinearity and phylogeny analysis showed that the innovation of PhAGO genes was mainly due to dispersed duplication and whole-genome duplication, which resulted in the enlarged PhAGO family. PhAGO genes were expressed in a temporal-spatial expression pattern, and they encoded proteins differently localized in the cytoplasm and/or nucleus. Overexpression of the PhAGO2 and PhAGO4 genes increased the number of tillers or leaves in Oryza sativa and affected the shoot architecture of Arabidopsis thaliana. These results provided insight into the fact that PhAGO genes play important roles in plant development.

The lncRNA1-miR6288b-3p-PpTCP4-PpD2 module regulates peach branch number by affecting brassinosteroid biosynthesis

Branch number is one of the most important agronomic traits of fruit trees such as peach. Little is known about how LncRNA and/or miRNA modules regulate branching through transcription factors. Here, we used molecular and genetic tools to clarify the molecular mechanisms underlying brassinosteroid (BR) altering plant branching. We found that the number of sylleptic branch and BR content in pillar peach ('Zhaoshouhong') was lower than those of standard type ('Okubo'), and exogenous BR application could significantly promote branching. PpTCP4 expressed great differentially comparing 'Zhaoshouhong' with 'Okubo'. PpTCP4 could directly bind to DWARF2 (PpD2) and inhibited its expression. PpD2 was the only one differentially expressed key gene in the path of BR biosynthesis. At the same time, PpTCP4 was identified as a target of miR6288b-3p. LncRNA1 could act as the endogenous target mimic of miR6288b-3p and repress expression of miR6288b-3p. Three deletions and five SNP sites of lncRNA1 promoter were found in 'Zhaoshouhong', which was an important cause of different mRNA level of PpTCP4 and BR content. Moreover, overexpressed PpTCP4 significantly inhibited branching. A novel mechanism in which the lncRNA1-miR6288b-3p-PpTCP4-PpD2 module regulates peach branching number was proposed.

TaSPL6B, a member of the Squamosa promoter binding protein-like family, regulates shoot branching and florescence in Arabidopsis thaliana

BACKGROUND

Squamosa promoter-binding protein-like (SPL) proteins are essential to plant growth and development as plant-specific transcription factors. However, the functions of SPL proteins in wheat need to be further explored.

RESULTS

We cloned and characterized TaSPL6B of wheat in this study. Analysis of physicochemical properties revealed that it contained 961 amino acids and had a molecular weight of 105 kDa. Full-length TaSPL6B transcription activity was not validated in yeast and subcellular localization analysis revealed that TaSPL6B was distributed in the nucleus. Ectopic expression of TaSPL6B in Arabidopsis led to increasing number of branches and early flowering. TaSPL6B was highly transcribed in internodes of transgenic Arabidopsis. The expression of AtSMXL6/AtSMXL7/AtSMXL8 (homologous genes of TaD53) was markedly increased, whereas the expression of AtSPL2 (homologous genes of TaSPL3) and AtBRC1 (homologous genes of TaTB1) was markedly reduced in the internodes of transgenic Arabidopsis. Besides, TaSPL6B, TaSPL3 and TaD53 interacted with one another, as demonstrated by yeast two-hybrid and bimolecular fluorescence complementation assays. Therefore, we speculated that TaSPL6B brought together TaD53 and TaSPL3 and enhanced the inhibition effect of TaD53 on TaSPL3 through integrating light and strigolactone signaling pathways, followed by suppression of TaTB1, a key repressor of tillering.

CONCLUSIONS

As a whole, our findings contribute to a better understanding of how SPL genes work in wheat and will be useful for further research into how TaSPL6B affects yield-related traits in wheat.

Carbohydrate distribution via SWEET17 is critical for Arabidopsis inflorescence branching under drought

Sugars Will Eventually be Exported Transporters (SWEETs) are the most recently discovered family of plant sugar transporters. By acting as uniporters, SWEETs facilitate the diffusion of sugars across cell membranes and play an important role in various physiological processes such as abiotic stress adaptation. AtSWEET17, a vacuolar fructose facilitator, was shown to be involved in the modulation of the root system during drought. In addition, previous studies have shown that overexpression of an apple homolog leads to increased drought tolerance in tomato plants. Therefore, SWEET17 might be a molecular element involved in plant responses to drought. However, the role and function of SWEET17 in above-ground tissues of Arabidopsis under drought stress remain elusive. By combining gene expression analysis and stem architecture with the sugar profiles of different above-ground tissues, we uncovered a putative role for SWEET17 in carbohydrate supply and thus cauline branch elongation, especially during periods of carbon limitation, as occurs under drought stress. Thus, SWEET17 seems to be involved in maintaining efficient plant reproduction under drought stress conditions.

OsNAC121 regulates root development, tillering, panicle morphology, and grain filling in rice plant

Transcription factors in coordination with phytohormones form an intricate regulatory network modulating vital cellular mechanisms like development, growth and senescence in plants. In this study, we have functionally characterized the transcription factor OsNAC121 by developing gene silencing and overexpressing transgenic rice plants, followed by detailed analyses of the plant architecture. Transgenic lines exhibited remodelling in crown root development, lateral root structure and density, tiller height and number, panicle and grain morphologies, underpinning the imbalanced auxin: cytokinin ratio due to perturbed auxin transportation. Application of cytokinin, auxin and abscisic acid increased OsNAC121 gene expression nearly 17-, 6- and 91-folds, respectively. qRT-PCR results showed differential expressions of auxin and cytokinin pathway genes, implying their altered levels. A 47-fold higher expression level of OsNAC121 during milky stage in untransformed rice, compared to 14-day old shoot tissue, suggests its crucial role in grain filling; as evidenced by a large number of undeveloped grains produced by the gene silenced lines. Crippled gravitropic response by the transgenic plants indicates their impaired auxin transport. Bioinformatics revealed that OsNAC121 interacts with co-repressor (TOPLESS) proteins and forms a part of the inhibitor complex OsIAA10, an essential core component of auxin signalling pathway. Therefore, OsNAC121 emerges as an important regulator of various aspects of plant architecture through modulation of crosstalk between auxin and cytokinin, altering their concentration gradient in the meristematic zones, and consequently modifying different plant organogenesis processes.

Exploring silique number in Brassica napus L.: Genetic and molecular advances for improving yield

Silique number is a crucial yield-related trait for the genetic enhancement of rapeseed (Brassica napus L.). The intricate molecular process governing the regulation of silique number involves various factors. Despite advancements in understanding the mechanisms regulating silique number in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), the molecular processes involved in controlling silique number in rapeseed remain largely unexplored. In this review, we identify candidate genes and review the roles of genes and environmental factors in regulating rapeseed silique number. We use genetic regulatory networks for silique number in Arabidopsis and grain number in rice to uncover possible regulatory pathways and molecular mechanisms involved in regulating genes associated with rapeseed silique number. A better understanding of the genetic network regulating silique number in rapeseed will provide a theoretical basis for the genetic improvement of this trait and genetic resources for the molecular breeding of high-yielding rapeseed.