Suppression of tiller bud activity in tillering dwarf mutants of rice

Harnessing neo-domestication of wild pigmented rice for enhanced nutrition and sustainable agriculture

Advances in precision gene editing have enabled the rapid domestication of wild crop relatives, a process known as neo-domestication. During domestication, breeding rice for maximum productivity under optimal growth conditions reduced genetic diversity, eliminating variants for stress tolerance and grain nutrients. Wild rice varieties have rich genetic diversity, including variants for disease resistance, stress tolerance, and grain nutritional quality. For example, the grain of pigmented wild rice has abundant antioxidants (anthocyanins, proanthocyanidins, and flavonoids), but low yield, poor plant architecture, and long life cycle limit its cultivation. In this review, we address the neo-domestication of wild pigmented rice, focusing on recent progress, CRISPR-Cas editing toolboxes, selection of key candidate genes for domestication, identifying species with superior potential via generating genomic and multi-omics resources, efficient crop transformation methods and highlight strategies for the promotion and application pigmented rice. We also address critical outstanding questions and potential solutions to enable efficient neo-domestication of wild pigmented rice and thus enhance food security and nutrition.

Root microbiota regulates tiller number in rice

Rice tillering is an important agronomic trait regulated by plant genetic and environmental factors. However, the role and mechanism of the root microbiota in modulating rice tillering have not been explored. Here, we examined the root microbiota composition and tiller numbers of 182 genome-sequenced rice varieties grown under field conditions and uncovered a significant correlation between root microbiota composition and rice tiller number. Using cultivated bacterial isolates, we demonstrated that various members of the root microbiota can regulate rice tillering in both laboratory and field conditions. Genetic, biochemical, and structural analyses revealed that cyclo(Leu-Pro), produced by the tiller-inhibiting bacterium Exiguobacterium R2567, activates the rice strigolactone (SL) signaling pathway by binding to the SL receptor OsD14, thus regulating tillering. The present work provides insight into how the root microbiota regulates key agronomic traits and offers a promising strategy for optimizing crop growth by harnessing the root microbiota in sustainable agriculture.

Mutation of strigolactone biosynthetic gene DWARF 17 impairs the responses of rice tillering to N supply

Tiller number is one important parameter for rice yield and is influenced by both strigolactone (SL) and nitrogen (N). However, how SL and N interact to regulate the tiller outgrowth in rice is unclear. In this study, we isolated a multi-tillering mutant, tin, from an ethyl methanesulfonate (EMS)-mutagenized population of Wuyunjing 7, a japonica cultivar. The tin mutant exhibited low sensitivity to varying N concentrations during the tiller development. Through bulk segregation analysis (BSA), we identified a missense mutation located in the exon of DWARF 17 (D17), a key gene involved in SL biosynthesis. Complementation experiments confirmed that D17 is responsible for the tin tiller phenotype, and exogenous application of the SL analogue GR24 restored the tiller response of tin to N. Transcriptome analysis further revealed that D17 and SL regulate the tiller response to N by modulating the expression of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes and ammonium transporter genes. These findings elucidate the mechanism by which SL and N coordinate to regulate rice tillering growth, providing valuable insights for optimizing rice plant architecture to enhance yield potential.

FZP modulates tillering via OsMADS57 in rice

The number of tillers in rice directly determines the number of panicles, which is crucial for enhancing plant architecture and achieving high yields. Some important genes regulating rice tillering have been identified, but their underlying mechanisms remain unclear. FRIZZY PANICLE (FZP) encodes an AP2/ERF transcription factor. Beyond its well-established role in promoting spikelet formation during the reproductive phase, here we demonstrate that FZP also inhibits axillary buds outgrowth in the vegetative phase by suppressing the expression of a MADS-box gene (OsMADS57) that functions as a growth promoter. Consequently, genome editing of the FZP-bound cis-motif in the promoter of OsMADS57 releases its expression, leading to more tillers. Furthermore, domestication analysis shows that FZP has undergone strong selection in cultivated rice, while the downstream gene OsMADS57 has been differentiated between indica and japonica subspecies. Four functional SNPs in the promoter of OsMADS57 can increase rice tillering in most indica accessions by enhancing its expression. Our findings expose hidden pleiotropy of classic spikelet identity genes that are redeployed to control stem form, potentially enriching the gene resources for rice genetic improvement.

Identification and functional analysis of strigolactone pathway genes regulating tillering traits in sugarcane

Saccharum officinarum and Saccharum spontaneum are two fundamental species of modern sugarcane cultivars, exhibiting divergent tillering patterns crucial for sugarcane architecture and yield. Strigolactones (SLs), a class of plant hormones, are considered to play a central role in shaping plant form and regulating tillering. Our study highlights the distinct tillering patterns observed between S. officinarum and S. spontaneum and implicates significant differences in SL levels in root exudates between the two species. Treatment with rac-GR24 (an artificial SL analog) suppressed tillering in S. spontaneum. Based on transcriptome analysis, we focused on two genes, TRANSCRIPTION ELONGATION FACTOR 1 (TEF1) and CIRCADIAN CLOCK ASSOCIATED1 (CCA1), which show higher expression in S. spontaneum or S. officinarum, respectively. While the overexpression of SoCCA1 did not lead to significant phenotypic differences, overexpression of SsTEF1 in rice stimulated tillering and inhibited plant height, demonstrating its role in tillering regulation. However, the overexpression of suggests that SoCCA1 may not be the key regulator of sugarcane tillering. Yeast one-hybrid assays identified four transcription factors (TFs) regulating SsTEF1 and four and five TFs regulating SsCCA1 and SoCCA1. This study provides a theoretical foundation for deciphering the molecular mechanisms underlying the different tillering behaviors between S. officinarum and S. spontaneum, providing valuable insights for the molecular-based design of sugarcane breeding strategies.

Prioritization of candidate genes regulating the dwarfness in rice by integration of whole-genome and transcriptome analyses

Dwarfism is a major trait for developing lodging-resistant rice cultivars. Gamma irradiation-induced mutagenesis has proven to be an effective method for generating dwarf rice mutants. In this research, we isolated a dwarf mutant from Anna R (4) in the M2 generation and subsequently stabilized the trait through successive selfing of progeny across the M3-M7 generations. We then employed whole-genome re-sequencing (WGRS) and RNA sequencing (RNA-seq) analyses of Anna R (4) and the mutant (designated as ACM-20001) to elucidate the underlying mechanisms and identify candidate genes associated with dwarfness. Numerous genetic variations were identified between Anna (R) 4 and ACM-20001 through WGRS. In total, 2049 genetic variants, including 343 InDels and 1706 nonsynonymous SNPs, were identified across 697 genes. Additionally, RNA-seq analysis revealed 2,881 differentially expressed genes between the wild-type Anna (R) 4 and the mutant ACM-20001, with 1,451 genes up-regulated and 1,430 genes down-regulated in ACM-20001 compared to Anna (R) 4. By integrating WGRS and RNA-seq data with functional annotation analysis, we identified the most likely candidate genes (i.e., Os02g0506400, Os05g0515200, Os06g0154200 and Os08g0250900) related to dwarfness. Quantitative real-time PCR analysis verified the expression of these genes. Collectively, our study provides valuable insights in to the genes and mechanisms underlying dwarfness in rice. Further studies are required to elucidate the roles of these candidate genes in dwarfness, which contribute to advancements rice breeding programs.

Identification of QTL-by-environment interaction by controlling polygenic background effect

The quantitative trait loci (QTL)-by-environment (Q × E) interaction effect is hard to detect because there are no effective ways to control the genomic background. In this study, we propose a linear mixed model that simultaneously analyzes data from multiple environments to detect Q × E interactions. This model incorporates two different kinship matrices derived from the genome-wide markers to control both main and interaction polygenic background effects. Simulation studies demonstrate that our approach is more powerful than the meta-analysis and inclusive composite interval mapping methods. We further analyze four agronomic traits of rice across four environments. A main effect QTL is identified for 1000-grain weight (KGW), while no QTL are found for tiller number. Additionally, a large QTL with a significant Q × E interaction is detected on chromosome 7 affecting grain number, yield, and KGW. This region harbors two important genes, PROG1 and Ghd7. Furthermore, we apply our mixed model to analyze lodging in barley across six environments. The six regions exhibiting Q × E interaction effects identified by our approach overlap with the SNPs previously identified using EM and MCMC-based Bayesian methods, further validating the robustness of our approach. Both simulation studies and empirical data analyses show that our method outperformed all other methods compared.

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.

Improving grain yield and salt tolerance by optimizing plant height with beneficial haplotypes in rice (Oryza sativa)

INTRODUCTION

Rice (Oryza sativa L.), a staple food for billions worldwide, is challenged by salt stress. Owing to the limited understanding of the physiological and genetic basis of rice salt tolerance, few genes have been identified as valuable in rice breeding, causing a major bottleneck in the development of high-yield, salt-tolerant rice varieties.

OBJECTIVE

This study aims to identify salt tolerance genes/quantitative trait loci (QTLs) with breeding potential in rice.

METHODS

Field trials were conducted with 166 Chinese rice cultivars from saline-affected regions and 412 global rice accessions to assess salt tolerance. Genome-wide association study (GWAS) was performed to identify key loci related to high yield and salt tolerance. Additionally, the impact of introducing beneficial haplotypes on grain yield and salt tolerance was assessed.

RESULTS

The optimal rice plant height of 100-120 cm was crucial for sustaining high yield under both normal and salt stress conditions. GWAS revealed 6 novel QTLs/genes associated with rice plant growth and grain yield across various environments, distinct from previously recognized salt stress-related genes. Notably, the gene PHS10.1, encoding a serine/threonine protein kinase, may regulate carbon metabolism, starch and sucrose metabolism, influencing plant growth and grain yield. Certain haplotypes of the genes regulating plant height and grain yield, including SD1, Ghd7.1, GH3.5, and PHS10.1, were selected in traditional breeding. Moreover, optimizing plant height through the introgression of beneficial alleles of these genes increased grain yield in recipient lines under both normal and saline conditions.

CONCLUSION

We propose that utilizing beneficial haplotypes to optimize plant height can effectively balance the growth-stress trade-offs in rice plants. This represents a promising breeding strategy for the development of crop varieties that are both high-yielding and salt-tolerant.

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

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

Novel mechanisms of strigolactone-induced DWARF14 degradation in Arabidopsis thaliana

In angiosperms, the strigolactone receptor is the α/β hydrolase DWARF14 (D14) that, upon strigolactone binding, undergoes conformational changes, triggers strigolactone-dependent responses, and hydrolyses strigolactones. Strigolactone signalling involves the formation of a complex between strigolactone-bound D14, the E3-ubiquitin ligase SCFMAX2, and the transcriptional corepressors SMXL6/7/8, which become ubiquitinated and degraded by the proteasome. Strigolactone also destabilizes the D14 receptor. The current model proposes that D14 degradation occurs after ubiquitination of the SMXLs via SCFMAX2 and proteasomal degradation. Using fluorescence and luminescence assays on transgenic lines expressing D14 fused to GREEN FLUORESCENT PROTEIN or LUCIFERASE, we showed that strigolactone-induced D14 degradation may also occur independently of SCFMAX2 and/or SMXL6/7/8 through a proteasome-independent mechanism. Furthermore, strigolactone hydrolysis was not essential for triggering either D14 or SMXL7 degradation. The activity of mutant D14 proteins predicted to be non-functional for strigolactone signalling was also examined, and their capability to bind strigolactones in vitro was studied using differential scanning fluorimetry. Finally, we found that under certain conditions, the efficiency of D14 degradation was not aligned with that of SMXL7 degradation. These findings indicate a more complex regulatory mechanism governing D14 degradation than previously anticipated and provide novel insights into the dynamics of strigolactone signalling in Arabidopsis.

The strigolactone receptor DWARF14 regulates flowering time in Arabidopsis

Multiple plant hormones, including strigolactone (SL), play key roles in regulating flowering time. The Arabidopsis (Arabidopsis thaliana) DWARF14 (AtD14) receptor perceives SL and recruits F-box protein MORE AXILLARY GROWTH2 (MAX2) and the SUPPRESSOR OF MAX2-LIKE (SMXL) family proteins. These interactions lead to the degradation of the SMXL repressor proteins, thereby regulating shoot branching, leaf shape, and other developmental processes. However, the molecular mechanism by which SL regulates plant flowering remains elusive. Here, we demonstrate that intact strigolactone biosynthesis and signaling pathways are essential for normal flowering in Arabidopsis. Loss-of-function mutants in both SL biosynthesis (max3) and signaling (Atd14 and max2) pathways display earlier flowering, whereas the repressor triple mutant smxl6/7/8 (s678) exhibits the opposite phenotype. Retention of AtD14 in the cytoplasm leads to its inability to repress flowering. Moreover, we show that nuclear-localized AtD14 employs dual strategies to enhance the function of the AP2 transcription factor TARGET OF EAT1 (TOE1). AtD14 directly binds to TOE1 in an SL-dependent manner and stabilizes it. In addition, AtD14-mediated degradation of SMXL7 releases TOE1 from the repressor protein, allowing it to bind to and inhibit the FLOWERING LOCUS T (FT) promoter. This results in reduced FT transcription and delayed flowering. In summary, AtD14 perception of SL enables the transcription factor TOE1 to repress flowering, providing insights into hormonal control of plant flowering.

Functions of exogenous strigolactone application and strigolactone biosynthesis genes GhMAX3/GhMAX4b in response to drought tolerance in cotton (Gossypium hirsutum L.)

BACKGROUND

Drought stress markedly constrains plant growth and diminishes crop productivity. Strigolactones (SLs) exert a beneficial influence on plant resilience to drought conditions. Nevertheless, the specific function of SLs in modulating cotton's response to drought stress remains to be elucidated.

RESULTS

In this study, we assess the impact of exogenous SL (rac-GR24) administration at various concentrations (0, 1, 5, 10, 20 µM) on cotton growth during drought stress. The findings reveal that cotton seedlings treated with 5 µM exogenous SL exhibit optimal mitigation of growth suppression induced by drought stress. Treatment with 5 µM exogenous SL under drought stress conditions enhances drought tolerance in cotton seedlings by augmenting photosynthetic efficiency, facilitating stomatal closure, diminishing reactive oxygen species (ROS) generation, alleviating membrane lipid peroxidation, enhancing the activity of antioxidant enzymes, elevating the levels of osmoregulatory compounds, and upregulating the expression of drought-responsive genes. The suppression of cotton SL biosynthesis genes, MORE AXILLARY GROWTH 3 (GhMAX3) and GhMAX4b, impairs the drought tolerance of cotton. Conversely, overexpression of GhMAX3 and GhMAX4b in respective Arabidopsis mutants ameliorates the drought-sensitive phenotype in these mutants.

CONCLUSION

These observations underscore that SLs significantly bolster cotton's resistance to drought stress.

The Psathyrostachys juncea DWARF27 gene encodes an all-trans-/9-cis-beta-carotene isomerase in the control of plant branches in Arabidopsis thaliana by strigolactones

Strigolactones (SLs), carotenoid-derived plant hormones, govern the growth and development of both monocotyledonous and dicotyledonous plants. DWARF27 (D27), a plastid-targeted protein located at the initiation site of the core pathway in SL synthesis, plays a crucial role in regulating plant tillering (branching). In rice (Oryza sativa) and wheat (Triticum aestivum), OsD27 and TaD27-B proteins modulate the number of plant tillers by participating in SL biosynthesis. Similarly, AtD27 in Arabidopsis thaliana is required for SL production and has a significant impact on phenotypic changes related to branching. At the same time, TaD27 in wheat has been confirmed as a functional orthologue of AtD27 in Arabidopsis, and both Psathyrostachys juncea and wheat belong to the Triticeae, so we speculate that PjD27 gene may also have the same function as AtD27 in Arabidopsis. In this study, we initially screened the PjD27 gene significantly associated with tillering regulation through transcriptome data analysis and subsequently validated its expression levels using qRT-PCR analysis. Furthermore, we conducted phylogenetic analysis using amino acid sequences from 41 species, including P. juncea, to identify closely related species of P. juncea. Here, we analyze the conservation of D27 protein among P. juncea, rice, wheat, and Arabidopsis and provide preliminary evidence suggesting that PjD27 protein is an orthologue of D27 protein in Arabidopsis. Through reverse genetics, we demonstrate the crucial role of PjD27 in regulating plant branching, establishing it as a functional orthologue of D27 in Arabidopsis. Furthermore, following transient expression in tobacco (Nicotiana tabacum), we demonstrate that the subcellular location of the PjD27 protein is consistent with the cellular location of TaD27-B in wheat. Quantitative analysis of SLs shows that PjD27 is a key gene regulating tillering (branching) by participating in SL biosynthesis. By elucidating the function of the PjD27 gene, our findings provide valuable genetic resources for new germplasm creation and improving grain yield in P. juncea.

Independent regulation of strigolactones and blumenols during arbuscular mycorrhizal symbiosis in rice

The apocarotenoid strigolactones (SLs) facilitate pre-symbiotic communication between arbuscular mycorrhizal (AM) fungi and plants. Related blumenol-C-glucosides (blumenols), have also been associated with symbiosis, but the cues that are involved in the regulation of blumenol accumulation during AM symbiosis remain unclear. In rice, our analyses demonstrated a strict correlation between foliar blumenol abundance and intraradical fungal colonisation. More specifically, rice mutants affected at distinct stages of the interaction revealed that fungal cortex invasion was required for foliar blumenol accumulation. Plant phosphate status and D14L hormone signalling had no effect, contrasting their known role in induction of SLs. This a proportion of the SL biosynthetic enzymes, D27 and D17, are equally required for blumenol production. These results importantly clarify that, while there is a partially shared biosynthetic pathway between SL and blumenols, the dedicated induction of the related apocarotenoids occurs in response to cues acting at distinct stages during the root colonisation process. However, we reveal that neither SLs nor blumenols are essential for fungal invasion of rice roots.

Temperature Effect on Rhizome Development in Perennial rice

Traditional agriculture is becoming increasingly not adapted to global climate change. Compared with annual rice, perennial rice has strong environmental adaptation and needs fewer natural resources and labor inputs. Rhizome, a kind of underground stem for rice to achieve perenniallity, can grow underground horizontally and then bend upward, developing into aerial stems. The temperature has a great influence on plant development. To date, the effect of temperature on rhizome development is still unknown. Fine temperature treatment of Oryza longistaminata (OL) proved that compared with higher temperatures (28-30 ℃), lower temperature (17-19 ℃) could promote the sprouting of axillary buds and enhance negative gravitropism of branches, resulting in shorter rhizomes. The upward growth of branches was earlier at low temperature than that at high temperature, leading to a high frequency of shorter rhizomes and smaller branch angles. Comparative transcriptome showed that plant hormones played an essential role in the response of OL to temperature. The expressions of ARF17, ARF25 and FucT were up-regulated at low temperature, resulting in prospectively asymmetric auxin distribution, which subsequently induced asymmetric expression of IAA20 and WOX11 between the upper and lower side of the rhizome, further leading to upward growth of the rhizome. Cytokinin and auxin are phytohormones that can promote and inhibit bud outgrowth, respectively. The auxin biosynthesis gene YUCCA1 and cytokinin oxidase/dehydrogenase gene CKX4 and CKX9 were up-regulated, while cytokinin biosynthesis gene IPT4 was down-regulated at high temperature. Moreover, the D3 and D14 in strigolactones pathways, negatively regulating bud outgrowth, were up-regulated at high temperature. These results indicated that cytokinin, auxins, and strigolactones jointly control bud outgrowth at different temperatures. Our research revealed that the outgrowth of axillary bud and the upward growth of OL rhizome were earlier at lower temperature, providing clues for understanding the rhizome growth habit under different temperatures, which would be helpful for cultivating perennial rice.

Transcriptome-Based Weighted Gene Co-Expression Network Analysis Reveals the Photosynthesis Pathway and Hub Genes Involved in Promoting Tiller Growth under Repeated Drought-Rewatering Cycles in Perennial Ryegrass

Drought stress, which often occurs repeatedly across the world, can cause multiple and long-term effects on plant growth. However, the repeated drought-rewatering effects on plant growth remain uncertain. This study was conducted to determine the effects of drought-rewatering cycles on aboveground growth and explore the underlying mechanisms. Perennial ryegrass plants were subjected to three watering regimes: well-watered control (W), two cycles of drought-rewatering (D2R), and one cycle of drought-rewatering (D1R). The results indicated that the D2R treatment increased the tiller number by 40.9% and accumulated 28.3% more aboveground biomass compared with W; whereas the D1R treatment reduced the tiller number by 23.9% and biomass by 42.2% compared to the W treatment. A time-course transcriptome analysis was performed using crown tissues obtained from plants under D2R and W treatments at 14, 17, 30, and 33 days (d). A total number of 2272 differentially expressed genes (DEGs) were identified. In addition, an in-depth weighted gene co-expression network analysis (WGCNA) was carried out to investigate the relationship between RNA-seq data and tiller number. The results indicated that DEGs were enriched in photosynthesis-related pathways and were further supported by chlorophyll content measurements. Moreover, tiller-development-related hub genes were identified in the D2R treatment, including F-box/LRR-repeat MAX2 homolog (D3), homeobox-leucine zipper protein HOX12-like (HOX12), and putative laccase-17 (LAC17). The consistency of RNA-seq and qRT-PCR data were validated by high Pearson's correlation coefficients ranging from 0.899 to 0.998. This study can provide a new irrigation management strategy that might increase plant biomass with less water consumption. In addition, candidate photosynthesis and hub genes in regulating tiller growth may provide new insights for drought-resistant breeding.

Unveiling the complexity of strigolactones: exploring structural diversity, biosynthesis pathways, and signaling mechanisms

Strigolactone is the collective name for compounds containing a butenolide as a part of their structure, first discovered as compounds that induce seed germination of root parasitic plants. They were later found to be rhizosphere signaling molecules that induce hyphal branching of arbuscular mycorrhizal fungi, and, finally, they emerged as a class of plant hormones. Strigolactones are found in root exudates, where they display a great variability in their chemical structure. Their structure varies among plant species, and multiple strigolactones can exist in one species. Over 30 strigolactones have been identified, yet the chemical structure of the strigolactone that functions as an endogenous hormone and is found in the above-ground parts of plants remains unknown. We discuss our current knowledge of the synthetic pathways of diverse strigolactones and their regulation, as well as recent progress in identifying strigolactones as plant hormones. Strigolactone is perceived by the DWARF14 (D14), receptor, an α/β hydrolase which originated by gene duplication of KARRIKIN INSENSITIVE 2 (KAI2). D14 and KAI2 signaling pathways are partially overlapping paralogous pathways. Progress in understanding the signaling mechanisms mediated by two α/β hydrolase receptors as well as remaining challenges in the field of strigolactone research are reviewed.

D27-like carotenoid isomerases: at the crossroads of strigolactone and abscisic acid biosynthesis

Strigolactones and abscisic acid (ABA) are apocarotenoid-derived plant hormones. Their biosynthesis starts with the conversion of trans-carotenes into cis forms, which serve as direct precursors. Iron-containing DWARF27 isomerases were shown to catalyse or contribute to the trans/cis conversions of these precursor molecules. D27 converts trans-β-carotene into 9-cis-β-carotene, which is the first committed step in strigolactone biosynthesis. Recent studies found that its paralogue, D27-LIKE1, also catalyses this conversion. A crucial step in ABA biosynthesis is the oxidative cleavage of 9-cis-violaxanthin and/or 9-cis-neoxanthin, which are formed from their trans isomers by unknown isomerases. Several lines of evidence point out that D27-like proteins directly or indirectly contribute to 9-cis-violaxanthin conversion, and eventually ABA biosynthesis. Apparently, the diversity of D27-like enzymatic activity is essential for the optimization of cis/trans ratios, and hence act to maintain apocarotenoid precursor pools. In this review, we discuss the functional divergence and redundancy of D27 paralogues and their potential direct contribution to ABA precursor biosynthesis. We provide updates on their gene expression regulation and alleged Fe-S cluster binding feature. Finally, we conclude that the functional divergence of these paralogues is not fully understood and we provide an outlook on potential directions in research.

Genome-Wide Identification and Expression Analysis of DWARF53 Gene in Response to GA and SL Related to Plant Height in Banana

Dwarfing is one of the common phenotypic variations in asexually reproduced progeny of banana, and dwarfed banana is not only windproof and anti-fallout but also effective in increasing acreage yield. As a key gene in the strigolactone signalling pathway, DWARF53 (D53) plays an important role in the regulation of the height of plants. In order to gain insight into the function of the banana D53 gene, this study conducted genome-wide identification of banana D53 gene based on the M. acuminata, M. balbisiana and M. itinerans genome database. Analysis of MaD53 gene expression under high temperature, low temperature and osmotic stress based on transcriptome data and RT-qPCR was used to analyse MaD53 gene expression in different tissues as well as in different concentrations of GA and SL treatments. In this study, we identified three MaD53, three MbD53 and two MiD53 genes in banana. Phylogenetic tree analysis showed that D53 Musa are equally related to D53 Asparagales and Poales. Both high and low-temperature stresses substantially reduced the expression of the MaD53 gene, but osmotic stress treatments had less effect on the expression of the MaD53 gene. GR24 treatment did not significantly promote the height of the banana, but the expression of the MaD53 gene was significantly reduced in roots and leaves. GA treatment at 100 mg/L significantly promoted the expression of the MaD53 gene in roots, but the expression of this gene was significantly reduced in leaves. In this study, we concluded that MaD53 responds to GA and SL treatments, but "Yinniaijiao" dwarf banana may not be sensitive to GA and SL.

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.

Strigolactone and abscisic acid synthesis and signaling pathways are enhanced in the wheat oligo-tillering mutant ot1

Tiller number greatly contributes to grain yield in wheat. Using ethylmethanesulfonate mutagenesis, we previously discovered the oligo-tillering mutant ot1. The tiller number was significantly lower in ot1 than in the corresponding wild type from the early tillering stage until the heading stage. Compared to the wild type, the thousand-grain weight and grain length were increased by 15.41% and 31.44%, respectively, whereas the plant height and spike length were decreased by 26.13% and 37.25%, respectively. Transcriptomic analysis was conducted at the regreening and jointing stages to identify differential expressed genes (DEGs). Functional enrichment analysis with the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases showed differential expression of genes associated with ADP binding, transmembrane transport, and transcriptional regulation during tiller development. Differences in tiller number in ot1 led to the upregulation of genes in the strigolactone (SL) and abscisic acid (ABA) pathways. Specifically, the SL biosynthesis genes DWARF (D27), D17, D10, and MORE AXILLARY GROWTH 1 (MAX1) were upregulated by 3.37- to 8.23-fold; the SL signal transduction genes D14 and D53 were upregulated by 1.81- and 1.32-fold, respectively; the ABA biosynthesis genes 9-CIS-EPOXICAROTENOID DIOXIGENASE 3 (NCED3) and NCED5 were upregulated by 1.66- and 3.4-fold, respectively; and SNF1-REGULATED PROTEIN KINASE2 (SnRK2) and PROTEIN PHOSPHATASE 2C (PP2C) genes were upregulated by 1.30- to 4.79-fold. This suggested that the tiller number reduction in ot1 was due to alterations in plant hormone pathways. Genes known to promote tillering growth were upregulated, whereas those known to inhibit tillering growth were downregulated. For example, PIN-FORMED 9 (PIN9), which promotes tiller development, was upregulated by 8.23-fold in ot1; Ideal Plant Architecture 1 (IPA1), which inhibits tiller development, was downregulated by 1.74-fold. There were no significant differences in the expression levels of TILLER NUMBER 1 (TN1) or TEOSINTE BRANCHED 1 (TB1), indicating that the tiller reduction in ot1 was not controlled by known genes. Our findings provide valuable data for subsequent research into the genetic bases and regulatory mechanisms of wheat tillering.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01450-3.

Perception of strigolactones and the coordinated phytohormonal regulation on rice (Oryza sativa) tillering is affected by endogenous ascorbic acid

Phytohormones play a key role in regulating tiller number. Ascorbic acid (Asc)-phytohormone interaction plays a pivotal role in the regulation of senescence. We analysed the relationship between Asc and the enzyme concentrations and gene transcript abundances related to the signal perception of strigolactones (SLs), the contents of four phytohormones (abscisic acid, ABA; jasmonic acid, JA; indole acetic acid, IAA; cytokinin, CTK), the enzyme concentrations and gene transcript abundances related to the synthesis or transportation of these four phytohormones. Our results showed that Asc deficiency leads to the upregulation of enzyme concentrations, gene transcript abundances related to the SL signal perception, ABA synthesis and IAA transport. The altered level of Asc also leads to a change in the contents of ABA, JA, IAA and CTK. These findings support the conclusion that Asc or Asc/DHA play an important role in the signal perception and transduction of SLs, and Asc may affect the coordinated regulation of SL, IAA and CTK on rice (Oryza sativa ) tillering.

miRNAs and genes as molecular regulators of rice grain morphology and yield

Rice is one of the most consumed crops worldwide and the genetic and molecular basis of its grain yield attributes are well understood. Various studies have identified different yield-related parameters in rice that are regulated by the microRNAs (miRNAs). MiRNAs are endogenous small non-coding RNAs that silence gene expression during or after transcription. They control a variety of biological or genetic activities in plants including growth, development and response to stress. In this review, we have summarized the available information on the genetic control of panicle architecture and grain yield (number and morphology) in rice. The miRNA nodes that are associated with their regulation are also described while focussing on the central role of miR156-SPL node to highlight the co-regulation of two master regulators that determine the fate of panicle development. Since abiotic stresses are known to negatively affect yield, the impact of abiotic stress induced alterations on the levels of these miRNAs are also discussed to highlight the potential of miRNAs for regulating crop yields.

Field-work reveals a novel function for MAX2 in a native tobacco's high-light adaptions

Laboratory studies have revealed that strigolatone (SL) and karrikin (KAR) signalling mediate responses to abiotic and biotic stresses, and reshape branching architecture that could increase reproductive performance and crop yields. To understand the ecological function of SL and KAR signalling, transgenic lines of wild tobacco Nicotiana attenuata, silenced in SL/KAR biosynthesis/signalling were grown in the glasshouse and in two field plots in the Great Basin Desert in Utah over four field seasons. Of the lines silenced in SL and KAR signalling components (irMAX2, irD14, irKAI2 and irD14 × irKAI2 plants), which exhibited the expected increases in shoot branching, only irMAX2 plants showed a strong leaf-bleaching phenotype when grown in the field. In the field, irMAX2 plants had lower sugar and higher leaf amino acid contents, lower lifetime fitness and were more susceptible to herbivore attack compared to wild-type plants. These irMAX2 phenotypes were not observed in glasshouse-grown plants. Transcriptomic analysis revealed dramatic responses to high-light intensity in irMAX2 leaves in the field: lutein contents decreased, and transcriptional responses to high-intensity light, singlet oxygen and hydrogen peroxide increased. PAR and UV-B manipulations in the field revealed that the irMAX2 bleaching phenotype is reversed by decreasing PAR, but not UV-B fluence. We propose that NaMAX2 functions in high-light adaptation and fitness optimisation by regulating high-light responses independently of its roles in the SL and KAR signalling pathways. The work provides another example of the value of studying the function of genes in the complex environments in which plants evolved, namely nature.

Conformational Dynamics of the D53-D3-D14 Complex in Strigolactone Signaling

Strigolactones (SLs) play fundamental roles in regulating plant architecture, which is a major factor determining crop yield. The perception and signal transduction of SLs require the formation of a complex containing the receptor DWARF14 (D14), an F-box protein D3 and a transcriptional regulator D53 in an SL-dependent manner. Structural and biochemical analyses of D14 and its orthologs DAD2 and AtD14, D3 and the complexes of ASK1-D3-AtD14 and D3CTH-D14 have made great contributions to understanding the mechanisms of SL perception. However, structural analyses of D53 and the D53-D3-D14 holo-complex are challenging, and the biochemical mechanism underlying the complex assembly remains poorly understood. Here, we found that apo-D53 was rather flexible and reconstituted the holo-complex containing D53, S-phase kinase-associated protein 1 (SKP1), D3 and D14 with rac-GR24. The cryo-electron microscopy (cryo-EM) structure of SKP1-D3-D14 in the presence of D53 was analyzed and superimposed on the crystal structure of ASK1-D3-AtD14 without D53. No large conformational rearrangement was observed, but a 9Å rotation appeared between D14 and AtD14. Using hydrogen-deuterium exchange monitored by mass spectrometry, we analyzed dynamic motifs of D14, D3 and D53 in the D53-SKP1-D3-D14 complex assembly process and further identified two potential interfaces in D53 that are located in the N and D2 domains, respectively. Together, our results uncovered the dynamic conformational changes and built a model of the holo-complex D53-SKP1-D3-D14, offering valuable information for the biochemical and genetic mechanisms of SL perception and signal transduction.

Activation of Strigolactone Biosynthesis by the DWARF14-LIKE/KARRIKIN-INSENSITIVE2 Pathway in Mycorrhizal Angiosperms, but Not in Arabidopsis, a Non-mycorrhizal Plant

Strigolactones (SLs) are a class of plant hormones that regulate many aspects of plant growth and development. SLs also improve symbiosis with arbuscular mycorrhizal fungi (AMF) in the rhizosphere. Recent studies have shown that the DWARF14-LIKE (D14L)/KARRIKIN-INSENSITIVE2 (KAI2) family, paralogs of the SL receptor D14, are required for AMF colonization in several flowering plants, including rice. In this study, we found that (-)-GR5, a 2'S-configured enantiomer of a synthetic SL analog (+)-GR5, significantly activated SL biosynthesis in rice roots via D14L. This result is consistent with a recent report, showing that the D14L pathway positively regulates SL biosynthesis in rice. In fact, the SL levels tended to be lower in the roots of the d14l mutant under both inorganic nutrient-deficient and -sufficient conditions. We also show that the increase in SL levels by (-)-GR5 was observed in other mycorrhizal plant species. In contrast, the KAI2 pathway did not upregulate the SL level and the expression of SL biosynthetic genes in Arabidopsis, a non-mycorrhizal plant. We also examined whether the KAI2 pathway enhances SL biosynthesis in the liverwort Marchantia paleacea, where SL functions as a rhizosphere signaling molecule for AMF. However, the SL level and SL biosynthetic genes were not positively regulated by the KAI2 pathway. These results imply that the activation of SL biosynthesis by the D14L/KAI2 pathway has been evolutionarily acquired after the divergence of bryophytes to efficiently promote symbiosis with AMF, although we cannot exclude the possibility that liverworts have specifically lost this regulatory system.

Integrating stay-green and PIN-FORMED genes: PIN-FORMED genes as potential targets for designing climate-resilient cereal ideotypes

Plant architecture modification (e.g. short-stature crops) is one of the key outcomes of modern crop breeding for high-yielding crop varieties. In cereals, delayed senescence, or stay-green, is an important trait that enables post-anthesis drought stress adaptation. Stay-green crops can prolong photosynthetic capacity during grain-filling period under post-anthesis drought stress, which is essential to ensure grain yield is not impacted under drought stress conditions. Although various stay-green quantitative trait loci have been identified in cereals, the underlying molecular mechanisms regulating stay-green remain elusive. Recent advances in various gene-editing technologies have provided avenues to fast-track crop improvement, such as the breeding of climate-resilient crops in the face of climate change. We present in this viewpoint the focus on using sorghum as the model cereal crop, to study PIN-FORMED (PIN) auxin efflux carriers as means to modulate plant architecture, and the potential to employ it as an adaptive strategy to address the environmental challenges posed by climate uncertainties.

Strigolactones positively regulate Verticillium wilt resistance in cotton via crosstalk with other hormones

Verticillium wilt caused by Verticillium dahliae is a serious vascular disease in cotton (Gossypium spp.). V. dahliae induces the expression of the CAROTENOID CLEAVAGE DIOXYGENASE 7 (GauCCD7) gene involved in strigolactone (SL) biosynthesis in Gossypium australe, suggesting a role for SLs in Verticillium wilt resistance. We found that the SL analog rac-GR24 enhanced while the SL biosynthesis inhibitor TIS108 decreased cotton resistance to Verticillium wilt. Knock-down of GbCCD7 and GbCCD8b genes in island cotton (Gossypium barbadense) decreased resistance, whereas overexpression of GbCCD8b in upland cotton (Gossypium hirsutum) increased resistance to Verticillium wilt. Additionally, Arabidopsis (Arabidopsis thaliana) SL mutants defective in CCD7 and CCD8 putative orthologs were susceptible, whereas both Arabidopsis GbCCD7- and GbCCD8b-overexpressing plants were more resistant to Verticillium wilt than wild-type (WT) plants. Transcriptome analyses showed that several genes related to the jasmonic acid (JA)- and abscisic acid (ABA)-signaling pathways, such as MYELOCYTOMATOSIS 2 (GbMYC2) and ABA-INSENSITIVE 5, respectively, were upregulated in the roots of WT cotton plants in responses to rac-GR24 and V. dahliae infection but downregulated in the roots of both GbCCD7- and GbCCD8b-silenced cotton plants. Furthermore, GbMYC2 suppressed the expression of GbCCD7 and GbCCD8b by binding to their promoters, which might regulate the homeostasis of SLs in cotton through a negative feedback loop. We also found that GbCCD7- and GbCCD8b-silenced cotton plants were impaired in V. dahliae-induced reactive oxygen species (ROS) accumulation. Taken together, our results suggest that SLs positively regulate cotton resistance to Verticillium wilt through crosstalk with the JA- and ABA-signaling pathways and by inducing ROS accumulation.

MORE PANICLES 3, a natural allele of OsTB1/FC1, impacts rice yield in paddy fields at elevated CO2 levels

Improving crop yield potential through an enhanced response to rising atmospheric CO₂ levels is an effective strategy for sustainable crop production in the face of climate change. Large-sized panicles (containing many spikelets per panicle) have been a recent ideal plant architecture (IPA) for high-yield rice breeding. However, few breeding programs have proposed an IPA under the projected climate change. Here, we demonstrate through the cloning of the rice (Oryza sativa) quantitative trait locus for MORE PANICLES 3 (MP3) that the improvement in panicle number increases grain yield at elevated atmospheric CO₂ levels. MP3 is a natural allele of OsTB1/FC1, previously reported as a negative regulator of tiller bud outgrowth. The temperate japonica allele advanced the developmental process in axillary buds, moderately promoted tillering, and increased the panicle number without negative effects on the panicle size or culm thickness in a high-yielding indica cultivar with large-sized panicles. The MP3 allele, containing three exonic polymorphisms, was observed in most accessions in the temperate japonica subgroups but was rarely observed in the indica subgroup. No selective sweep at MP3 in either the temperate japonica or indica subgroups suggested that MP3 has not been involved and utilized in artificial selection during domestication or breeding. A free-air CO₂ enrichment experiment revealed a clear increase of grain yield associated with the temperate japonica allele at elevated atmospheric CO₂ levels. Our findings show that the moderately increased panicle number combined with large-sized panicles using MP3 could be a novel IPA and contribute to an increase in rice production under climate change with rising atmospheric CO₂ levels.

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.

Strigolactones: diversity, perception, and hydrolysis

Strigolactones (SLs) are a unique and novel class of phytohormones that regulate numerous processes of growth and development in plants. Besides their endogenous functions as hormones, SLs are exuded by plant roots to stimulate critical interactions with symbiotic fungi but can also be exploited by parasitic plants to trigger their seed germination. In the past decade, since their discovery as phytohormones, rapid progress has been made in understanding the SL biosynthesis and signaling pathway. Of particular interest are the diversification of natural SLs and their exact mode of perception, selectivity, and hydrolysis by their dedicated receptors in plants. Here we provide an overview of the emerging field of SL perception with a focus on the diversity of canonical, non-canonical, and synthetic SL probes. Moreover, this review offers useful structural insights into SL perception, the precise molecular adaptations that define receptor-ligand specificities, and the mechanisms of SL hydrolysis and its attenuation by downstream signaling components.

Maize domestication phenotypes reveal strigolactone networks coordinating grain size evolution with kernel-bearing cupule architecture

The maize (Zea mays) ear represents one of the most striking domestication phenotypes in any crop species, with the cob conferring an exceptional yield advantage over the ancestral form of teosinte. Remodeling of the grain-bearing surface required profound developmental changes. However, the underlying mechanisms remain unclear and can only be partly attributed to the known domestication gene Teosinte glume architecture 1 (Tga1). Here we show that a more complete conversion involves strigolactones (SLs), and that these are prominent players not only in the Tga1 phenotype but also other domestication features of the ear and kernel. Genetic combinations of a teosinte tga1 allele with three SL-related mutants progressively enhanced ancestral morphologies. The SL mutants, in addition to modulating the tga1 phenotype, also reshaped kernel-bearing pedicels and cupules in a teosinte-like manner. Genetic and molecular evidence are consistent with SL regulation of TGA1, including direct interaction of TGA1 with components of the SL-signaling system shown here to mediate TGA1 availability by sequestration. Roles of the SL network extend to enhancing maize seed size and, importantly, coordinating increased kernel growth with remodeling of protective maternal tissues. Collectively, our data show that SLs have central roles in releasing kernels from restrictive maternal encasement and coordinating other factors that increase kernel size, physical support, and their exposure on the grain-bearing surface.

Identification of new potential downstream transcriptional targets of the strigolactone pathway including glucosinolate biosynthesis

Strigolactones regulate shoot branching and many aspects of plant growth, development, and allelopathy. Strigolactones are often discussed alongside auxin because they work together to inhibit shoot branching. However, the roles and mechanisms of strigolactones and how they act independently of auxin are still elusive. Additionally, there is still much in general to be discovered about the network of molecular regulators and their interactions in response to strigolactones. Here, we conducted an experiment in Arabidopsis with physiological treatments and strigolactone mutants to determine transcriptional pathways associated with strigolactones. The three physiological treatments included shoot tip removal with and without auxin treatment and treatment of intact plants with the auxin transport inhibitor, N-1-naphthylphthalamic acid (NPA). We identified the glucosinolate biosynthesis pathway as being upregulated across strigolactone mutants indicating strigolactone-glucosinolate crosstalk. Additionally, strigolactone application cannot restore the highly branched phenotype observed in glucosinolate biosynthesis mutants, placing glucosinolate biosynthesis downstream of strigolactone biosynthesis. Oxidative stress genes were enriched across the experiment suggesting that this process is mediated through multiple hormones. Here, we also provide evidence supporting non-auxin-mediated, negative feedback on strigolactone biosynthesis. Increases in strigolactone biosynthesis gene expression seen in strigolactone mutants could not be fully restored by auxin. By contrast, auxin could fully restore auxin-responsive gene expression increases, but not sugar signaling-related gene expression. Our data also point to alternative roles of the strigolactone biosynthesis genes and potential new signaling functions of strigolactone precursors. In this study, we identify a strigolactone-specific regulation of glucosinolate biosynthesis genes indicating that the two are linked and may work together in regulating stress and shoot ranching responses in Arabidopsis. Additionally, we provide evidence for non-auxinmediated feedback on strigolactone biosynthesis and discuss this in the context of sugar signaling.

Prohexadione calcium enhances rice growth and tillering under NaCl stress

Salt stress affects crop quality and reduces crop yields, and growth regulators enhance salt tolerance of crop plants. In this report, we examined the effects of prohexadione-calcium (Pro-Ca) on improving rice (Oryza sativa L.) growth and tillering under salt stress. We found that NaCl stress inhibited the growth of two rice varieties and increased malondialdehyde (MDA) levels, electrolyte leakage, and the activities of the antioxidant enzymes. Foliar application of Pro-Ca reduced seedling height and increased stem base width and lodging resistance of rice. Further analyses showed that Pro-Ca application reduced MDA content, electrolyte leakage, and membrane damage in rice leaves under NaCl stress. Pro-Ca enhanced the net photosynthetic rate (Pn), stomatal conductance (Gs), and intercellular CO₂ concentration (Ci) of rice seedlings, while increasing the activities of superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbic acid peroxidase (APX) at the tillering stage under salt stress. Overall, Pro-Ca improves salt tolerance of rice seedlings at the tillering stage by enhancing lodging resistance, reducing membrane damages, and enhancing photosynthesis and antioxidant capacities of rice seedlings.

Potentially Useful Dwarfing or Semi-dwarfing Genes in Rice Breeding in Addition to the sd1 Gene

The "Green revolution" gene sd1 has been used widely in the breeding of modern rice varieties for over half a century. The application of this gene has increased rice yields and thereby supported a significant proportion of the global population. The use of a single gene, however, has raised concerns in the scientific community regarding its durability, especially given the bottleneck in genetic background and the need for large input of fertilizer. New dwarfing or semi-dwarfing genes are needed to alleviate our dependence on the sole "Green revolution" gene. In the past few years, several new dwarfing and semi-dwarfing genes as well as their mutants have been reported. Here, we provide an extensive review of the recent discoveries concerning newly identified genes that are potentially useful in rice breeding, including methods employed to create and effectively screen new rice mutants, the phenotypic characteristics of the new dwarfing and semi-dwarfing mutants, potential values of the new dwarfing and semi-dwarfing genes in rice breeding, and potential molecular mechanisms associated with the newly identified genes.

Candidate loci for leaf angle in maize revealed by a combination of genome-wide association study and meta-analysis

Leaf angle (LA) is a key component of maize plant architecture that can simultaneously govern planting density and improve final yield. However, the genetic mechanisms underlying LA have not been fully addressed. To broaden our understanding of its genetic basis, we scored three LA-related traits on upper, middle, and low leaves of 492 maize inbred lines in five environments. Phenotypic data revealed that the three LA-related traits were normally distributed, and significant variation was observed among environments and genotypes. A genome-wide association study (GWAS) was then performed to dissect the genetic factors that control natural variation in maize LA. In total, 85 significant SNPs (involving 32 non-redundant QTLs) were detected (p ≤ 2.04 × 10-6), and individual QTL explained 4.80%-24.09% of the phenotypic variation. Five co-located QTL were detected in at least two environments, and two QTLs were co-located with multiple LA-related traits. Forty-seven meta-QTLs were identified based on meta-analysis combing 294 LA-related QTLs extracted from 18 previously published studies, 816 genes were identified within these meta-QTLs, and seven co-located QTLs were jointly identified by both GWAS and meta-analysis. ZmULA1 was located in one of the co-located QTLs, qLA7, and its haplotypes, hap1 and hap2, differed significantly in LA-related traits. Interestingly, the temperate materials with hap2 had smallest LA. Finally, we also performed haplotype analysis using the reported genes that regulate LA, and identified a lot of maize germplasms that aggregated favorable haplotypes. These results will be helpful for elucidating the genetic basis of LA and breeding new maize varieties with ideal plant architecture.

Arbuscular mycorrhizal fungi induce lateral root development in angiosperms via a conserved set of MAMP receptors

Root systems regulate their branching patterns in response to environmental stimuli. Lateral root development in both monocotyledons and dicotyledons is enhanced in response to inoculation with arbuscular mycorrhizal (AM) fungi, which has been interpreted as a developmental response to specific, symbiosis-activating chitinaceous signals. Here, we report that generic instead of symbiosis-specific, chitin-derived molecules trigger lateral root formation. We demonstrate that this developmental response requires the well-known microbe-associated molecular pattern (MAMP) receptor, ChitinElicitorReceptorKinase 1 (CERK1), in rice, Medicago truncatula, and Lotus japonicus, as well as the non-host of AM fungi, Arabidopsis thaliana, lending further support for a broadly conserved signal transduction mechanism across angiosperms. Using rice mutants impaired in strigolactone biosynthesis and signaling, we show that strigolactone signaling is necessary to regulate this developmental response. Rice CERK1 operates together with either Chitin Elicitor Binding Protein (CEBiP) or Nod Factor Receptor 5 (NFR5) in immunity and symbiosis signaling, respectively; for the lateral root response, however, all three LysM receptors are required. Our work, therefore, reveals an overlooked but a conserved role of LysM receptors integrating MAMP perception with developmental responses in plants, an ability that might influence the interaction between roots and the rhizosphere biota.

Dwarf and High Tillering1 represses rice tillering through mediating the splicing of D14 pre-mRNA

Strigolactones (SLs) constitute a class of plant hormones that regulate many aspects of plant development, including repressing tillering in rice (Oryza sativa). However, how SL pathways are regulated is still poorly understood. Here, we describe a rice mutant dwarf and high tillering1 (dht1), which exhibits pleiotropic phenotypes (such as dwarfism and increased tiller numbers) similar to those of mutants defective in SL signaling. We show that DHT1 encodes a monocotyledon-specific hnRNP-like protein that acts as a previously unrecognized intron splicing factor for many precursor mRNAs (pre-mRNAs), including for the SL receptor gene D14. We find that the dht1 (DHT1I232F) mutant protein is impaired in its stability and RNA binding activity, causing defective splicing of D14 pre-mRNA and reduced D14 expression, and consequently leading to the SL signaling-defective phenotypes. Overall, our findings deepen our understanding of the functional diversification of hnRNP-like proteins and establish a connection between posttranscriptional splicing and SL signaling in the regulation of plant development.

Strigolactones and Cytokinin Interaction in Buds in the Control of Rice Tillering

Shoot branching is among the most crucial morphological traits in rice (Oryza sativa L.) and is physiologically modulated by auxins, cytokinins (CKs), and strigolactones (SLs) cumulatively in rice. A number of studies focused on the interplay of these three hormones in regulating rice tiller extension. The present study primarily aimed at determining the impact of different treatments, which were used to regulate rice tiller and axillary bud development on node 2 at the tillering stage and full heading stage, respectively. Transcription levels of several genes were quantified through qRT-PCR analysis, and an endogenous auxin and four types of CKs were determined through LC-MS/MS. Both nutrient deficiency and exogenous SL supply were found to inhibit rice tiller outgrowth by reducing the CK content in the tiller buds. Furthermore, supplying the inhibitor of both exogenous SLs and endogenous SL synthesis could also affect the expression level of OsCKX genes but not the OsIPT genes. Comparison of OsCKX gene expression pattern under exogenous SL and CK supply suggested that the induction of OsCKX expression was most likely via a CK-induced independent pathway. These results combined with the expression of CK type-A RR genes in bud support a role for SLs in regulating bud outgrowth through the regulation of local CK levels. SL functioned antagonistically with CK in regulating the outgrowth of buds on node 2, by promoting the OsCKX gene expression in buds.

The miR528-D3 Module Regulates Plant Height in Rice by Modulating the Gibberellin and Abscisic Acid Metabolisms

Plant height, as one of the important agronomic traits of rice, is closely related to yield. In recent years, plant height-related genes have been characterized and identified, among which the DWARF3 (D3) gene is one of the target genes of miR528, and regulates rice plant height and tillering mainly by affecting strigolactone (SL) signal transduction. However, it remains unknown whether the miR528 and D3 interaction functions in controlling plant height, and the underlying regulatory mechanism in rice. In this study, we found that the plant height, internode length, and cell length of internodes of d3 mutants and miR528-overexpressing (OE-miR528) lines were greatly shorter than WT, D3-overexpressing (OE-D3), and miR528 target mimicry (OE-MIM528) transgenic plants. Knockout of D3 gene (d3 mutants) or miR528-overexpressing (OE-miR528) triggers a substantial reduction of gibberellin (GA) content, but a significant increase of abscisic acid (ABA) accumulation than in WT. The d3 and OE-miR528 transgenic plants were much more sensitive to GA, but less sensitive to ABA than WT. Moreover, the expression level of GA biosynthesis-related key genes, including OsCPS1, OsCPS2, OsKO2 and OsKAO was remarkably higher in OE-D3 plants, while the NECD2 expression, a key gene involved in ABA biosynthesis, was significantly higher in d3 mutants than in WT and OE-D3 plants. The results indicate that the miR528-D3 module negatively regulates plant height in rice by modulating the GA and ABA homeostasis, thereby further affecting the elongation of internodes, and resulting in lower plant height, which adds a new regulatory role to the D3-mediated plant height controlling in rice.

QTL mapping of morphological characteristics that correlated to drought tolerance in St. Augustinegrass

St. Augustinegrass is a warm-season grass species widely utilized as turf in the southeastern U.S. It shows significant variation in plant growth and morphological characteristics, some of which are potentially associated with drought tolerance. However, the genetic basis of these variations is not well understood. Detecting quantitative trait loci (QTL) associated with morphological traits will provide a foundation for the application of genetic and molecular breeding in St. Augustinegrass. In this study, we report QTL associated with morphological traits, including leaf blade width (LW), leaf blade length (LL), canopy density (CD), and shoot growth orientation (SGO) in a St. Augustinegrass ‘Raleigh’ x ‘Seville’ mapping population containing 115 F1 hybrids. Phenotypic data were collected from one greenhouse and two field trials. Single and joint trial analyses were performed, finding significant phenotypic variance among the hybrids for all traits. Interval mapping (IM) and multiple QTL method (MQM) analysis detected seven QTL for CD, four for LL, five for LW, and two for SGO, which were distributed on linkage groups RLG1, RLG9, SLG3, SLG7, SLG8 and SLG9. In addition, three genomic regions where QTL colocalized were identified on Raleigh LG1 and Seville LG3. One genomic region on Seville LG3 overlapped with two previously reported drought-related QTL for leaf relative water content (RWC) and percent green cover (GC). Several candidate genes related to plant development and drought stress response were identified within QTL intervals. The QTL identified in this study represent a first step in identifying genes controlling morphological traits that might accelerate progress in selection of St. Augustinegrass lines with lower water usage.

A conformational switch in the SCF-D3/MAX2 ubiquitin ligase facilitates strigolactone signalling

Strigolactones (SLs) are a class of plant hormones that regulate numerous processes of growth and development. SL perception and signal activation involves interaction between F-box E3 ubiquitin ligase D3/MAX2 and DWARF14 (D14) α/β-hydrolase in a SL-dependent manner and targeting of D53/SMXL6/7/8 transcriptional repressors (SMXLs) for proteasome-mediated degradation. D3/MAX2 has been shown to exist in multiple conformational states in which the C-terminal helix (CTH) undergoes a closed-to-open dynamics and regulates D14 binding and SL perception. Despite the multiple modes of D3-D14 interactions found in vitro, the residues that regulate the conformational switch of D3/MAX2 CTH in targeting D53/SMXLs and the subsequent effect on SL signalling remain unclear. Here we elucidate the functional dynamics of ASK1-D3/MAX2 in SL signalling by leveraging conformational switch mutants in vitro and in plants. We report the crystal structure of a dislodged CTH of the ASK1-D3 mutant and demonstrate that disruptions in CTH plasticity via either CRISPR-Cas9 genome editing or expression of point mutation mutants result in impairment of SL signalling. We show that the conformational switch in ASK1-D3/MAX2 CTH directly regulates ubiquitin-mediated protein degradation. A dislodged conformation involved in D53/SMXLs SL-dependent recruitment and ubiquitination and an engaged conformation are required for the release of polyubiquitinated D53/SMXLs and subsequently D14 for proteasomal degradation. Finally, we uncovered an organic acid metabolite that can directly trigger the D3/MAX2 CTH conformational switch. Our findings unravel a new regulatory function of a SKP1-CUL1-F-box ubiquitin ligase in plant signalling.

Wheat breeding history reveals synergistic selection of pleiotropic genomic sites for plant architecture and grain yield

Diversity surveys of crop germplasm are important for gaining insights into the genomic basis for plant architecture and grain yield improvement, which is still poorly understood in wheat. In this study, we exome sequenced 287 wheat accessions that were collected in the past 100 years. Population genetics analysis identified that 6.7% of the wheat genome falls within the selective sweeps between landraces and cultivars, which harbors the genes known for yield improvement. These regions were asymmetrically distributed on the A and B subgenomes with regulatory genes being favorably selected. Genome-wide association study (GWAS) identified genomic loci associated with traits for yield potential, and two underlying genes, TaARF12 encoding an auxin response factor and TaDEP1 encoding the G-protein γ-subunit, were located and characterized to pleiotropically regulate both plant height and grain weight. Elite single-nucleotide haplotypes with increased allele frequency in cultivars relative to the landraces were identified and found to have accumulated over the course of breeding. Interestingly, we found that TaARF12 and TaDEP1 function in epistasis with the classical plant height Rht-1 locus, leading to propose a "Green Revolution"-based working model for historical wheat breeding. Collectively, our study identifies selection signatures that fine-tune the gibberellin pathway during modern wheat breeding and provides a wealth of genomic diversity resources for the wheat research community.

Identification of One Major QTL and a Novel Gene OsIAA17q5 Associated with Tiller Number in Rice Using QTL Analysis

Rice tillers are one of the most important traits for the yield and development of rice, although little is known about its mode of inheritance. Tiller numbers were recorded every 7 days a total of nine times, starting 30 days after transplantation. Quantitative trait locus (QTL) based analysis on a set of double haploid population derivatives of a cross between the Cheongcheong and Nagdong varieties identified a major effect of locus RM18130-RM3381 on chromosome 5, which was expressed in eight different growth stages. Within the target region RM18130-RM3381 (physical distance: 2.08 Mb), 61 candidate genes were screened by annotation. Among the candidate genes, Os05g0230700 (named OsIAA17q5), which belongs to the family of auxin-responsive genes, was selected as a target. Auxin promotes cell division and meristem maintenance and is an effective plant regulator which influences plant growth and development by altering the expression of various genes. OsIAA17q5 is expected to control the number of tillers. The present study provides further understanding of the basic genetic mechanisms that selectively express the control of tiller numbers in different growth stages, as well as provides valuable information for future research aimed at cloning the target gene. These results may contribute to developing a comprehensive understanding of the basic genetic processes regulating the developmental behavior of tiller numbers in rice.

Fine mapping of the tiller inhibition gene TIN4 contributing to ideal plant architecture in common wheat

A tiller inhibition gene, TIN4, was mapped to an approximately 311 kb genomic interval on chromosome arm 2DL of wheat. The tiller is one of the key components of plant morphological architecture and a central agronomic trait affecting spike number in wheat. Low tiller number has been proposed as a major component of crop ideotypes for high yield potential. In this study, we characterized the development of tillering in near-isogenic lines (NIL7A and NIL7B), indicating that the TIN4 gene inhibited the growth of tillering buds and negatively regulated tiller number. Low-tillering was controlled by a single gene (TIN4) located on chromosome 2DL by genetic analysis and bulked segregant RNA-seq analysis. A total of 17 new polymorphic markers were developed in this study, and 61 recombinants were identified in the secondary F2 population containing 4,266 individuals. TIN4 was finally mapped on a 0.35 cM interval, co-segregated with molecular marker M380, within a 311 kb genomic interval of the wheat cultivar Chinese Spring reference genome sequence that contained twelve predicted genes. Yield experiments showed that the yield of low-tillering lines was higher than that of high-tillering lines at a higher density. Overall, this study provides a foundation for the construction of a low-tillering ideotype for improving wheat yield and further cloning TIN4 by map-based cloning approach.

RGN1 controls grain number and shapes panicle architecture in rice

Yield in rice is determined mainly by panicle architecture. Using map-based cloning, we identified an R2R3 MYB transcription factor REGULATOR OF GRAIN NUMBER1 (RGN1) affecting grain number and panicle architecture. Mutation of RGN1 caused an absence of lateral grains on secondary branches. We demonstrated that RGN1 controls lateral grain formation by regulation of LONELY GUY (LOG) expression, thus controlling grain number and shaping panicle architecture. A novel favourable allele, RGN1^C , derived from the Or-I group in wild rice affected panicle architecture by means longer panicles. Identification of RGN1 provides a theoretical basis for understanding the molecular mechanism of lateral grain formation in rice; RGN1 will be an important gene resource for molecular breeding for higher yield.

Mapping novel QTLs for yield related traits from a popular rice hybrid KRH-2 derived doubled haploid (DH) population

A doubled haploid (DH) population consisting of 125 DHLs derived from the popular rice hybrid, KRH-2 (IR58025A/KMR3R) was utilized for Quantitative Trait Loci (QTL) mapping to identify novel genomic regions associated with yield related traits. A genetic map was constructed with 126 polymorphic SSR and EST derived markers, which were distributed across rice genome. QTL analysis using inclusive composite interval mapping (ICIM) method identified a total of 24 major and minor effect QTLs. Among them, twelve major effect QTLs were identified for days to fifty percent flowering (qDFF12-1), total grain yield/plant (qYLD3-1 and qYLD6-1), test (1,000) grain weight (qTGW6-1 and qTGW7-1), panicle weight (qPW9-1), plant height (qPH12-1), flag leaf length (qFLL6-1), flag leaf width (qFLW4-1), panicle length (qPL3-1 and qPL6-1) and biomass (qBM4-1), explaining 29.95-56.75% of the phenotypic variability with LOD scores range of 2.72-16.51. Chromosomal regions with gene clusters were identified on chromosome 3 for total grain yield/plant (qYLD3-1) and panicle length (qPL3-1) and on chromosome 6 for total grain yield/plant (qYLD6-1), flag leaf length (qFLL6-1) and panicle length (qPL6-1). Majority of the QTLs identified were observed to be co-localized with the previously reported QTL regions. Five novel, major effect QTLs associated with panicle weight (qPW9-1), plant height (qPH12-1), flag leaf width (qFLW4-1), panicle length (qPL3-1) and biomass (qBM4-1) and three novel minor effect QTLs for panicle weight (qPW3-1 and qPW8-1) and fertile grains per panicle (qFGP5-1) were identified. These QTLs can be used in breeding programs aimed to yield improvement after their validation in alternative populations.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03045-7.

Strigolactones Modulate Cellular Antioxidant Defense Mechanisms to Mitigate Arsenate Toxicity in Rice Shoots

Metalloid contamination, such as arsenic poisoning, poses a significant environmental problem, reducing plant productivity and putting human health at risk. Phytohormones are known to regulate arsenic stress; however, the function of strigolactones (SLs) in arsenic stress tolerance in rice is rarely investigated. Here, we investigated shoot responses of wild-type (WT) and SL-deficient d10 and d17 rice mutants under arsenate stress to elucidate SLs’ roles in rice adaptation to arsenic. Under arsenate stress, the d10 and d17 mutants displayed severe growth abnormalities, including phenotypic aberrations, chlorosis and biomass loss, relative to WT. Arsenate stress activated the SL-biosynthetic pathway by enhancing the expression of SL-biosynthetic genes D10 and D17 in WT shoots. No differences in arsenic levels between WT and SL-biosynthetic mutants were found from Inductively Coupled Plasma-Mass Spectrometry analysis, demonstrating that the greater growth defects of mutant plants did not result from accumulated arsenic in shoots. The d10 and d17 plants had higher levels of reactive oxygen species, water loss, electrolyte leakage and membrane damage but lower activities of superoxide dismutase, ascorbate peroxidase, glutathione peroxidase and glutathione S-transferase than did the WT, implying that arsenate caused substantial oxidative stress in the SL mutants. Furthermore, WT plants had higher glutathione (GSH) contents and transcript levels of OsGSH1, OsGSH2, OsPCS1 and OsABCC1 in their shoots, indicating an upregulation of GSH-assisted arsenic sequestration into vacuoles. We conclude that arsenate stress activated SL biosynthesis, which led to enhanced arsenate tolerance through the stimulation of cellular antioxidant defense systems and vacuolar sequestration of arsenic, suggesting a novel role for SLs in rice adaptation to arsenic stress. Our findings have significant implications in the development of arsenic-resistant rice varieties for safe and sustainable rice production in arsenic-polluted soils.