OsSHI1 Regulates Plant Architecture Through Modulating the Transcriptional Activity of IPA1 in Rice

The molecular mechanism of transcription factor regulation of grain size in rice

Rice is a crucial food crop in China, and the continuous and stable improvement of rice yield is of great significance for ensuring national food security. Grain size in rice is closely related to thousand-grain weight, making it a key factor influencing yield. Identifying genes associated with grain size and elucidating their molecular mechanisms are essential for breeding high-yield, high-quality rice varieties. Transcription factors play a vital role in regulating plant growth and development, and many transcription factor families are crucial in controlling grain size in rice. Here, we review the mechanisms by which transcription factors regulate rice grain size, summarize and evaluate the regulatory mechanisms of transcription factors that have been discovered in recent decades to regulate rice grain size, construct two possible super networks composed of transcription factors as links to regulate rice grain size, and points out the application of transcription factors regulating grain size in rice breeding. This review will provide a roadmap for understanding the regulatory mechanisms of rice grain size and applying these genes to rice breeding using molecular breeding techniques.

Pan-Genome-Based Characterization of the SRS Transcription Factor Family in Foxtail Millet

The Short Internodes-Related Sequence (SRS) family, a class of plant-specific transcription factors crucial for diverse biological processes, was systematically investigated in foxtail millet using pan-genome data from 110 core germplasm resources as well as two high-quality genomes (xm and Yu1). We identified SRS members and analyzed their intra-species distribution patterns, including copy number variation (CNV) and interchromosomal translocations. A novel standardized nomenclature (Accession_SiSRSN[.n]_xDy or xTy) was proposed to unify gene family nomenclature, enabling the direct visualization of member number variation across germplasms and the identification of core/variable members while highlighting chromosomal translocations. Focusing on the two high-quality genomes, both harboring six core SRS members, we performed whole-genome collinearity analysis with Arabidopsis, rice, maize, soybean, and green foxtail. Ka/Ks analysis of collinear gene pairs revealed purifying selection acting on SiSRS genes. Promoter analysis identified abundant stress-responsive cis-elements. Among core members, the xm_SiSRS5 gene exhibited the highest expression during vegetative growth but showed significant downregulation under drought and salt stress, suggesting its role as a key negative regulator in abiotic stress responses. This study demonstrates the utility of pan-genomics in resolving gene family dynamics and establishes SiSRS5 as a critical target for stress tolerance engineering in foxtail millet.

Strigolactone promotes cotton fiber cell elongation by de-repressing DWARF53 on linolenic acid biosynthesis

Strigolactone (SL) is a plant hormone required for plant development. DWARF53 (D53) functions as a transcription repressor in SL signaling. However, the role of D53 in cotton (Gossypium hirsutum, Gh) fiber development remains unclear. Here, we identify that GhD53 suppresses fiber elongation by repressing transcription of GhFAD3 genes, which control linolenic acid (C18:3) biosynthesis. Mechanistically, GhD53 interacts with SL-related transcriptional activate factor (GhSLRF) to prevent its binding on Omega-3 fatty acid desaturase gene (GhFAD3) promoters, thereby inhibiting GhFAD3 transcription. Upon SL exposure, GhD53 is degraded and leads to GhSLRF activation. This activation further promotes GhFAD3 transcription, C18:3 biosynthesis, and fiber elongation. Our findings identify the molecular mechanism of how SL controls cell elongation via D53 and offer potential strategies to improve cotton quality through SL application.

LTD1 plays a key role in rice tillering regulation through cooperation with CycH1;1 and TFB2 subunits of the TFIIH complex

Tillering contributes greatly to grain yield in rice (Oryza sativa). At present, many genes involved in rice tillering regulation have been cloned and characterized. However, the identification of more novel genes is still necessary to fully understand the molecular mechanisms regulating rice tillering. In this study, we isolated a low-tillering and dwarf 1 (ltd1) mutant in indica rice. Map-based cloning and MutMap analysis showed that the candidate gene LTD1 (LOC_Os01g19760) encodes a putative FAM91A1 protein with an unknown function in plants. LTD1-complementation and -RNAi confirmed that LTD1 is responsible for the mutant phenotype of ltd1. The LTD1 protein is localized to the plasma membrane, endoplasmic reticulum, and multi-vesicular bodies. Furthermore, protein interaction and colocalization assays showed that LTD1 interacts with both the TFB2 subunit of the core subcomplex and the CycH1;1 subunit of the cyclin-dependent kinase-activating kinase (CAK) subcomplex of the TFIIH complex, and TFB2 also interacts with CycH1;1. qRT-PCR demonstrated that the expression levels of most genes related to the cell cycle are changed significantly in the ltd1 tiller buds, and flow cytometry assays revealed that there are more polyploid nuclei in the ltd1 leaves and roots, suggesting that LTD1 could be involved in cell cycle regulation. Taken together, our findings indicated that LTD1 plays a key role in rice tillering regulation by involvement in the cell cycle through cooperation with CycH1;1 and TFB2 subunits of TFIIH. This work also sheds light on the biological function of FAM91A1 in regulating important agronomic traits of rice.

Molecular mechanisms of high tiller development based on transcriptome and proteome correlation analysis in Poa pratensis

Poa pratensis, a high-quality forage and turfgrass, plays a significant role in grassland construction, biodiversity maintenance, and ecological restoration, and has considerable ecological value. Exploring the molecular mechanisms of high tillering occurrence in Kentucky bluegrass is an effective approach for understanding nutrient dense germplasm materials. Additionally, it provides a theoretical foundation for enhancements in plant yield and competitive survival. In this study, statistical analyses of tiller number and tiller node diameter in two wild Kentucky bluegrass germplasms from Gansu Province were conducted. Transcriptome and proteomic analyses were performed on the tillering nodes of these grasses at various tillering stages, aiming to identify the genes, proteins, and pathways that regulate tillering formation. The 'SN' variety was found to possess stronger tillering abilities and greater tillering potential. Through RNA sequencing (RNA-Seq) and DIA quantitative proteomics, a total of 331,749 Unigenes and 21,140 proteins were identified. Among these, 29,932 Unigenes exhibited differential expression and 6974 proteins demonstrated differential accumulation between the tillering nodes of the two varieties of Kentucky bluegrass. KEGG analysis indicated that differentially expressed genes and proteins were significantly enriched in pathways such as phenylpropanoid biosynthesis, plant hormone signal transduction, glutathione metabolism, starch and sucrose metabolism, as well as secondary metabolite biosynthesis. Joint transcriptome and proteome analysis identified 784, 733, and 483 genes/proteins that were coordinately expressed between the 'SN' and 'QS' varieties at the prophase, peak, and anaphase stages of tillering, respectively. KEGG analysis was conducted on these genes and proteins, revealing that pathways such as phenylpropanoid biosynthesis, glutathione metabolism, and photosynthesis were likely involved in regulating the growth and development of tillers. This study elucidated the biological and metabolic characteristics of Kentucky bluegrass at different tillering stages, aiding in the identification of genes and proteins associated with tillering formation. This work establishes a theoretical foundation for exploring the mechanisms of tillering formation in Kentucky bluegrass.

Genome-wide association and selection studies reveal genomic insight into saline-alkali tolerance in rice

Saline-alkali stress has detrimental effects on growth and development of rice (Oryza sativa L.). Domesticated rice cultivars with high saline-alkali tolerance (SAT) are essential for sustainable agriculture. To explore the genomic basis underlying SAT in rice, we integrate genome-wide association study (GWAS) with selective sweep analysis using a core population consisting of 234 cultivars grown in the saline and normal fields across three consecutive years and identify 70 genes associated with SAT with signals of selection and evolution between subpopulations of tolerance and sensitivity. We detected and subsequently characterized GATA19 trans-regulated SAT1/OsCYL4 that regulated SAT through reactive oxygen species (ROS) scavenging pathway. Our results provide a comprehensive insight into genome-wide natural variants and selection sweep underlying saline-alkali tolerance and pave avenues for SAT breeding through genome editing and genomic selection in rice.

Genome-wide association study of rice (Oryza sativa L.) inflorescence architecture

Rice yield strongly depends on panicle size and architecture but the genetics underlying these traits and their coordination with environmental cues through various signaling pathways have remained elusive. A genome-wide association study (GWAS) was performed to pinpoint the underlying genetic determinants for rice panicle architecture by analyzing 20 panicle-related traits using a data set consisting of 44,100 SNPs. We defined QTL windows around significant SNPs by the rate of LD decay for each chromosome and used these windows to identify putative candidate genes associated with the trait. Using a publicly available RNA-seq data set we performed analyses to identify the differentially expressed genes between stem and panicle with putative functions in panicle architecture. In total, 52 significant SNPs were identified, corresponding to 41 unique QTLs across the 12 rice chromosomes, with the most signals appearing on chromosome 1 (nine associated SNPs), and seven significant SNPs for each of chromosomes 8 and 12. Some novel genes such as Ankyrin, Duf, Kinesin and Brassinosteroid insensitive were found to be associated with panicle size. A haplotype analysis showed that genetic variation in haplotypes qMIL2 and qNSBBH21 were related to two traits, MIL, the greatest distance between two nodes on the rachis, and NSBBH, the number of primary branches in the bottom half of a panicle, respectively. Analysis of epistatic interactions revealed a marker affecting clustered traits. Several QTLs were identified on different chromosomes for the first time which may explain the phenotypic diversity of rice panicle architecture we observe in our collection of accessions. The identified candidate genes and haplotypes could be used in marker-assisted selection to improve rice yield through gene pyramiding.

Enhancing crop yields to ensure food security by optimizing photosynthesis

The crop yields achieved through traditional plant breeding techniques appear to be nearing a plateau. Therefore, it is essential to accelerate advancements in photosynthesis, the fundamental process by which plants convert light energy into chemical energy, to further enhance crop yields. Research focused on improving photosynthesis holds significant promise for increasing sustainable agricultural productivity and addressing challenges related to global food security. This review examines the latest advancements and strategies aimed at boosting crop yields by enhancing photosynthetic efficiency. There has been a linear increase in yield over the years in historically released germplasm selected through traditional breeding methods, and this increase is accompanied by improved photosynthesis. We explore various aspects of the light reactions designed to enhance crop yield, including light harvest efficiency through smart canopy systems, expanding the absorbed light spectrum to include far-red light, optimizing non-photochemical quenching, and accelerating electron transport flux. At the same time, we investigate carbon reactions that can enhance crop yield, such as manipulating Rubisco activity, improving the Calvin-Benson-Bassham (CBB) cycle, introducing CO2 concentrating mechanisms (CCMs) in C3 plants, and optimizing carbon allocation. These strategies could significantly impact crop yield enhancement and help bridge the yield gap.

Genetic Mapping by 55K Single-Nucleotide Polymorphism Array Reveals Candidate Genes for Tillering Trait in Wheat Mutant dmc

BACKGROUND

The tiller number is a key agronomic trait for increasing the yield potential of wheat (Triticum aestivum L.). A number of quantitative trait loci (QTLs) and key genes controlling tillering have been identified, but the regulatory mechanisms remain unclear.

METHODS

In this study, we utilized the dwarf-monoculm mutant (dmc) obtained from the ethyl methane sulfonate (EMS)-treated wheat cultivar Guomai 301. The F2 populations were constructed using the dmc mutant crossed to multiple tiller parents. The F2 populations were surveyed for tillering traits at the critical fertility stage for genetic analyses. The extreme-tillering-phenotype plants from the F2 population were used to construct mixing pools that were analyzed by a wheat 55K SNP array. The tillering genes of dmc were mapped using the wheat 55K SNP array combined with transcriptomic data.

RESULTS

The results showed that the genetic phenotype of dmc is controlled by two dominant genes. The tillering genes of dmc were mapped on the 60-100 Mb region of chromosome 5B and the 135-160 Mb region of chromosome 7A. A total of sixteen candidate genes associated with the tillering trait of dmc were identified. Two candidate genes, TraesCS5B02G058800 and TraesCS7A02G184200, were predicted to be involved in indole acetic acid (IAA) response and transport, which were considered as potential regulatory genes.

CONCLUSIONS

This study elucidated the genetic basis of the dmc mutant and provided two valuable reference genes for studying the development and regulatory mechanisms of wheat tillering.

Regulation of tillering and panicle branching in rice and wheat

Branching is a critical aspect of plant architecture that significantly impacts the yield and adaptability of staple cereal crops like rice and wheat. Cereal crops develop tillers during the vegetative stage and panicle or spike branches during the reproductive stage, respectively, both of which are significantly impacted by hormones and genetic factors. Tillering and panicle branching are closely interconnected and exhibit high environmental plasticity. Here, we summarize the recent progress in genetic, hormonal, and environmental factors regulation in the branching of rice and wheat. This review not only provides a comprehensive overview of the current knowledge on branching mechanisms in rice and wheat, but also explores the prospects for future research aimed at optimizing crop architecture for enhanced productivity.

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.

Natural variation in LONELY GUY-Like 1 regulates rice grain weight under warmer night conditions

Global nighttime temperatures are rising at twice the rate of daytime temperatures and pose a challenge for rice (Oryza sativa) production. High nighttime temperature (HNT) stress affects rice yield by reducing grain weight, size, and fertility. Although the genes associated with these yield parameters have been identified and characterized under normal temperatures, the genetic basis of grain weight regulation under HNT stress remains less explored. We examined the natural variation for rice single grain weight (SGW) under HNT stress imposed during grain development. A genome-wide association analysis identified several loci associated with grain weight under HNT stress. A locus, SGW1, specific to HNT conditions resolved to LONELY GUY-Like 1 (LOGL1), which encodes a putative cytokinin-activation enzyme. We demonstrated that LOGL1 contributes to allelic variation at SGW1. Accessions with lower LOGL1 transcript abundance had higher grain weight under HNT. This was supported by the higher grain weight of logl1-mutants relative to the wild type under HNT. Compared to logl1-mutants, LOGL1 over-expressers showed increased sensitivity to HNT. We showed that LOGL1 regulates the thiamin biosynthesis pathway, which is under circadian regulation, which in turn is likely perturbed by HNT stress. These findings provide a genetic source to enhance rice adaptation to warming night temperatures and improve our mechanistic understanding of HNT stress tolerance pathways.

A transcription factor of SHI family AaSHI1 activates artemisinin biosynthesis genes in Artemisia annua

BACKGROUND

Transcription factors (TFs) of plant-specific SHORT INTERNODES (SHI) family play a significant role in regulating development and metabolism in plants. In Artemisia annua, various TFs from different families have been discovered to regulate the accumulation of artemisinin. However, specific members of the SHI family in A. annua (AaSHIs) have not been identified to regulate the biosynthesis of artemisinin.

RESULTS

We found five AaSHI genes (AaSHI1 to AaSHI5) in the A. annua genome. The expression levels of AaSHI1, AaSHI2, AaSHI3 and AaSHI4 genes were higher in trichomes and young leaves, also induced by light and decreased when the plants were subjected to dark treatment. The expression pattern of these four AaSHI genes was consistent with the expression pattern of four structural genes of artemisinin biosynthesis and their specific regulatory factors. Dual-luciferase reporter assays, yeast one-hybrid assays, and transient transformation in A. annua provided the evidence that AaSHI1 could directly bind to the promoters of structural genes AaADS and AaCYP71AV1, and positively regulate their expressions. This study has presented candidate genes, with AaSHI1 in particular, that can be considered for the metabolic engineering of artemisinin biosynthesis in A. annua.

CONCLUSIONS

Overall, a genome-wide analysis of the AaSHI TF family of A. annua was conducted. Five AaSHIs were identified in A. annua genome. Among the identified AaSHIs, AaSHI1 was found to be localized to the nucleus and activate the expression of structural genes of artemisinin biosynthesis including AaADS and AaCYP71AV1. These results indicated that AaSHI1 had positive roles in modulating artemisinin biosynthesis, providing candidate genes for obtaining high-quality new A. annua germplasms.

Identification and Functional Studies on the Role of PlSPL14 in Herbaceous Peony Stem Development

Stem strength plays a crucial role in the growth and development of plants, as well as in their flowering and fruiting. It not only impacts the lodging resistance of crops, but also influences the ornamental value of ornamental plants. Stem development is closely linked to stem strength; however, the roles of the SPL transcription factors in the stem development of herbaceous peony (Paeonia lactiflora Pall.) are not yet fully elucidated. In this study, we obtained and cloned the full-length sequence of PlSPL14, encoding 1085 amino acids. Quantitative real-time PCR (qRT-PCR) analysis revealed that the expression level of PlSPL14 gradually increased with the stem development of P. lactiflora and was significantly expressed in vascular bundles. Subsequently, utilizing the techniques of virus-induced gene silencing (VIGS) and heterologous overexpression in tobacco (Nicotiana tabacum L.), it was determined that PlSPL14-silenced P. lactiflora had a thinner xylem thickness, a decreased stem diameter, and weakened stem strength, while PlSPL14-overexpressing tobacco resulted in a thicker xylem thickness, an increased stem diameter, and enhanced stem strength. Further screening of the interacting proteins of PlSPL14 using a yeast two-hybrid (Y2H) assay revealed an interactive relationship between PlSPL14 and PlSLR1 protein, which acts as a negative regulator of gibberellin (GA). Additionally, the expression level of PlSLR1 gradually decreased during the stem development of P. lactiflora. The above results suggest that PlSPL14 may play a positive regulatory role in stem development and act in the xylem, making it a potential candidate gene for enhancing stem straightness in plants.

The elite haplotype OsGATA8-H coordinates nitrogen uptake and productive tiller formation in rice

Excessive nitrogen promotes the formation of nonproductive tillers in rice, which decreases nitrogen use efficiency (NUE). Developing high-NUE rice cultivars through balancing nitrogen uptake and the formation of productive tillers remains a long-standing challenge, yet how these two processes are coordinated in rice remains elusive. Here we identify the transcription factor OsGATA8 as a key coordinator of nitrogen uptake and tiller formation in rice. OsGATA8 negatively regulates nitrogen uptake by repressing transcription of the ammonium transporter gene OsAMT3.2. Meanwhile, it promotes tiller formation by repressing the transcription of OsTCP19, a negative modulator of tillering. We identify OsGATA8-H as a high-NUE haplotype with enhanced nitrogen uptake and a higher proportion of productive tillers. The geographical distribution of OsGATA8-H and its frequency change in historical accessions suggest its adaption to the fertile soil. Overall, this study provides molecular and evolutionary insights into the regulation of NUE and facilitates the breeding of rice cultivars with higher NUE.

OsPRMT6a-mediated arginine methylation of OsJAZ1 regulates jasmonate signaling and spikelet development in rice

Although both protein arginine methylation (PRMT) and jasmonate (JA) signaling are crucial for regulating plant development, the relationship between these processes in the control of spikelet development remains unclear. In this study, we used the CRISPR/Cas9 technology to generate two OsPRMT6a loss-of-function mutants that exhibit various abnormal spikelet structures. Interestingly, we found that OsPRMT6a can methylate arginine residues in JA signal repressors OsJAZ1 and OsJAZ7. We showed that arginine methylation of OsJAZ1 enhances the binding affinity of OsJAZ1 with the JA receptors OsCOI1a and OsCOI1b in the presence of JAs, thereby promoting the ubiquitination of OsJAZ1 by the SCFOsCOI1a/OsCOI1b complex and degradation via the 26S proteasome. This process ultimately releases OsMYC2, a core transcriptional regulator in the JA signaling pathway, to activate or repress JA-responsive genes, thereby maintaining normal plant (spikelet) development. However, in the osprmt6a-1 mutant, reduced arginine methylation of OsJAZ1 impaires the interaction between OsJAZ1 and OsCOI1a/OsCOI1b in the presence of JAs. As a result, OsJAZ1 proteins become more stable, repressing JA responses, thus causing the formation of abnormal spikelet structures. Moreover, we discovered that JA signaling reduces the OsPRMT6a mRNA level in an OsMYC2-dependent manner, thereby establishing a negative feedback loop to balance JA signaling. We further found that OsPRMT6a-mediated arginine methylation of OsJAZ1 likely serves as a switch to tune JA signaling to maintain normal spikelet development under harsh environmental conditions such as high temperatures. Collectively, our study establishes a direct molecular link between arginine methylation and JA signaling in rice.

Blocking of amino acid transporter OsAAP7 promoted tillering and yield by determining basic and neutral amino acids accumulation in rice

BACKGROUND

Amino acids are not only the main form of N in rice, but also are vital for its growth and development. These processes are facilitated by amino acid transporters within the plant. Despite their significance, only a few AAP amino acid transporters have been reported.

RESULTS

In this study, we observed that there were differences in the expression of amino acid transporter OsAAP7 among 521 wild cultivated rice varieties, and it directly negatively correlated with tillering and grain yield per plant. We revealed that OsAAP7 protein was localized to the endoplasmic reticulum and had absorption and transport affinity for amino acids such as phenylalanine (Phe), lysine (Lys), leucine (Leu), and arginine (Arg) using subcellular localization, yeast substrate testing, fluorescent amino acid uptake, and amino acid content determination. Further hydroponic studies showed that exogenous application of amino acids Phe, Lys and Arg inhibited the growth of axillary buds in the overexpression lines, and promoted the elongation of axillary buds in the mutant lines. Finally, RNA-seq analysis showed that the expression patterns of genes related to nitrogen, auxin and cytokinin pathways were changed in axillary buds of OsAAP7 transgenic plants.

CONCLUSIONS

This study revealed the gene function of OsAAP7, and found that blocking of amino acid transporter OsAAP7 with CRISPR/Cas9 technology promoted tillering and yield by determining basic and neutral amino acids accumulation in rice.

AmDHN4, a winter accumulated SKn-type dehydrin from Ammopiptanthus mongolicus, and regulated by AmWRKY45, enhances the tolerance of Arabidopsis to low temperature and osmotic stress

Ammopiptanthus mongolicus, a rare temperate evergreen broadleaf shrub, exhibits remarkable tolerance to low temperature and drought stress in winter. Late embryogenesis abundant (LEA) proteins, a kind of hydrophilic protein with a protective function, play significant roles in enhancing plant tolerance to abiotic stress. In this present study, we analyzed the evolution and expression of LEA genes in A. mongolicus, and investigated the function and regulatory mechanism of dehydrin under abiotic stresses. Evolutionary analysis revealed that 14 AmLEA genes underwent tandem duplication events, and 36 AmLEA genes underwent segmental duplication events Notably, an expansion in SKn-type dehydrins was observed. Expression analysis showed that AmDHN4, a SKn-type dehydrin, was up-regulated in winter and under low temperature and osmotic stresses. Functional analysis showcased that the heterologous expression of the AmDHN4 enhanced the tolerance of yeast and tobacco to low temperature stress. Additionally, the overexpression of AmDHN4 significantly improved the tolerance of transgenic Arabidopsis to low temperature, drought, and osmotic stress. Further investigations identified AmWRKY45, a downstream transcription factor in the jasmonic acid signaling pathway, binding to the AmDHN4 promoter and positively regulating its expression. In summary, these findings contribute to a deeper understanding of the functional and regulatory mechanisms of dehydrin.

OsCSN2 orchestrates Oryza sativa L. growth and development through modulation of the GA and BR pathways

The COP9 signalosome (CSN) is a conserved protein complex found in higher eukaryotes, consisting of eight subunits, and it plays a crucial role in regulating various processes of plant growth and development. Among these subunits, CSN2 is one of the most conserved components within the COP9 signalosome complex. Despite its prior identification in other species, its specific function in Oryza sativa L. (Rice) has remained poorly understood. In this study, we investigated the role of CSN2 in rice using gene editing CRISPR/Cas9 technology and overexpression techniques. We created two types of mutants: the oscsn2 mutant and the OsCSN2-OE mutant, both in the background of rice, and also generated point mutants of OsCSN2 (OsCSN2K64E, OsCSN2K67E, OsCSN2K71E and OsCSN2K104E) to further explore the regulatory function of OsCSN2. Phenotypic observation and gene expression analysis were conducted on plants from the generated mutants, tracking their growth from the seedling to the heading stages. The results showed that the loss and modification of OsCSN2 had limited effects on plant growth and development during the early stages of both the wild-type and mutant plants. However, as the plants grew to 60 days, significant differences emerged. The OsCSN2 point mutants exhibited increased tillering compared to the OsCSN2-OE mutant plants, which were already at the tillering stage. On the other hand, the OsCSN2 point mutant had already progressed to the heading and flowering stages, with the shorter plants. These results, along with functional predictions of the OsCSN2 protein, indicated that changes in the 64th, 67th, 71st, and 104th amino acids of OsCSN2 affected its ubiquitination site, influencing the ubiquitination function of CSN and consequently impacting the degradation of the DELLA protein SLR1. Taken together, it can be speculated that OsCSN2 plays a key role in GA and BR pathways by influencing the functional regulation of the transcription factor SLR1 in CSN, thereby affecting the growth and development of rice and the number of tillers.

Potential of rice tillering for sustainable food production

Tillering, also known as shoot branching, is a fundamental trait for cereal crops such as rice to produce sufficient panicle numbers. Effective tillering that guarantees successful panicle production is essential for achieving high crop yields. Recent advances in molecular biology have revealed the mechanisms underlying rice tillering; however, in rice breeding and cultivation, there remain limited genes or alleles suitable for effective tillering and high yields. A recently identified quantitative trait locus (QTL) called MORE PANICLES 3 (MP3) has been cloned as a single gene and shown to promote tillering and to moderately increase panicle number. This gene is an ortholog of the maize domestication gene TB1, and it has the potential to increase grain yield under ongoing climate change and in nutrient-poor environments. This review reconsiders the potential and importance of tillering for sustainable food production. Thus, I provide an overview of rice tiller development and the currently understood molecular mechanisms that underly it, focusing primarily on the biosynthesis and signaling of strigolactones, effective QTLs, and the importance of MP3 (TB1). The possible future benefits in using promising QTLs such as MP3 to explore agronomic solutions under ongoing climate change and in nutrient-poor environments are also highlighted.

The OsNLP3/4-OsRFL module regulates nitrogen-promoted panicle architecture in rice

Rice panicles, a major component of yield, are regulated by phytohormones and nutrients. How mineral nutrients promote panicle architecture remains largely unknown. Here, we report that NIN-LIKE PROTEIN3 and 4 (OsNLP3/4) are crucial positive regulators of rice panicle architecture in response to nitrogen (N). Loss-of-function mutants of either OsNLP3 or OsNLP4 produced smaller panicles with reduced primary and secondary branches and fewer grains than wild-type, whereas their overexpression plants showed the opposite phenotypes. The OsNLP3/4-regulated panicle architecture was positively correlated with N availability. OsNLP3/4 directly bind to the promoter of OsRFL and activate its expression to promote inflorescence meristem development. Furthermore, OsRFL activates OsMOC1 expression by binding to its promoter. Our findings reveal the novel N-responsive OsNLP3/4-OsRFL-OsMOC1 module that integrates N availability to regulate panicle architecture, shedding light on how N nutrient signals regulate panicle architecture and providing candidate targets for the improvement of crop yield.

LESION SIMULATING DISEASE 3 regulates disease resistance via fine-tuning histone acetylation in cassava

Bacterial blight seriously affects the growth and production of cassava (Manihot esculenta Crantz), but disease resistance genes and the underlying molecular mechanism remain unknown. In this study, we found that LESION SIMULATING DISEASE 3 (MeLSD3) is essential for disease resistance in cassava. MeLSD3 physically interacts with SIRTUIN 1 (MeSRT1), inhibiting MeSRT1-mediated deacetylation modification at the acetylation of histone 3 at K9 (H3K9Ac). This leads to increased H3K9Ac levels and transcriptional activation of SUPPRESSOR OF BIR1 (SOBIR1) and FLAGELLIN-SENSITIVE2 (FLS2) in pattern-triggered immunity, resulting in immune responses in cassava. When MeLSD3 was silenced, the release of MeSRT1 directly decreased H3K9Ac levels and inhibited the transcription of SOBIR1 and FLS2, leading to decreased disease resistance. Notably, DELLA protein GIBBERELLIC ACID INSENSITIVE 1 (MeGAI1) also interacted with MeLSD3, which enhanced the interaction between MeLSD3 and MeSRT1 and further strengthened the inhibition of MeSRT1-mediated deacetylation modification at H3K9Ac of defense genes. In summary, this study illustrates the mechanism by which MeLSD3 interacts with MeSRT1 and MeGAI1, thereby mediating the level of H3K9Ac and the transcription of defense genes and immune responses in cassava.

Unlocking the Multifaceted Mechanisms of Bud Outgrowth: Advances in Understanding Shoot Branching

Shoot branching is a complex and tightly regulated developmental process that is essential for determining plant architecture and crop yields. The outgrowth of tiller buds is a crucial step in shoot branching, and it is influenced by a variety of internal and external cues. This review provides an extensive overview of the genetic, plant hormonal, and environmental factors that regulate shoot branching in several plant species, including rice, Arabidopsis, tomato, and wheat. We especially highlight the central role of TEOSINTE BRANCHED 1 (TB1), a key gene in orchestrating bud outgrowth. In addition, we discuss how the phytohormones cytokinins, strigolactones, and auxin interact to regulate tillering/branching. We also shed light on the involvement of sugar, an integral component of plant development, which can impact bud outgrowth in both trophic and signaling ways. Finally, we emphasize the substantial influence of environmental factors, such as light, temperature, water availability, biotic stresses, and nutrients, on shoot branching. In summary, this review offers a comprehensive evaluation of the multifaced regulatory mechanisms that underpin shoot branching and highlights the adaptable nature of plants to survive and persist in fluctuating environmental conditions.

Identification of SRS transcription factor family in Solanum lycopersicum, and functional characterization of their responses to hormones and abiotic stresses

The SHI RELATED SEQUENCE (SRS) family plays a vital role in the development of multiple plant organs such as floral meristem determinacy, organ morphogenesis, and signal transduction. Nevertheless, there is little understanding of the biological significance of tomato SRS family at this point. Our research identified eight SlSRS family members and classified them into three subfamilies based on phylogenetics, conserved motifs, and characteristic domain analysis. The intraspecies and interspecies collinearity analysis revealed clues of SRS family evolution. Many cis-elements related to hormones, stresses, and plant development can be found in the promoter region of SlSRS genes. All of eight SlSRS proteins were located in the nucleus and possessed transcriptional activity, half of which were transcriptional activators, and the other half were transcriptional repressors. Except for SlSRS1, which showed high transcript accumulation in vegetative organs, most SlSRS genes expressed ubiquitously in all flower organs. In addition, all SlSRS genes could significantly respond to at least four different plant hormones. Further, expression of SlSRS genes were regulated by various abiotic stress conditions. In summary, we systematically analyzed and characterized the SlSRS family, reviewed the expression patterns and preliminarily investigated the protein function, and provided essential information for further functional research of the tomato SRS genes in the determination of reproductive floral organs and the development of plants, and possibly other plants.

OsMDH12: A Peroxisomal Malate Dehydrogenase Regulating Tiller Number and Salt Tolerance in Rice

Salinity is an important environmental factor influencing crop growth and yield. Malate dehydrogenase (MDH) catalyses the reversible conversion of oxaloacetate (OAA) to malate. While many MDHs have been identified in various plants, the biochemical function of MDH in rice remains uncharacterised, and its role in growth and salt stress response is largely unexplored. In this study, the biochemical function of OsMDH12 was determined, revealing its involvement in regulating tiller number and salt tolerance in rice. OsMDH12 localises in the peroxisome and is expressed across various organs. In vitro analysis confirmed that OsMDH12 converts OAA to malate. Seedlings of OsMDH12-overexpressing (OE) plants had shorter shoot lengths and lower fresh weights than wild-type (WT) plants, while osmdh12 mutants displayed the opposite. At maturity, OsMDH12-OE plants had fewer tillers than WT, whereas osmdh12 mutants had more, suggesting OsMDH12's role in tiller number regulation. Moreover, OsMDH12-OE plants were sensitive to salt stress, but osmdh12 mutants showed enhanced salt tolerance. The Na+/K+ content ratio increased in OsMDH12-OE plants and decreased in osmdh12 mutants, suggesting that OsMDH12 might negatively affect salt tolerance through influencing the Na+/K+ balance. These findings hint at OsMDH12's potential as a genetic tool to enhance rice growth and salt tolerance.

Advances in cis-element- and natural variation-mediated transcriptional regulation and applications in gene editing of major crops

Transcriptional regulation is crucial to control of gene expression. Both spatio-temporal expression patterns and expression levels of genes are determined by the interaction between cis-acting elements and trans-acting factors. Numerous studies have focused on the trans-acting factors that mediate transcriptional regulatory networks. However, cis-acting elements, such as enhancers, silencers, transposons, and natural variations in the genome, are also vital for gene expression regulation and could be utilized by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated gene editing to improve crop quality and yield. In this review, we discuss current understanding of cis-element-mediated transcriptional regulation in major crops, including rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays), as well as the latest advancements in gene editing techniques and their applications in crops to highlight prospective strategies for crop breeding.

Revitalizing miRNAs mediated agronomical advantageous traits improvement in rice

One of the key enigmas in conventional and modern crop improvement programmes is how to introduce beneficial traits without any penalty impairment. Rice (Oryza sativa L.), among the essential staple food crops grown and utilized worldwide, needs to improve genotypes in multifaceted ways. With the global view to feed ten billion under the climatic perturbation, only a potent functional master regulator can withstand with hope for the next green revolution and food security. miRNAs are such, miniature, fine tuners for crop improvement and provide a value addition in emerging technologies, namely large-scale genotyping, phenotyping, genome editing, marker-assisted selection, and genomic selection, to make rice production feasible. There has been surplus research output generated since the last decade on miRNAs in rice, however, recent functional knowledge is limited to reaping the benefits for conventional and modern improvements in rice to avoid ambiguity and redundancy in the generated data. Here, we present the latest functional understanding of miRNAs in rice. In addition, their biogenesis, intra- and inter-kingdom signaling and communication, implication of amiRNAs, and consequences upon integration with CRISPR-Cas9. Further, highlights refer to the application of miRNAs for rice agronomical trait improvements, broadly classified into three functional domains. The majority of functionally established miRNAs are responsible for growth and development, followed by biotic and abiotic stresses. Tabular cataloguing reveals and highlights two multifaceted modules that were extensively studied. These belong to miRNA families 156 and 396, orchestrate multifarious aspects of advantageous agronomical traits. Moreover, updated and exhaustive functional aspects of different supplemental miRNA modules that would strengthen rice improvement are also being discussed.

Genome assembly and resequencing analyses provide new insights into the evolution, domestication and ornamental traits of crape myrtle

Crape myrtle (Lagerstroemia indica) is a globally used ornamental woody plant and is the representative species of Lagerstroemia. However, studies on the evolution and genomic breeding of L. indica have been hindered by the lack of a reference genome. Here we assembled the first high-quality genome of L. indica using PacBio combined with Hi-C scaffolding to anchor the 329.14-Mb genome assembly into 24 pseudochromosomes. We detected a previously undescribed independent whole-genome triplication event occurring 35.5 million years ago in L. indica following its divergence from Punica granatum. After resequencing 73 accessions of Lagerstroemia, the main parents of modern crape myrtle cultivars were found to be L. indica and L. fauriei. During the process of domestication, genetic diversity tended to decrease in many plants, but this was not observed in L. indica. We constructed a high-density genetic linkage map with an average map distance of 0.33 cM. Furthermore, we integrated the results of quantitative trait locus (QTL) using genetic mapping and bulk segregant analysis (BSA), revealing that the major-effect interval controlling internode length (IL) is located on chr1, which contains CDL15, CRG98, and GID1b1 associated with the phytohormone pathways. Analysis of gene expression of the red, purple, and white flower-colour flavonoid pathways revealed that differential expression of multiple genes determined the flower colour of L. indica, with white flowers having the lowest gene expression. In addition, BSA of purple- and green-leaved individuals of populations of L. indica was performed, and the leaf colour loci were mapped to chr12 and chr17. Within these intervals, we identified MYB35, NCED, and KAS1. Our genome assembly provided a foundation for investigating the evolution, population structure, and differentiation of Myrtaceae species and accelerating the molecular breeding of L. indica.

A high-resolution genotype-phenotype map identifies the TaSPL17 controlling grain number and size in wheat

BACKGROUND

Large-scale genotype-phenotype association studies of crop germplasm are important for identifying alleles associated with favorable traits. The limited number of single-nucleotide polymorphisms (SNPs) in most wheat genome-wide association studies (GWASs) restricts their power to detect marker-trait associations. Additionally, only a few genes regulating grain number per spikelet have been reported due to sensitivity of this trait to variable environments.

RESULTS

We perform a large-scale GWAS using approximately 40 million filtered SNPs for 27 spike morphology traits. We detect 132,086 significant marker-trait associations and the associated SNP markers are located within 590 associated peaks. We detect additional and stronger peaks by dividing spike morphology into sub-traits relative to GWAS results of spike morphology traits. We propose that the genetic dissection of spike morphology is a powerful strategy to detect signals for grain yield traits in wheat. The GWAS results reveal that TaSPL17 positively controls grain size and number by regulating spikelet and floret meristem development, which in turn leads to enhanced grain yield per plant. The haplotypes at TaSPL17 indicate geographical differentiation, domestication effects, and breeding selection.

CONCLUSION

Our study provides valuable resources for genetic improvement of spike morphology and a fast-forward genetic solution for candidate gene detection and cloning in wheat.

The transcriptional hub SHORT INTERNODES1 integrates hormone signals to orchestrate rice growth and development

Plants have evolved sophisticated mechanisms to coordinate their growth and stress responses via integrating various phytohormone signaling pathways. However, the precise molecular mechanisms orchestrating integration of the phytohormone signaling pathways remain largely obscure. In this study, we found that the rice (Oryza sativa) short internodes1 (shi1) mutant exhibits typical auxin-deficient root development and gravitropic response, brassinosteroid (BR)-deficient plant architecture and grain size as well as enhanced abscisic acid (ABA)-mediated drought tolerance. Additionally, we found that the shi1 mutant is also hyposensitive to auxin and BR treatment but hypersensitive to ABA. Further, we showed that OsSHI1 promotes the biosynthesis of auxin and BR by activating the expression of OsYUCCAs and D11, meanwhile dampens ABA signaling by inducing the expression of OsNAC2, which encodes a repressor of ABA signaling. Furthermore, we demonstrated that 3 classes of transcription factors, AUXIN RESPONSE FACTOR 19 (OsARF19), LEAF AND TILLER ANGLE INCREASED CONTROLLER (LIC), and OsZIP26 and OsZIP86, directly bind to the promoter of OsSHI1 and regulate its expression in response to auxin, BR, and ABA, respectively. Collectively, our results unravel an OsSHI1-centered transcriptional regulatory hub that orchestrates the integration and self-feedback regulation of multiple phytohormone signaling pathways to coordinate plant growth and stress adaptation.

Rice microRNA156/529-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE7/14/17 modules regulate defenses against bacteria

Rice (Oryza sativa L.) microRNA156/529-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE7/14/17 (miR156/529-SPL7/14/17) modules have pleiotropic effects on many biological pathways. OsSPL7/14 can interact with DELLA protein SLENDER RICE1 (SLR1) to modulate gibberellin acid (GA) signal transduction against the bacterial pathogen Xanthomonas oryzae pv. oryzae. However, whether the miR156/529-OsSPL7/14/17 modules also regulate resistance against other pathogens is unclear. Notably, OsSPL7/14/17 functioning as transcriptional activators, their target genes, and the corresponding downstream signaling pathways remain largely unexplored. Here, we demonstrate that miR156/529 play negative roles in plant immunity and that miR156/529-regulated OsSPL7/14/17 confer broad-spectrum resistance against 2 devastating bacterial pathogens. Three OsSPL7/14/17 proteins directly bind to the promoters of rice Allene Oxide Synthase 2 (OsAOS2) and NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 (OsNPR1) and activate their transcription, regulating jasmonic acid (JA) accumulation and the salicylic acid (SA) signaling pathway, respectively. Overexpression of OsAOS2 or OsNPR1 impairs the susceptibility of the osspl7/14/17 triple mutant. Exogenous application of JA enhances resistance of the osspl7/14/17 triple mutant and the miR156 overexpressing plants. In addition, genetic evidence confirms that bacterial pathogen-activated miR156/529 negatively regulate pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) responses, such as pattern recognition receptor Xa3/Xa26-initiated PTI. Our findings demonstrate that bacterial pathogens modulate miR156/529-OsSPL7/14/17 modules to suppress OsAOS2-catalyzed JA accumulation and the OsNPR1-promoted SA signaling pathway, facilitating pathogen infection. The uncovered miR156/529-OsSPL7/14/17-OsAOS2/OsNPR1 regulatory network provides a potential strategy to genetically improve rice disease resistance.

Natural variation in Tiller Number 1 affects its interaction with TIF1 to regulate tillering in rice

Tiller number per plant-a cardinal component of ideal plant architecture-affects grain yield potential. Thus, alleles positively affecting tillering must be mined to promote genetic improvement. Here, we report a Tiller Number 1 (TN1) protein harbouring a bromo-adjacent homology domain and RNA recognition motifs, identified through genome-wide association study of tiller numbers. Natural variation in TN1 affects its interaction with TIF1 (TN1 interaction factor 1) to affect DWARF14 expression and negatively regulate tiller number in rice. Further analysis of variations in TN1 among indica genotypes according to geographical distribution revealed that low-tillering varieties with TN1-hap^L are concentrated in Southeast Asia and East Asia, whereas high-tillering varieties with TN1-hap^H are concentrated in South Asia. Taken together, these results indicate that TN1 is a tillering regulatory factor whose alleles present apparent preferential utilization across geographical regions. Our findings advance the molecular understanding of tiller development.

A conserved brassinosteroid-mediated BES1-CERP-EXPA3 signaling cascade controls plant cell elongation

Continuous plant growth is achieved by cell division and cell elongation. Brassinosteroids control cell elongation and differentiation throughout plant life. However, signaling cascades underlying BR-mediated cell elongation are unknown. In this study, we introduce cotton fiber, one of the most representative single-celled tissues, to decipher cell-specific BR signaling. We find that gain of function of GhBES1, a key transcriptional activator in BR signaling, enhances fiber elongation. The chromatin immunoprecipitation sequencing analysis identifies a cell-elongation-related protein, GhCERP, whose transcription is directly activated by GhBES1. GhCERP, a downstream target of GhBES1, transmits the GhBES1-mediated BR signaling to its target gene, GhEXPA3-1. Ultimately, GhEXPA3-1 promotes fiber cell elongation. In addition, inter-species functional analysis of the BR-mediated BES1-CERP-EXPA3 signaling cascade also promotes Arabidopsis root and hypocotyl growth. We propose that the BES1-CERP-EXPA3 module may be a broad-spectrum pathway that is universally exploited by diverse plant species to regulate BR-promoted cell elongation.

Identification of candidate genes responsible for chasmogamy in wheat

BACKGROUND

The flowering biology of wheat plants favours self-pollination which causes obstacles in wheat hybrid breeding. Wheat flowers can be divided into two groups, the first one is characterized by flowering and pollination within closed flowers (cleistogamy), while the second one possesses the ability to open flowers during processes mentioned above (chasmogamy). The swelling of lodicules is involved in the flowering of cereals and among others their morphology, calcium and potassium content differentiate between cleistogamic and non-cleistogamous flowers. A better understanding of the chasmogamy mechanism can lead to the development of tools for selection of plants with the desired outcrossing rate. To learn more, the sequencing of transcriptomes (RNA-Seq) and Representational Difference Analysis products (RDA-Seq) were performed to investigate the global transcriptomes of wheat lodicules in two highly chasmogamous (HCH, Piko and Poezja) and two low chasmogamous (LCH, Euforia and KWS Dacanto) varieties at two developmental stages-pre-flowering and early flowering.

RESULTS

The differentially expressed genes were enriched in five, main pathways: "metabolism", "organismal systems", "genetic information processing", "cellular processes" and "environmental information processing", respectively. Important genes with opposite patterns of regulation between the HCH and LCH lines have been associated with the lodicule development i.e. expression levels of MADS16 and MADS58 genes may be responsible for quantitative differences in chasmogamy level in wheat.

CONCLUSIONS

We conclude that the results provide a new insight into lodicules involvement in the wheat flowering process. This study generated important genomic information to support the exploitation of the chasmogamy in wheat hybrid breeding programs.

Combined genome-wide association study and epistasis analysis reveal multifaceted genetic architectures of plant height in Asian cultivated rice

Plant height (PH) in rice (Oryza sativa) is an important trait for its adaptation and agricultural performance. Discovery of the semi-dwarf1 (SD1) mutation initiated the Green Revolution, boosting rice yield and fitness, but the underlying genetic regulation of PH in rice remains largely unknown. Here, we performed genome-wide association study (GWAS) and identified 12 non-repetitive QTL/genes regulating PH variation in 619 Asian cultivated rice accessions. One of these was an SD1 structural variant, not normally detected in standard GWAS analyses. Given the strong effect of SD1 on PH, we also divided 619 accessions into subgroups harbouring distinct SD1 haplotypes, and found a further 85 QTL/genes for PH, revealing genetic heterogeneity that may be missed by analysing a broad, diverse population. Moreover, we uncovered two epistatic interaction networks of PH-associated QTL/genes in the japonica (Geng)-dominant SD1^NIP subgroup. In one of them, the hub QTL/gene qphSN1.4/GAMYB interacted with qphSN3.1/OsINO80, qphSN3.4/HD16/EL1, qphSN6.2/LOC_Os06g11130, and qphSN10.2/MADS56. Sequence variations in GAMYB and MADS56 were associated with their expression levels and PH variations, and MADS56 was shown to physically interact with MADS57 to coregulate expression of gibberellin (GA) metabolic genes OsGA2ox3 and Elongated Uppermost Internode1 (EUI1). Our study uncovered the multifaceted genetic architectures of rice PH, and provided novel and abundant genetic resources for breeding semi-dwarf rice and new candidates for further mechanistic studies on regulation of PH in rice.

A regulatory loop establishes the link between the circadian clock and abscisic acid signaling in rice

There is a close regulatory relationship between the circadian clock and the abscisic acid (ABA) signaling pathway in regulating many developmental processes and stress responses. However, the exact feedback regulation mechanism between them is still poorly understood. Here, we identified the rice (Oryza sativa) clock component PSEUDO-RESPONSE REGULATOR 95 (OsPRR95) as a transcriptional regulator that accelerates seed germination and seedling growth by inhibiting ABA signaling. We also found that OsPRR95 binds to the ABA receptor gene REGULATORY COMPONENTS OF ABA RECEPTORS10 (OsRCAR10) DNA and inhibits its expression. Genetic analysis showed OsRCAR10 acts downstream of OsPRR95 in mediating ABA responses. In addition, the induction of OsPRR95 by ABA partly required a functional OsRCAR10, and the ABA-responsive element-binding factor ABSCISIC ACID INSENSITIVE5 (OsABI5) bound directly to the promoter of OsPRR95 and activated its expression, thus establishing a regulatory feedback loop between OsPRR95, OsRCAR10, and OsABI5. Taken together, our results demonstrated that the OsRCAR10-OsABI5-OsPRR95 feedback loop modulates ABA signaling to fine-tune seed germination and seedling growth, thus establishing the molecular link between ABA signaling and the circadian clock.

The DnaJ domain-containing heat-shock protein NAL11 determines plant architecture by mediating gibberellin homeostasis in rice (Oryza sativa)

Ideal Plant Architecture 1 (IPA1) is a key regulator of plant architecture. However, knowledge of downstream genes applicable for improving rice plant architecture is very limited. We identified the plant architecture regulatory gene NARROW LEAF 11 (NAL11), which encodes a heat-shock protein (HSP) containing a DnaJ domain. A promising rare allele of NAL11 (NAL11^-923del-1552 ) positively selected in Aus cultivars was identified; this allele exhibited increased expression and generated relatively few tillers, thick stems, and large panicles, components of the ideal plant architecture (IPA). NAL11 is involved in regulating the cell cycle and cell proliferation. NAL11 loss-of-function mutants present impaired chloroplast development and gibberellin (GA) defects. Biochemical analyses show that IPA1 directly binds to elements in the missing fragment of the NAL11^-923del-1552 promoter and negatively regulates NAL11 expression. Genetic analyses support the hypothesis that NAL11 acts downstream of IPA1 to regulate IPA by modulating GA homeostasis, and NAL11 may be an essential complement for IPA1. Our work revealed that avoidance of the inhibition of NAL11^-923del-1552 caused by IPA1 represents a positive strategy for rescuing GA defects accompanied by the upregulation of IPA1 in breeding high-yield rice.

A wheat integrative regulatory network from large-scale complementary functional datasets enables trait-associated gene discovery for crop improvement

Gene regulation is central to all aspects of organism growth, and understanding it using large-scale functional datasets can provide a whole view of biological processes controlling complex phenotypic traits in crops. However, the connection between massive functional datasets and trait-associated gene discovery for crop improvement is still lacking. In this study, we constructed a wheat integrative gene regulatory network (wGRN) by combining an updated genome annotation and diverse complementary functional datasets, including gene expression, sequence motif, transcription factor (TF) binding, chromatin accessibility, and evolutionarily conserved regulation. wGRN contains 7.2 million genome-wide interactions covering 5947 TFs and 127 439 target genes, which were further verified using known regulatory relationships, condition-specific expression, gene functional information, and experiments. We used wGRN to assign genome-wide genes to 3891 specific biological pathways and accurately prioritize candidate genes associated with complex phenotypic traits in genome-wide association studies. In addition, wGRN was used to enhance the interpretation of a spike temporal transcriptome dataset to construct high-resolution networks. We further unveiled novel regulators that enhance the power of spike phenotypic trait prediction using machine learning and contribute to the spike phenotypic differences among modern wheat accessions. Finally, we developed an interactive webserver, wGRN (http://wheat.cau.edu.cn/wGRN), for the community to explore gene regulation and discover trait-associated genes. Collectively, this community resource establishes the foundation for using large-scale functional datasets to guide trait-associated gene discovery for crop improvement.

The plant specific SHORT INTERNODES/STYLISH (SHI/STY) proteins: Structure and functions

Plant specific SHORT INTERNODES/STYLISH (SHI/STY) protein is a transcription factor involved in the formation and development of early lateral organs in plants. However, research on the SHI/STY protein family is not focused enough. In this article, we review recent studies on SHI/STY genes and explore the evolution and structure of SHI/STY. The biological functions of SHI/STYs are discussed in detail in this review, and the application of each biological function to modern agriculture is discussed. All SHI/STY proteins contain typical conserved RING-like zinc finger domain and IGGH domain. SHI/STYs are involved in the formation and development of lateral root, stem extension, leaf morphogenesis, and root nodule development. They are also involved in the regulation of pistil and stamen development and flowering time. At the same time, the regulation of some GA, JA, and auxin signals also involves these family proteins. For each aspect, unanswered or poorly understood questions were identified to help define future research areas. This review will provide a basis for further functional study of this gene family.

The coordinated regulation mechanism of rice plant architecture and its tolerance to stress

Rice plant architecture and stress tolerance have historically been primary concerns for rice breeders. The "Green Revolution" and super-rice breeding practices have demonstrated that ideal plant architecture can effectively improve both stress tolerance and yield. The synergistic selection and breeding of rice varieties with ideal architecture and stress tolerance can increase and stabilize yield. While rice plant plant architecture and stress tolerance are separately regulated by complicated genetic networks, the molecular mechanisms underlying their relationships and synergism have not yet been explored. In this paper, we review the regulatory mechanism between plant architecture, stress tolerance, and biological defense at the different level to provide a theoretical basis for the genetic network of the synergistic regulation and improvement of multiple traits.

Natural variation of RGN1a regulates grain number per panicle in japonica rice

The grain number per panicle (GNP) is an important yield component. Identifying naturally favorable variations in GNP will benefit high-yield rice breeding. Here, we performed a genome-wide association study using a mini-core collection of 266 cultivated rice accessions with deep sequencing data and investigated the phenotype for three years. Three genes, i.e., TOTOU1 (TUT1), Grain height date 7 (Ghd7), and Days to heading 7/Grain height date 7.1/Pseudo-Response Regulator37 (DTH7/Ghd7.1/OsPRR37), which regulate GNP, were found in the quantitative trait loci (QTL) identified in this study. A stable QTL, qGNP1.3, which showed a strong correlation with variations in GNP, was repeatedly detected. After functional and transgenic phenotype analysis, we identified a novel gene, regulator of grain number 1a (RGN1a), which codes for protein kinase, controlling GNP in rice. The RGN1a mutation caused 37.2%, 27.8%, 51.2%, and 25.5% decreases in grain number, primary branch number per panicle, secondary branch number per panicle, and panicle length, respectively. Furthermore, breeding utilization analysis revealed that the additive effects of the dominant allelic variants of RGN1a and DTH7 played a significant role in increasing the grain number per panicle in japonica rice. Our findings enrich the gene pool and provide an effective strategy for the genetic improvement of grain numbers.

Genome-Wide Identification and Expression Profiling of the SRS Gene Family in Melilotus albus Reveals Functions in Various Stress Conditions

The plant-specific SHI-related sequence (SRS) family of transcription factors plays a vital role in growth regulation, plant development, phytohormone biosynthesis, and stress response. However, the genome-wide identification and role in the abiotic stress-related functions of the SRS gene family were not reported in white sweet clover (Melilotus albus). In this study, nine M. albus SRS genes (named MaSRS01-MaSRS09) were identified via a genome-wide search method. All nine genes were located on six out of eight chromosomes in the genome of M. albus and duplication analysis indicated eight segmentally duplicated genes in the MaSRS family. These MaSRS genes were classified into six groups based on their phylogenetic relationships. The gene structure and motif composition results indicated that MaSRS members in the same group contained analogous intron/exon and motif organizations. Further, promoter region analysis of MaSRS genes uncovered various growth, development, and stress-responsive cis-acting elements. Protein interaction networks showed that each gene has both functions of interacting with other genes and members within the family. Moreover, real-time quantitative PCR was also performed to verify the expression patterns of nine MaSRS genes in the leaves of M. albus. The results showed that nine MaSRSs were up- and down-regulated at different time points after various stress treatments, such as salinity, low-temperature, salicylic acid (SA), and methyl jasmonate (MeJA). This is the first systematic study of the M. albus SRS gene family, and it can serve as a strong foundation for further elucidation of the stress response and physiological improvement of the growth functions in M. albus.

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.

Rice DWARF AND LOW-TILLERING and the homeodomain protein OSH15 interact to regulate internode elongation via orchestrating brassinosteroid signaling and metabolism

Brassinosteroid (BR) phytohormones play crucial roles in regulating internode elongation in rice (Oryza sativa). However, the underlying mechanism remains largely unclear. The dwarf and low-tillering (dlt) mutant is a mild BR-signaling-defective mutant. Here, we identify two dlt enhancers that show more severe shortening of the lower internodes compared to the uppermost internode (IN1). Both mutants carry alleles of ORYZA SATIVA HOMEOBOX 15 (OSH15), the founding gene for dwarf6-type mutants, which have shortened lower internodes but not IN1. Consistent with the mutant phenotype, OSH15 expression is much stronger in lower internodes, particularly in IN2, than IN1. The osh15 single mutants have impaired BR sensitivity accompanied by enhanced BR synthesis in seedlings. DLT physically interacts with OSH15 to co-regulate many genes in seedlings and internodes. OSH15 targets and promotes the expression of the BR receptor gene BR INSENSITIVE1 (OsBRI1), and DLT facilitates this regulation in a dosage-dependent manner. In osh15, dlt, and osh15 dlt, BR levels are higher in seedlings and panicles, but unexpectedly lower in internodes compared with the wild-type. Taken together, our results suggest that DLT interacts with OSH15, which functions in the lower internodes, to modulate rice internode elongation via orchestrating BR signaling and metabolism.

Nitrate signaling and use efficiency in crops

Nitrate (NO₃^-) is not only an essential nutrient but also an important signaling molecule for plant growth. Low nitrogen use efficiency (NUE) of crops is causing increasingly serious environmental and ecological problems. Understanding the molecular mechanisms of NO₃^- regulation in crops is crucial for NUE improvement in agriculture. During the last several years, significant progress has been made in understanding the regulation of NO₃^- signaling in crops, and some key NO₃^- signaling factors have been shown to play important roles in NO₃^- utilization. However, no detailed reviews have yet summarized these advances. Here, we focus mainly on recent advances in crop NO₃^- signaling, including short-term signaling, long-term signaling, and the impact of environmental factors. We also review the regulation of crop NUE by crucial genes involved in NO₃^- signaling. This review provides useful information for further research on NO₃^- signaling in crops and a theoretical basis for breeding new crop varieties with high NUE, which has great significance for sustainable agriculture.

Wheat genomic study for genetic improvement of traits in China

Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.

Genome-wide identification, structural analysis and expression profiles of short internodes related sequence gene family in quinoa

Based on the whole genome data information of Chenopodium quinoa Willd, the CqSRS gene family members were systematically identified and analyzed by bioinformatics methods, and the responses of CqSRS genes to NaCl (100 mmol/L), salicylic acid (200 umol/L) and low temperature (4°C) were detected by qRT-PCR. The results showed that a total of 10 SHI related sequence genes were identified in quinoa, and they were distributed on 9 chromosomes, and there were four pairs of duplicated genes. The number of amino acids encoded ranged from 143 aa to 370 aa, and the isoelectric point ranged from 4.81 to 8.90. The secondary structure was mainly composed of random coil (Cc). Most of the SRS gene encoding proteins were located in the cytoplasm (5 CqSRS). Phylogenetic analysis showed that the CqSRS genes were divided into three groups, and the gene structure showed that the number of exons of CqSRS was between two-five. Promoter analysis revealed that there are a total of 44 elements related to plant hormone response elements, light response elements, stress response elements and tissue-specific expression in the upstream regin of the gene. Protein interaction showed that all 10 CqSRS proteins appeared in the known protein interaction network diagram in Arabidopsis. Expression profile analysis showed that CqSRS genes had different expression patterns, and some genes had tissue-specific expression. qRT-PCR showed that all SRS family genes responded to ABA、NaCl、drought and low-temperature treatments, but the expression levels of different CqSRS genes were significantly different under various stresses. This study lays a foundation for further analyzed the function of CqSRS genes.

Molecular evolutionary analysis of the SHI/STY gene family in land plants: A focus on the Brassica species

The plant-specific SHORT INTERNODES/STYLISH (SHI/STY) proteins belong to a family of transcription factors that are involved in the formation and development of early lateral roots. However, the molecular evolution of this family is rarely reported. Here, a total of 195 SHI/STY genes were identified in 21 terrestrial plants, and the Brassica species is the focus of our research. Their physicochemical properties, chromosome location and duplication, motif distribution, exon-intron structures, genetic evolution, and expression patterns were systematically analyzed. These genes are divided into four clades (Clade 1/2/3/4) based on phylogenetic analysis. Motif distribution and gene structure are similar in each clade. SHI/STY proteins are localized in the nucleus by the prediction of subcellular localization. Collinearity analysis indicates that the SHI/STYs are relatively conserved in evolution. Whole-genome duplication is the main factor for their expansion. SHI/STYs have undergone intense purifying selection, but several positive selection sites are also identified. Most promoters of SHI/STY genes contain different types of cis-elements, such as light, stress, and hormone-responsive elements, suggesting that they may be involved in many biological processes. Protein-protein interaction predicted some important SHI/STY interacting proteins, such as LPAT4, MBOATs, PPR, and UBQ3. In addition, the RNA-seq and qRT-PCR analysis were studied in detail in rape. As a result, SHI/STYs are highly expressed in root and bud, and can be affected by Sclerotinia sclerotiorum, drought, cold, and heat stresses. Moreover, quantitative real-time PCR (qRT-PCR) analyses indicates that expression levels of BnSHI/STYs are significantly altered in different treatments (cold, salt, drought, IAA, auxin; ABA, abscisic acid; 6-BA, cytokinin). It provides a new understanding of the evolution and expansion of the SHI/STY family in land plants and lays a foundation for further research on their functions.

Genetic and molecular factors in determining grain number per panicle of rice

It was suggested that the most effective way to improve rice grain yield is to increase the grain number per panicle (GN) through the breeding practice in recent decades. GN is a representative quantitative trait affected by multiple genetic and environmental factors. Understanding the mechanisms controlling GN has become an important research field in rice biotechnology and breeding. The regulation of rice GN is coordinately controlled by panicle architecture and branch differentiation, and many GN-associated genes showed pleiotropic effect in regulating tillering, grain size, flowering time, and other domestication-related traits. It is also revealed that GN determination is closely related to vascular development and the metabolism of some phytohormones. In this review, we summarize the recent findings in rice GN determination and discuss the genetic and molecular mechanisms of GN regulators.

OsSPL14 acts upstream of OsPIN1b and PILS6b to modulate axillary bud outgrowth by fine-tuning auxin transport in rice

As a multigenic trait, rice tillering can optimize plant architecture for the maximum agronomic yield. SQUAMOSA PROMOTER BINDING PROTEIN-LIKE14 (OsSPL14) has been demonstrated to be necessary and sufficient to inhibit rice branching, but the underlying mechanism remains largely unclear. Here, we demonstrated that OsSPL14, which is cleaved by miR529 and miR156, inhibits tillering by fine-tuning auxin transport in rice. RNA interference of OsSPL14 or miR529 and miR156 overexpression significantly increased the tiller number, whereas OsSPL14 overexpression decreased the tiller number. Histological analysis revealed that the OsSPL14-overexpressing line had normal initiation of axillary buds but inhibited outgrowth of tillers. Moreover, OsSPL14 was found to be responsive to indole-acetic acid and 1-naphthylphthalamic acid, and RNA interference of OsSPL14 reduced polar auxin transport and increased 1-naphthylphthalamic acid sensitivity of rice plants. Further analysis revealed that OsSPL14 directly binds to the promoter of PIN-FORMED 1b (OsPIN1b) and PIN-LIKE6b (PILS6b) to regulate their expression positively. OsPIN1b and PILS6b were highly expressed in axillary buds and proved involved in bud outgrowth. Loss of function of OsPIN1b or PILS6b increased the tiller number of rice. Taken together, our findings suggested that OsSPL14 could control axillary bud outgrowth and tiller number by activating the expression of OsPIN1b and PILS6b to fine-tune auxin transport in rice.