Suppressing a phosphohydrolase of cytokinin nucleotide enhances grain yield in rice

Coexpression Regulation of New and Ancient Genes in the Dynamic Transcriptome Landscape of Stem and Rhizome Development in "Bainianzhe"-An Ancient Chinese Sugarcane Variety Ratooned for Nearly 300 Years

The sucrose yield in sugarcane largely depends on stem morphology, including length, diameter and sugar content, making sugarcane stem a key trait in breeding. The "Bainianzhe" variety from Songxi County, Fujian Province, possesses both aerial stems and rhizomes, providing a unique model for studying stem development. We performed a spatiotemporal transcriptomic analysis of the base, middle and apical sections of both aerial stems and rhizomes. The analysis categorized transcriptomes by developmental stage-base, middle and apical-rather than environmental differences. Apical segments were enriched with genes related to cell proliferation, while base segments were linked to senescence and fibrosis. Gene regulatory networks revealed key TFs involved in stem development. Orphan genes may be involved in rhizome development through coexpression networks. Plant hormones, especially genes involved in ABA and GAs synthesis, were highly expressed in rhizomes. Thiamine-related genes were also more prevalent in rhizomes. Furthermore, the apical segments of rhizomes enriched in photosynthesis-related genes suggest adaptations to light exposure. Low average temperatures in Songxi have led to unique cold acclimation in Bainianzhe, with rhizomes showing higher expression of genes linked to unsaturated fatty acid synthesis and cold-responsive calcium signalling. This indicates that rhizomes may have enhanced cold tolerance, aiding in the plant's overwintering success.

The cytokinin efflux transporter ABCC4 participates in Arabidopsis root system development

The directional and sequential flow of cytokinin in plants is organized by a complex network of transporters. Genes involved in several aspects of cytokinin transport have been characterized; however, much of the elaborate system remains elusive. In this study, we used a transient expression system in tobacco (Nicotiana benthamiana) leaves to screen Arabidopsis (Arabidopsis thaliana) transporter genes and isolated ATP-BINDING CASSETTE TRANSPORTER C4 (ABCC4). Validation through drug-induced expression in Arabidopsis and heterologous expression in budding yeast revealed that ABCC4 effluxes the active form of cytokinins. During the seedling stage, ABCC4 was highly expressed in roots, and its expression was upregulated in response to cytokinin application. Loss-of-function mutants of ABCC4 displayed enhanced primary root elongation, similar to mutants impaired in cytokinin biosynthesis or signaling, that was suppressed by exogenous trans-zeatin treatment. In contrast, overexpression of the gene led to suppression of root elongation. These results suggest that ABCC4 plays a role in the efflux of active cytokinin, thereby contributing to root growth regulation. Additionally, cytokinin-dependent enlargement of stomatal aperture was impaired in the loss-of-function and overexpression lines. Our findings contribute to unraveling the many complexities of cytokinin flow and enhance our understanding of the regulatory mechanisms underlying root system development and stomatal opening in plants.

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.

Transcription factor AtNAC002 positively regulates Cu toxicity tolerance in Arabidopsis thaliana

Copper (Cu) is an essential micronutrient for plant growth and development, but environmental Cu pollution has become increasingly severe, adversely affecting both ecosystems and crop productivity. In this study, we identified the AtNAC002 gene as a positive regulator of Cu toxicity in Arabidopsis thaliana. We found that AtNAC002 expression was induced by Cu excess, and the atnac002 mutant was Cu-sensitive, accumulating more Cu than the wild-type. Additionally, atnac002 mutants exhibit reduced activities of antioxidant enzymes (SOD, POD, and CAT), leading to increased levels of reactive oxygen species and malondialdehyde, which decrease Cu resistance. AtNAC002 might play a role in vacuolar and mitochondrial Cu compartmentalization by regulating genes involved in Cu detoxification, specifically COX11 and HCC1. Furthermore, AtNAC002 was implicated in flavone and flavanol biosynthesis, with the atnac002 mutant showing reduced flavonoid content. Our findings suggest that AtNAC002 is integral to the regulation of Cu toxicity tolerance in A. thaliana. This knowledge is critical for advancing our understanding and offers potential molecular breeding targets to enhance plant performance under Cu excess, which is significant for improving global food security and forest restoration.

Nucleotides and nucleotide derivatives as signal molecules in plants

In reaction to a stimulus, signaling molecules are made, generate a response, and are then degraded. Nucleotides are classically associated with central metabolism and nucleic acid biosynthesis, but there are a number of nucleotides and nucleotide derivatives in plants to which this simple definition of a signaling molecule applies in whole or at least in part. These include cytokinins and chloroplast guanosine tetraposphate (ppGpp), as well as extracellular canonical nucleotides such as extracellular ATP (eATP) and NAD+ (eNAD+). In addition, there is a whole series of compounds derived from NAD+ such as ADP ribose (ADPR), and ATP-ADPR dinucleotides and their hydrolysis products (e.g. pRib-AMP) together with different variants of cyclic ADPR (cADPR, 2´-cADPR, 3´-cADPR), and also cyclic nucleotides such as 3´,5´-cAMP and 2´,3´-cyclic nucleoside monophosphates. Interestingly, some of these compounds have recently been shown to play a central role in pathogen defense. In this review, we highlight these exciting new developments. We also review nucleotide derivatives that are considered as candidates for signaling molecules, for example purine deoxynucleosides, and discuss more controversial cases.

Engineering rice genomes towards green super rice

Rice, cultivated for millennia across diverse geographical regions, has witnessed tremendous advancements in recent decades, epitomized by the emergence of Green Super Rice. These efforts aim to address challenges such as climate change, pest and disease threats, and sustainable agriculture. Driven by the advent of multiomics big data, breakthroughs in genomic tools and resources, hybrid rice breeding techniques, and the extensive utilization of green genes, rice genomes are undergoing delicate modifications to produce varieties with high yield, superior quality, enhanced nutrient efficiency, and resilience to pests and environmental stresses, leading to the development of green agriculture in China. Additionally, the utilization of wild relatives and the promotion of genomic breeding approaches have further enriched our understanding of rice improvement. In the future, international efforts to develop next-generation green rice varieties remain both challenging and imperative for the whole community.

Manipulating hormones to mitigate trade-offs in crops

Addressing trait coupling due to gene pleiotropy presents challenges in conventional breeding system. However, targeted hormonal manipulation and precise genetic engineering designs hold promise to alleviate trade‐offs and unlock the potential of crops for multiple desirable traits.

Identification and segregation of two closely linked major QTLs for kernel row number in advanced maize-teosinte populations

KEY MESSAGE

Two closely linked novel loci, qKRN2-1 and qKRN2-2, associated with kernel row number were fine-mapped on chromosome 2, and a key candidate gene for qKRN2-1 was identified through expression analysis. Kernel row number (KRN) is a crucial factor influencing maize yield and serves as a significant target for maize breeding. The use of wild progenitor species can aid in identifying the essential traits for domestication and breeding. In this study, teosinte (MT1) served as the donor parent, the inbred maize line of Mo17 was used as the recurrent parent, we identified a major quantitative trait locus (QTL) for KRN, designated qKRN2, into two closely linked loci, qKRN2-1 and qKRN2-2. Here, fine mapping was performed to investigate two QTLs, qKRN2-1 and qKRN2-2, within a genomic range of 272 kb and 775 kb, respectively. This was achieved using a progeny test strategy in an advanced backcross population, with the two QTLs explaining 33.49% and 35.30% of the phenotypic variance. Molecular marker-assisted selection resulted in the development of two nearly isogenic lines (NILs), qKRN2-1 and qKRN2-2, which differed only in the segment containing the QTL. Notably, the maize (Mo17) alleles increased the KRN relative to teosinte by approximately 1.4 and 1.2 rows for qKRN2-1 and qKRN2-2, respectively. Zm00001d002989 encodes a cytokinin oxidase/dehydrogenase and its expression in the immature ears exhibited significant differences among the qKRN2-1 NILs. In situ hybridization localized Zm00001d002989 to the primordia of the inflorescence meristem and spikelet pair meristems, is predicted to be the causal gene of qKRN2-1. The findings of this study deepen our understanding of the genetic basis of KRN and hold significant potential for improving maize grain yields.

OsIAA23 Promotes Heading by Directly Downregulating Ghd7 in rice

Ghd7 is a central regulator to multiple growth and development processes in rice. While it is not clear how Ghd7 is regulated by upstream factors. To identify its upstream regulator, the truncated Ghd7 promoter fragments were used to screen cis elements binding to rice total nuclear proteins. Electrophoretic mobility shift assays screened one truncated fragment f3 binding to the proteins. Subsequently, the fragment f3 was employed to screen a yeast one-hybrid library, and a transcription factor OsIAA23 was screened as a direct upstream regulator of Ghd7. Dual-luciferase transient assay demonstrated the transcriptional repression effect of OsIAA23 on the activity of Ghd7, and the location of the cis elements binding to OsIAA23 in the region 1264 to 1255 bp upstream of ATG. Genetic analysis between the wild type Ghd7-OsIAA23 and single/double mutants further verified that OsIAA23 downregulated Ghd7 expression and led to a delayed heading under long day conditions. Moreover, natural variations in fragment f3 were associated with heading and geographic distribution in rice. This study sheds light on the direct regulatory mechanism of OsIAA23 on Ghd7, which enriches the understanding of the Ghd7 involved flowering regulatory network in rice.

Evolutionary Analysis and Catalytic Function of LOG Proteins in Plants

BACKGROUND

The plant hormone cytokinin is a conserved regulator of plant development. LONELY GUY (LOG) proteins are pivotal in cytokinin biosynthesis. However, their origin, evolutionary history, and enzymatic characteristics remain largely uncharacterized.

METHODS

To elucidate LOG family evolution history and protein motif composition, we conducted phylogenetic and motif analyses encompassing representative species across the whole green plant lineage. Catalytic activity and structure analysis were conducted to thoroughly characterize the LOG proteins.

RESULTS

Our phylogeny showed that LOG proteins could be divided into five groups and revealed three major duplication events giving rise to four distinct groups of vascular LOG proteins. LOG proteins share a conserved structure characterized by a canonical motif arrangement comprising motifs 1, 2, 3, 4, 5, 6, and 7. Two significant changes in LOG motif composition occurred during the transition to land plants: the emergence of motif 3 in charophyte LOG sequences and the subsequent acquisition of motif 8 at the C-terminus of LOG proteins. Enzymatic assays demonstrated that LOG proteins can be classified into two groups based on their enzyme activity. One group act as cytokinin riboside 5'-monophosphate phosphoribohydrolase and primarily convert iPRMP to iP, while the other group act as 5'-ribonucleotide phosphohydrolase, and preferentially produce iPR from the same substrates. TaLOG5-4A1, TaLOG5-4A2, TaLOG5-5B2, and TaLOG5-D1 shared conserved residues in the critical motif and were predicted to have similar protein structures, but displayed distinct enzymatic activities.

CONCLUSIONS

Our findings provide a comprehensive overview of LOG protein phylogeny and lay a foundation for further investigations into their functional diversification.

Epigenetics and plant hormone dynamics: a functional and methodological perspective

Plant hormones, pivotal regulators of plant growth, development, and response to environmental cues, have recently emerged as central modulators of epigenetic processes governing gene expression and phenotypic plasticity. This review addresses the complex interplay between plant hormones and epigenetic mechanisms, highlighting the diverse methodologies that have been harnessed to decipher these intricate relationships. We present a comprehensive overview to understand how phytohormones orchestrate epigenetic modifications, shaping plant adaptation and survival strategies. Conversely, we explore how epigenetic regulators ensure hormonal balance and regulate the signalling pathways of key plant hormones. Furthermore, our investigation includes a search for novel genes that are regulated by plant hormones under the control of epigenetic processes. Our review offers a contemporary overview of the epigenetic-plant hormone crosstalk, emphasizing its significance in plant growth, development, and potential agronomical applications.

Seed yield as a function of cytokinin-regulated gene expression in wild Kentucky bluegrass (Poa pratensis)

BACKGROUND

Kentucky bluegrass (Poa pratensis L.) panicle development is a coordinated process of cell proliferation and differentiation with distinctive phases and architectural changes that are pivotal to determine seed yield. Cytokinin (CK) is a key factor in determining seed yield that might underpin the second "Green Revolution". However, whether there is a difference between endogenous CK content and seed yields of Kentucky bluegrass, and how CK-related genes are expressed to affect enzyme regulation and downstream seed yield in Kentucky bluegrass remains enigmatic.

RESULTS

In order to establish a potential link between CK regulation and seed yield, we dissected and characterized the Kentucky bluegrass young panicle, and determined the changes in nutrients, 6 types of endogenous CKs, and 16 genes involved in biosynthesis, activation, inactivation, re-activation and degradation of CKs during young panicle differentiation of Kentucky bluegrass. We found that high seed yield material had more meristems compared to low seed yield material. Additionally, it was found that seed-setting rate (SSR) and lipase activity at the stage of spikelet and floret primordium differentiation (S3), as well as 1000-grain weight (TGW) and zeatin-riboside (ZR) content at the stages of first bract primordium differentiation (S1) and branch primordium differentiation (S2) showed a significantly positive correlation in the two materials. And zeatin, ZR, dihydrozeatin riboside, isopentenyl adenosine and isopentenyl adenosine riboside contents were higher in seed high yield material than those in seed low yield material at S3 stage. Furthermore, the expressions of PpITP3, PpITP5, PpITP8 and PpLOG1 were positively correlated with seed yield, while the expressions of PpCKX2, PpCKX5 and PpCKX7 were negatively correlated with seed yield in Kentucky bluegrass.

CONCLUSIONS

Overall, our study established a relationship between CK and seed yield in Kentucky bluegrass. Perhaps we can increase SSR and TGW by increasing lipase activity and ZR content. Of course, using modern gene editing techniques to manipulate CK related genes such as PpITP3/5/8, PpLOG1 and PpCKX2/5/7, will be a more direct and effective method in Kentucky bluegrass, which requires further trial validation.

Spatially distributed cytokinins: Metabolism, signaling, and transport

Cytokinins are mobile phytohormones that regulate plant growth, development, and environmental adaptability. The major cytokinin species include isopentenyl adenine (iP), trans-zeatin (tZ), cis-zeatin (cZ), and dihydrozeatin (DZ). The spatial distributions of different cytokinin species in different organelles, cells, tissues, and organs are primarily shaped by biosynthesis via isopentenyltransferases (IPT), cytochrome P450 monooxygenase, and 5'-ribonucleotide phosphohydrolase and by conjugation or catabolism via glycosyltransferase or cytokinin oxidase/dehydrogenase. Cytokinins bind to histidine receptor kinases in the endoplasmic reticulum or plasma membrane and relay signals to response regulators in the nucleus via shuttle proteins known as histidine phosphotransfer proteins. The movements of cytokinins from sites of biosynthesis to sites of signal perception usually require long-distance, intercellular, and intracellular transport. In the past decade, ATP-binding cassette (ABC) transporters, purine permeases (PUP), AZA-GUANINE RESISTANT (AZG) transporters, equilibrative nucleoside transporters (ENT), and Sugars Will Eventually Be Exported transporters (SWEET) have been characterized as involved in cytokinin transport processes. This review begins by introducing the spatial distributions of various cytokinins and the subcellular localizations of the proteins involved in their metabolism and signaling. Highlights focus on an inventory of the characterized transporters involved in cytokinin compartmentalization, including long-distance, intercellular, and intracellular transport, and the regulation of the spatial distributions of cytokinins by environmental cues. Future directions for cytokinin research are also discussed.

Natural variation in MORE GRAINS 1 regulates grain number and grain weight in rice

Grain yield is determined mainly by grain number and grain weight. In this study, we identified and characterized MORE GRAINS1 (MOG1), a gene associated with grain number and grain weight in rice (Oryza sativa L.), through map-based cloning. Overexpression of MOG1 increased grain yield by 18.6%-22.3% under field conditions. We determined that MOG1, a bHLH transcription factor, interacts with OsbHLH107 and directly activates the expression of LONELY GUY (LOG), which encodes a cytokinin-activating enzyme and the cell expansion gene EXPANSIN-LIKE1 (EXPLA1), positively regulating grain number per panicle and grain weight. Natural variations in the promoter and coding regions of MOG1 between Hap-LNW and Hap-HNW alleles resulted in changes in MOG1 expression level and transcriptional activation, leading to functional differences. Haplotype analysis revealed that Hap-HNW, which results in a greater number and heavier grains, has undergone strong selection but has been poorly utilized in modern lowland rice breeding. In summary, the MOG1-OsbHLH107 complex activates LOG and EXPLA1 expression to promote cell expansion and division of young panicles through the cytokinin pathway, thereby increasing grain number and grain weight. These findings suggest that Hap-HNW could be used in strategies to breed high-yielding temperate japonica lowland rice.

A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice

Transposable elements (TEs) are ubiquitous genomic components and hard to study due to being highly repetitive. Here we assembled 232 chromosome-level genomes based on long-read sequencing data. Coupling the 232 genomes with 15 existing assemblies, we developed a pan-TE map comprising both cultivated and wild Asian rice. We detected 177 084 high-quality TE variations and inferred their derived state using outgroups. We found TEs were one source of phenotypic variation during rice domestication and differentiation. We identified 1246 genes whose expression variation was associated with TEs but not single-nucleotide polymorphisms (SNPs), such as OsRbohB, and validated OsRbohB's relative expression activity using a dual-Luciferase (LUC) reporter assays system. Our pan-TE map allowed us to detect multiple novel loci associated with agronomic traits. Collectively, our findings highlight the contributions of TEs to domestication, differentiation and agronomic traits in rice, and there is massive potential for gene cloning and molecular breeding by the high-quality Asian pan-TE map we generated.

Dissecting the molecular basis of spike traits by integrating gene regulatory networks and genetic variation in wheat

Spike architecture influences both grain weight and grain number per spike, which are the two major components of grain yield in bread wheat (Triticum aestivum L.). However, the complex wheat genome and the influence of various environmental factors pose challenges in mapping the causal genes that affect spike traits. Here, we systematically identified genes involved in spike trait formation by integrating information on genomic variation and gene regulatory networks controlling young spike development in wheat. We identified 170 loci that are responsible for variations in spike length, spikelet number per spike, and grain number per spike through genome-wide association study and meta-QTL analyses. We constructed gene regulatory networks for young inflorescences at the double ridge stage and the floret primordium stage, in which the spikelet meristem and the floret meristem are predominant, respectively, by integrating transcriptome, histone modification, chromatin accessibility, eQTL, and protein-protein interactome data. From these networks, we identified 169 hub genes located in 76 of the 170 QTL regions whose polymorphisms are significantly associated with variation in spike traits. The functions of TaZF-B1, VRT-B2, and TaSPL15-A/D in establishment of wheat spike architecture were verified. This study provides valuable molecular resources for understanding spike traits and demonstrates that combining genetic analysis and developmental regulatory networks is a robust approach for dissection of complex traits.

Boosting Triticeae crop grain yield by manipulating molecular modules to regulate inflorescence architecture: insights and knowledge from other cereal crops

One of the challenges for global food security is to reliably and sustainably improve the grain yield of cereal crops. One solution is to modify the architecture of the grain-bearing inflorescence to optimize for grain number and size. Cereal inflorescences are complex structures, with determinacy, branching patterns, and spikelet/floret growth patterns that vary by species. Recent decades have witnessed rapid advancements in our understanding of the genetic regulation of inflorescence architecture in rice, maize, wheat, and barley. Here, we summarize current knowledge on key genetic factors underlying the different inflorescence morphologies of these crops and model plants (Arabidopsis and tomato), focusing particularly on the regulation of inflorescence meristem determinacy and spikelet meristem identity and determinacy. We also discuss strategies to identify and utilize these superior alleles to optimize inflorescence architecture and, ultimately, improve crop grain yield.

Analysis of Genetic Diversity in Adzuki Beans (Vigna angularis): Insights into Environmental Adaptation and Early Breeding Strategies for Yield Improvement

Adzuki beans are widely cultivated in East Asia and are one of the earliest domesticated crops. In order to gain a deeper understanding of the genetic diversity and domestication history of adzuki beans, we conducted Genotyping by Sequencing (GBS) analysis on 366 landraces originating from Korea, China, and Japan, resulting in 6586 single-nucleotide polymorphisms (SNPs). Population structure analysis divided these 366 landraces into three subpopulations. These three subpopulations exhibited distinctive distributions, suggesting that they underwent extended domestication processes in their respective regions of origin. Phenotypic variance analysis of the three subpopulations indicated that the Korean-domesticated subpopulation exhibited significantly higher 100-seed weights, the Japanese-domesticated subpopulation showed significantly higher numbers of grains per pod, and the Chinese-domesticated subpopulation displayed significantly higher numbers of pods per plant. We speculate that these differences in yield-related traits may be attributed to varying emphases placed by early breeders in these regions on the selection of traits related to yield. A large number of genes related to biotic/abiotic stress resistance and defense were found in most quantitative trait locus (QTL) for yield-related traits using genome-wide association studies (GWAS). Genomic sliding window analysis of Tajima's D and a genetic differentiation coefficient (Fst) revealed distinct domestication selection signatures and genotype variations on these QTLs within each subpopulation. These findings indicate that each subpopulation would have been subjected to varied biotic/abiotic stress events in different origins, of which these stress events have caused balancing selection differences in the QTL of each subpopulation. In these balancing selections, plants tend to select genotypes with strong resistance under biotic/abiotic stress, but reduce the frequency of high-yield genotypes to varying degrees. These biotic/abiotic stressors impact crop yield and may even lead to selection purging, resulting in the loss of several high-yielding genotypes among landraces. However, this also fuels the flow of crop germplasms. Overall, balancing selection appears to have a more significant impact on the three yield-related traits compared to breeder-driven domestication selection. These findings are crucial for understanding the impact of domestication selection history on landraces and yield-related traits, aiding in the improvement of adzuki bean varieties.

Tapping into the plasticity of plant architecture for increased stress resilience

Plant architecture develops post-embryonically and emerges from a dialogue between the developmental signals and environmental cues. Length and branching of the vegetative and reproductive tissues were the focus of improvement of plant performance from the early days of plant breeding. Current breeding priorities are changing, as we need to prioritize plant productivity under increasingly challenging environmental conditions. While it has been widely recognized that plant architecture changes in response to the environment, its contribution to plant productivity in the changing climate remains to be fully explored. This review will summarize prior discoveries of genetic control of plant architecture traits and their effect on plant performance under environmental stress. We review new tools in phenotyping that will guide future discoveries of genes contributing to plant architecture, its plasticity, and its contributions to stress resilience. Subsequently, we provide a perspective into how integrating the study of new species, modern phenotyping techniques, and modeling can lead to discovering new genetic targets underlying the plasticity of plant architecture and stress resilience. Altogether, this review provides a new perspective on the plasticity of plant architecture and how it can be harnessed for increased performance under environmental stress.