The rice HIGH-TILLERING DWARF1 encoding an ortholog of Arabidopsis MAX3 is required for negative regulation of the outgrowth of axillary buds

Cadmium stress suppresses the tillering of perennial ryegrass and is associated with the transcriptional regulation of genes controlling axillary bud outgrowth

Perennial ryegrass (Lolium perenne L.), a grass species with superior tillering capacity, plays a potential role in the phytoremediation of cadmium (Cd)-contaminated soils. Tiller production is inhibited in response to serious Cd stress. However, the regulatory mechanism of Cd stress-induced inhibition of tiller development is not well documented. To address this issue, we investigated the phenotype, the expression levels of genes involved in axillary bud initiation and bud outgrowth, and endogenous hormone biosynthesis and signaling pathways in seedlings of perennial ryegrass under Cd stress. The results showed that the number of tillers and axillary buds in the Cd-treated seedlings decreased by 67% and 21%, respectively. The suppression of tiller production in the Cd-treated seedlings was more closely associated with the inhibition of axillary bud outgrowth than with bud initiation. Cd stress upregulated the expression level of genes related to axillary bud dormancy and downregulated bud activity genes. Additionally, genes involved in strigolactone biosynthesis and signaling, auxin transport and signaling, and cytokinin degradation were upregulated in Cd-treated seedlings, and cytokinin biosynthesis gene expression were decreased by Cd stress. The content of zeatin in the Cd-treated pants was significantly reduced by 69~85% compared to the control plants. The content of indole-3-acetic acid (IAA) remains constant under Cd stress. Overall, Cd stress induced axillary bud dormancy and subsequently inhibited axillary bud outgrowth. The decrease of zeatin content and upregulation of genes involved in strigolactone signaling and bud dormancy might be responsible for the inhibition of axillary bud outgrowth.

HIGH-TILLERING AND DWARF 12 modulates photosynthesis and plant architecture by affecting carotenoid biosynthesis in rice

Photosynthesis and plant architecture are important factors influencing grain yield in rice (Oryza sativa L.). Here, we identified a high-tillering and dwarf 12 (htd12) mutant and analyzed the effects of the HTD12 mutation on these important factors. HTD12 encodes a 15-cis-ζ-carotene isomerase (Z-ISO) belonging to the nitrite and nitric oxide reductase U (NnrU) protein family, as revealed by positional mapping and transformation experiments. Sequence analysis showed that a single nucleotide transition from guanine (G) to adenine (A) in the 3' acceptor site between the first intron and second exon of HTD12 alters its mRNA splicing in htd12 plants, resulting in a 49-amino acid deletion that affects carotenoid biosynthesis and photosynthesis. In addition, compared with the wild type, htd12 had significantly lower concentrations of ent-2'-epi-5-deoxystrigol (epi-5DS), a native strigolactone, in both roots and root exudates, resulting in an obvious increase in tiller number and decrease in plant height. These findings indicate that HTD12, the rice homolog of Z-ISO, regulates chloroplast development and photosynthesis by functioning in carotenoid biosynthesis, and modulates plant architecture by affecting strigolactone concentrations.

A transporter for delivering zinc to the developing tiller bud and panicle in rice

Tiller number is one of the most important agronomic traits that determine rice (Oryza sativa) yield. Active growth of tiller bud (TB) requires high amount of mineral nutrients; however, the mechanism underlying the distribution of mineral nutrients to TB with low transpiration is unknown. Here, we found that the distribution of Zn to TB is mediated by OsZIP4, one of the ZIP (ZRT, IRT-like protein) family members. The expression of OsZIP4 was highly detected in TB and nodes, and was induced by Zn deficiency. Immunostaining analysis revealed that OsZIP4 was mainly expressed in phloem of diffuse vascular bundles in the nodes and the axillary meristem. The mutation of OsZIP4 did not affect the total Zn uptake, but altered Zn distribution; less Zn was delivered to TB and new leaf, but more Zn was retained in the basal stems at the vegetative growth stage. Bioimaging analysis showed that the mutant aberrantly accumulated Zn in enlarged and transit vascular bundles of the basal node, whereas in wild-type high accumulation of Zn was observed in the meristem part. At the reproductive stage, mutation of OsZIP4 resulted in delayed panicle development, which is associated with decreased Zn distribution to the panicles. Collectively, OsZIP4 is involved in transporting Zn to the phloem of diffuse vascular bundles in the nodes for subsequent distribution to TBs and other developing tissues. It also plays a role in transporting Zn to meristem cells in the TBs.

Strigolactone biosynthesis, transport and perception

Strigolactones (SLs) are plant hormones that regulate diverse developmental processes and environmental responses. They are also known to be root-derived chemical signals that regulate symbiotic and parasitic interactions with arbuscular mycorrhizal fungi and root parasitic plants, respectively. Since the discovery of the hormonal function of SLs in 2008, there has been much progress in the SL research field. In particular, a number of breakthroughs have been achieved in our understanding of SL biosynthesis, transport and perception. The discovery of the hormonal function of SL was quite valuable not only as the identification of a new class of plant hormones, but also as the discovery of the long-sought-after SL biosynthetic and response mutants. These mutants in several plant species provided us the genetic resources to address fundamental questions regarding SL biosynthesis and perception. Such mutants were further characterized later, and biochemical analyses of these genetically identified factors have uncovered the outline of SL biosynthesis and perception so far. Moreover, new genes involved in SL transport have been discovered through reverse genetic analyses. In this review, we summarize recent advances in SL research with a focus on biosynthesis, transport and perception.

Genetic architecture to cause dynamic change in tiller and panicle numbers revealed by genome-wide association study and transcriptome profile in rice

Panicle number (PN) is one of the three yield components in rice. As one of the most unstable traits, the dynamic change in tiller number (DCTN) may determine the final PN. However, the genetic basis of DCTN and its relationship with PN remain unclear. Here, 377 deeply re-sequenced rice accessions were used to perform genome-wide association studies (GWAS) for tiller/PN. It was found that the DCTN pattern rather than maximum tiller number or effective tiller ratio is the determinant factor of high PN. The DCTN pattern that affords more panicles exhibits a period of stable tillering peak between 30 and 45 days after transplant (called DT30 and DT45, respectively), which was believed as an ideal pattern contributing to the steady transition from tiller development to panicle development (ST-TtP). Consistently, quantitative trait loci (QTL) expressed near DT30-DT45 were especially critical to the rice DCTN and in supporting the ST-TtP. The spatio-temporal expression analysis showed that the expression pattern of keeping relatively high expression in root at 24:00 (R24-P2) from about DT30 to DT45 is a typical expression pattern of cloned tiller genes, and the candidate genes with R24-P2 can facilitate the prediction of PN. Moreover, gene OsSAUR27 was identified by an integrated approach combining GWAS, bi-parental QTL mapping and transcription. These findings related to the genetic basis underlying the DCTN will provide the genetic theory in making appropriate decisions on field management, and in developing new varieties with high PN and ideal dynamic plant architecture.

Phytohormone-Mediated Molecular Mechanisms Involving Multiple Genes and QTL Govern Grain Number in Rice

Increasing the grain number is the most direct route toward enhancing the grain yield in cereals. In rice, grain number can be amplified through increasing the shoot branching (tillering), panicle branching, panicle length, and seed set percentage. Phytohormones have been conclusively shown to control the above characteristics by regulating molecular factors and their cross-interactions. The dynamic equilibrium of cytokinin levels in both shoot and inflorescence meristems, maintained by the regulation of its biosynthesis, activation, and degradation, determines the tillering and panicle branching, respectively. Auxins and gibberellins are known broadly to repress the axillary meristems, while jasmonic acid is implicated in the determination of reproductive meristem formation. The balance of auxin, gibberellin, and cytokinin determines meristematic activities in the inflorescence. Strigolactones have been shown to repress the shoot branching but seem to regulate panicle branching positively. Ethylene, brassinosteroids, and gibberellins regulate spikelet abortion and grain filling. Further studies on the optimization of endogenous hormonal levels can help in the expansion of the grain yield potential of rice. This review focuses on the molecular machinery, involving several genes and quantitative trait loci (QTL), operational in the plant that governs hormonal control and, in turn, gets governed by the hormones to regulate grain number and yield in rice.

Associations between phytohormones and cellulose biosynthesis in land plants

BACKGROUND

Phytohormones are small molecules that regulate virtually every aspect of plant growth and development, from basic cellular processes, such as cell expansion and division, to whole plant environmental responses. While the phytohormone levels and distribution thus tell the plant how to adjust itself, the corresponding growth alterations are actuated by cell wall modification/synthesis and internal turgor. Plant cell walls are complex polysaccharide-rich extracellular matrixes that surround all plant cells. Among the cell wall components, cellulose is typically the major polysaccharide, and is the load-bearing structure of the walls. Hence, the cell wall distribution of cellulose, which is synthesized by large Cellulose Synthase protein complexes at the cell surface, directs plant growth.

SCOPE

Here, we review the relationships between key phytohormone classes and cellulose deposition in plant systems. We present the core signalling pathways associated with each phytohormone and discuss the current understanding of how these signalling pathways impact cellulose biosynthesis with a particular focus on transcriptional and post-translational regulation. Because cortical microtubules underlying the plasma membrane significantly impact the trajectories of Cellulose Synthase Complexes, we also discuss the current understanding of how phytohormone signalling impacts the cortical microtubule array.

CONCLUSION

Given the importance of cellulose deposition and phytohormone signalling in plant growth and development, one would expect that there is substantial cross-talk between these processes; however, mechanisms for many of these relationships remain unclear and should be considered as the target of future studies.

6-Benzylaminopurine (6-BA) ameliorates drought stress response in tall fescue via the influencing of biochemicals and strigolactone-signaling genes

Drought is a major agricultural and societal concern that causes farmers worldwide billions of dollars in annual losses. By revealing the as-of-yet unknown details of the biochemical and phytohormonal crosstalk occurring in drought-stressed plants, novel strategies can be pioneered to enhance drought tolerance in crop plants. Toward this goal, exogenous treatments containing the synthetic cytokinin 6-Benzylaminopurine (6-BA) were applied to the perennial monocot grass Festuca arundinacea (Tall Fescue). These plants were subjected to three irrigation levels: 100% ± 5%, 50% ± 5%, and 25% ± 5% of field capacity, at which a number of morpho-physiological and biochemical responses were evaluated. Furthermore, to elucidate the crosstalk between cytokinin (CK) and strigolactone (SL), we evaluated the activities of several SL-responsive genes. Drought conditions were shown to have widespread effects on morpho-physiological and biochemical indices. However, foliar application of 6-BA on tall fescue largely ameliorated drought stress symptoms. Water-soluble carbohydrates also declined significantly in response to CK over the course of drought progression, with virtually no change to starch content. Severe drought stress also upregulated a number of SL-response genes in the leaves of plants, indicating a correlation between the degree of drought severity and the quantity of SLs in tall fescue. Furthermore, the drought‒mediated induction of SL-signaling genes (including FaD14 and FaMax2) was inhibited in response to exogenous application of 6-BA, implying that 6-BA is a drought-dependent suppressor of SL-signaling genes. However, our results also hint at the existence of an as-of-yet poorly-characterized system of complex phytohormonal responses coordinated from multiple signaling pathways in response to drought.

Functional Analysis of the teosinte branched 1 Gene in the Tetraploid Switchgrass (Panicum virgatum L.) by CRISPR/Cas9-Directed Mutagenesis

Tillering is an important biomass yield component trait in switchgrass (Panicum virgatum L.). Teosinte branched 1 (tb1)/Branched 1 (BRC1) gene is a known regulator for tillering/branching in several plant species; however, its role on tillering in switchgrass remains unknown. Here, we report physiological and molecular characterization of mutants created by CRISPR/Cas9. We successfully obtained nonchimeric Pvtb1a and Pvtb1b mutants from chimeric T0 mutants using nodal culture. The biallelic Pvtb1a-Pvtb1b mutant plants produced significantly more tillers and higher fresh weight biomass than the wild-type plants. The increased tiller number in the mutant plants resulted primarily from hastened outgrowth of lower axillary buds. Increased tillers were also observed in transgene-free BC1 monoallelic mutants for either Pvtb1a-Pvtb1b or Pvtb1b gene alone, suggesting Pvtb1 genes act in a dosage-dependent manner. Transcriptome analysis showed 831 genes were differentially expressed in the Pvtb1a-Pvtb1b double knockdown mutant. Gene Ontology analysis revealed downregulation of Pvtb1 genes affected multiple biological processes, including transcription, flower development, cell differentiation, and stress/defense responses in edited plants. This study demonstrates that Pvtb1 genes play a pivotal role in tiller production as a negative regulator in switchgrass and provides opportunities for further research aiming to elucidate the molecular pathway regulating tillering in switchgrass.

Rice dwarf and low tillering 10 (OsDLT10) regulates tiller number by monitoring auxin homeostasis

Tiller number is a crucial agronomic trait that directly affects the number of effective panicles and yield formation in rice. Here, we report a semi-dwarf and low tillering mutant Osdlt10 (dwarf and low tillering 10) that exhibited reduced tiller number, semi-dwarfism, increased grain width, low seed-setting rate, curled leaf tip and a series of abnormalities of agronomic traits. Phenotypic observations showed that Osdlt10 mutants had defects in tiller bud formation and grew slowly at the tillering stage. Map-based cloning revealed that LOC_Os10g41310 was the responsible gene for OsDLT10, which was subsequently demonstrated using the CRISPR/Cas9 system and a complementary experiment. Expression pattern analysis indicated that OsDLT10 was primarily expressed in the stem node, the basic part of axillary bud and leaf sheath, pulvinus. The hormone treatment investigation indicated that extremely high of exogenous auxin concentrations can inhibit the expression of OsDLT10. Endogenous auxin content decreased significantly at the base of stem node and axillary bud in Osdlt10 mutants. The results showed that OsDLT10 was related to auxin. qPCR analysis results further showed that the expression levels of auxin transport genes (PINs) and early response genes (IAAs) were significantly increased. The expression levels of WUS-like and FON1 were substantially decreased in the Osdlt10 mutants. These results revealed that OsDLT10 played a critical role in influencing tiller number, likely in association with hormone signals and the WUS-CLV pathway, to regulate axillary bud development in rice.

Regulation of Rice Tillering by RNA-Directed DNA Methylation at Miniature Inverted-Repeat Transposable Elements

Tillering is a major determinant of rice plant architecture and grain yield. Here, we report that depletion of rice OsNRPD1a and OsNRPD1b, two orthologs of the largest subunit of RNA polymerase IV, leads to a high-tillering phenotype, in addition to dwarfism and smaller panicles. OsNRPD1a and OsNRPD1b are required for the production of 24-nt small interfering RNAs that direct DNA methylation at transposable elements (TEs) including miniature inverted-repeat TEs (MITEs). Interestingly, many genes are regulated either positively or negatively by TE methylation. Among them, OsMIR156d and OsMIR156j, which promote rice tillering, are repressed by CHH methylation at two MITEs in the promoters. By contrast, D14, which suppresses rice tillering, is activated by CHH methylation at an MITE in its downstream. Our findings reveal regulation of rice tillering by RNA-directed DNA methylation at MITEs and provide potential targets for agronomic trait enhancement through epigenome editing.

A Strigolactone Biosynthesis Gene Contributed to the Green Revolution in Rice

Plant architecture is a complex agronomic trait and a major factor of crop yield, which is affected by several important hormones. Strigolactones (SLs) are identified as a new class hormoneinhibiting branching in many plant species and have been shown to be involved in various developmental processes. Genetical and chemical modulation of the SL pathway is recognized as a promising approach to modify plant architecture. However, whether and how the genes involved in the SL pathway could be utilized in breeding still remain elusive. Here, we demonstrate that a partial loss-of-function allele of the SL biosynthesis gene, HIGH TILLERING AND DWARF 1/DWARF17 (HTD1/D17), which encodes CAROTENOID CLEAVAGE DIOXYGENASE 7 (CCD7), increases tiller number and improves grain yield in rice. We found that the HTD1 gene had been widely utilized and co-selected with Semidwarf 1 (SD1), both contributing to the improvement of plant architecture in modern rice varieties since the Green Revolution in the 1960s. Understanding how phytohormone pathway genes regulate plant architecture and how they have been utilized and selected in breeding will lay the foundation for developing the rational approaches toward improving crop yield.

Transcriptome analyses provide insights into the homeostatic regulation of axillary buds in upland cotton (G. hirsutum L.)

BACKGROUND

The axillary bud is an important index of cotton plant-type traits, and the molecular mechanism of axillary bud development in upland cotton has not yet been reported. We obtained a mutant (designated mZ571) with a high-budding phenotype in axillary bud development from the low-budding phenotype variety G. hirsutum Z571 (CCRI 9A02), which provided ideal materials for the study of complex regulatory networks of axillary bud development. In this study, RNA sequencing was carried out to detect gene expression levels during three stages of axillary buds in Z571 (LB, low budding) and mZ571 mutant (HB, high budding).

RESULTS

A total of 7162 DEGs were identified in the three groups (HB-E vs. LB-E, HB-G1 vs. LB-G1, HB-G2 vs. LB-G2), including 4014 downregulated and 3184 upregulated DEGs. Additionally, 221 DEGs were commonly identified in all three groups, accounting for approximately 3.09% of the total DEGs. These DEGs were identified, annotated and classified. A significant number of DEGs were related to hormone metabolism, hormone signal transduction, and starch and sucrose metabolism. In addition, 45, 22 and 9 DEGs involved in hormone metabolic pathways and 67, 22 and 19 DEGs involved in hormone signal transduction pathwayspathway were identified in HB-E vs. LB-E, HB-G1 vs. LB-G1, and HB-G2 vs. LB-G2, respectively, suggesting that endogenous hormones are the primary factors influencing cotton axillary bud growth. Hormone and soluble sugar content measurements revealed that mZ571 exhibited higher concentrations of zeatin, gibberellins and soluble sugar in all three stages, which confirmed that these hormone metabolism-, hormone signal transduction- and starch metabolism-related genes showed interaction effects contributing to the divergence of axillary bud growth between mZ571 and Z571.

CONCLUSIONS

Our results confirmed the importance of endogenous hormones and sugars in the development of axillary buds, and we found that mZ571 plants, with a high-budding phenotype of axillary buds, exhibited higher endogenous hormone and sugar concentrations. Overall, we present a model for the emergence and development of cotton axillary buds that provides insights into the complexity and dynamic nature of the regulatory network during axillary bud emergence and development.

Marker-assisted selection for grain number and yield-related traits of rice (Oryza sativa L.)

Continuous rise in the human population has resulted in an upsurge in food demand, which in turn demand grain yield enhancement of cereal crops, including rice. Rice yield is estimated via the number of tillers, grain number per panicles, and the number of spikes present per panicle. Marker-assisted selection (MAS) serve as one of the best ways to introduce QTLs/gene associated with yield in the rice plant. MAS has also been employed effectively in dissecting several other complex agricultural traits, for instance, drought, cold tolerance, salinity, etc. in rice plants. Thus, in this review, authors attempted to collect information about various genes/QTLs associated with high yield, including grain number, in rice and how different scheme of MAS can be employed to introduce them in rice (Oryza sativa L.) plant, which in turn will enhance rice yield. Information obtained to date suggest that, numerous QTLs, e.g., Gn1a, Dep1, associated with grain number and yield-related traits, have been identified either via mapping or cloning approaches. These QTLs have been successfully introduced into rice plants using various schemes of MAS for grain yield enhancement in rice. However, sometimes, MAS does not perform well in breeding, which might be due to lack of resources, skilled labors, reliable markers, and high costs associated with MAS. Thus, by overcoming these problems, we can enhance the application of MAS in plant breeding, which, in turn, may help us in increasing yield, which subsequently may help in bridging the gap between demand and supply of food for the continuously growing population.

Strigolactones and Brassinosteroids Antagonistically Regulate the Stability of the D53-OsBZR1 Complex to Determine FC1 Expression in Rice Tillering

Rice tillering, a key architecture trait determining grain yield, is highly regulated by a class of newly identified phytohormones, strigolactones (SLs). However, the whole SL signaling pathway from the receptor to downstream transcription factors to finally inhibit tillering remains unrevealed. In this study, we first found that brassinosteroids (BRs) strongly enhance tillering by promoting bud outgrowth in rice, which is largely different from the function of BRs in Arabidopsis. Genetic and biochemical analyses indicated that both the SL and BR signaling pathways control rice tillering by regulating the stability of D53 and/or the OsBZR1-RLA1-DLT module, a transcriptional complex in the rice BR signaling pathway. We further found that D53 interacts with OsBZR1 to inhibit the expression of FC1, a local inhibitor of tillering, and that this inhibition depends on direct DNA binding by OsBZR1, which recruits D53 to the FC1 promoter in rice buds. Taken together, these findings uncover a mechanism illustrating how SLs and BRs coordinately regulate rice tillering via the early responsive gene FC1.

CRISPR-mediated accelerated domestication of African rice landraces

African Oryza glaberrima and Oryza sativa landraces are considered valuable resources for breeding traits due to their adaptation to local environmental and soil conditions. They often possess superior resistance to endemic pests and tolerance to drought and nutrient deficiencies when compared to the "imported" high production Asian rice varieties. In contrast, "domestication traits" such as seed shattering, lodging, and seed yield are not well established in these African landraces. Therefore, the use of these African varieties for high production agriculture is limited by unpredictable yield and grain quality. We are addressing this shortcoming by developing protocols for genetically transforming African landraces to allow the use of CRISPR-Cas mediated breeding approaches. Here we use as proof of concept the cultivated African landrace Kabre to target selected known "domestication loci" and improve the agronomic potential of Kabre rice. Stable genetic transformation with CRISPR-Cas9-based vectors generated single and simultaneous multiple gene knockouts. Plants with reduced stature to diminish lodging were generated by disrupting the HTD1 gene. Furthermore, three loci shown to control seed size and/or yield (GS3, GW2 and GN1A) were targeted using a multiplex CRISPR-Cas9 construct. This resulted in mutants with significantly improved seed yield. Our study provides an example of how new breeding technologies can accelerate the development of highly productive African landrace rice varieties, an important advancement considering that Africa is a hotspot for worldwide population growth and therefore prone to food shortage.

The synthesis of strigolactone is affected by endogenous ascorbic acid in transgenic rice for l-galactono-1, 4-lactone dehydrogenase suppressed or overexpressing

Rice tillering, which determines the panicle number per plant, is an important agronomic trait for grain production. In higher plants, ascorbic acid (Asc) plays a major role in ROS-scavenging activity. l-Galactono-1, 4-lactone dehydrogenase (GalLDH, EC1.3.2.3) is an enzyme that catalyzes the last step of Asc biosynthesis in plants. Previously, we have reported that homozygous L-GalLDH-suppressed transgenic rice plants (GI) display a reduced tiller number and a lower level of foliar carotenoids (Car) compared with wild type. Strigolactones (SL), which play an important role in the suppression of shoot branching, are synthesized in the roots of rice plant using Car as substrates. In this paper, the relationship between Asc, SL, the accumulation of H₂O₂, changes in antioxidant capacity, enzyme activities, and gene transcriptions related to the synthesis of SL were analyzed in transgenic rice plants for L-GalLDH suppressed (GI-1 and GI-2) and overexpressing (GO-2). The results showed that the altered level of Asc in the L-GalLDH transgenic rice plants leads to a change in redox homeostasis, resulting in a marked accumulation of H₂O₂ and decreased antioxidant capacity in GI-1 and GI-2, but lower H₂O₂ content and increased antioxidant capacity in GO-2. Meanwhile, the altered level of Asc also leads to altered enzyme activities and gene transcript abundances related to SL synthesis in L-GalLDH transgenics. These observations support the conclusion that Asc influences tiller number in the L-GalLDH transgenics by affecting H₂O₂ accumulation and antioxidant capacity, and altering those enzyme activities and gene transcript abundances related to SL synthesis.

Strigolactones Decrease Leaf Angle in Response to Nutrient Deficiencies in Rice

Strigolactones (SLs) are a class of plant hormones that are synthesized from β-carotene through sequential reactions catalyzed by DWARF (D) 27, D17, D10, and OsMORE AXILLARY GROWTH (MAX) 1 in rice (Oryza sativa L.). In rice, endogenous SL levels increase in response to deficiency of nitrogen, phosphate, or sulfate (-N, -P, or -S). Rice SL mutants show increased lamina joint (LJ) angle as well as dwarfism, delayed leaf senescence, and enhanced shoot branching. The LJ angle is an important trait that determines plant architecture. To evaluate the effect of endogenous SLs on LJ angle in rice, we measured LJ angle and analyzed the expression of SL-biosynthesis genes under macronutrient deficiencies. In the "Shiokari" background, LJ angle was significantly larger in SL mutants than in the wild-type (WT). In WT and SL-biosynthesis mutants, direct treatment with the SL synthetic analog GR24 decreased the LJ angle. In WT, deficiency of N, P, or S, but not of K, Ca, Mg, or Fe decreased LJ angle. In SL mutants, deficiency of N, P, or S had no such effect. We analyzed the time course of SL-related gene expression in the LJ of WT deficient in N, P, or S, and found that expression of SL-biosynthesis genes increased 2 or 3 days after the onset of deficiency. Expression levels of both the SL-biosynthesis and signaling genes was particularly strongly increased under -P. Rice cultivars "Nipponbare", "Norin 8", and "Kasalath" had larger LJ angle than "Shiokari", interestingly with no significant differences between WT and SL mutants. In "Nipponbare", endogenous SL levels increased and the LJ angle was decreased under -N and -P. These results indicate that SL levels increased in response to nutrient deficiencies, and that elevated endogenous SLs might negatively regulate leaf angle in rice.

Fusion of the Cas9 endonuclease and the VirD2 relaxase facilitates homology-directed repair for precise genome engineering in rice

Precise genome editing by systems such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) requires high-efficiency homology-directed repair (HDR). Different technologies have been developed to improve HDR but with limited success. Here, we generated a fusion between the Cas9 endonuclease and the Agrobacterium VirD2 relaxase (Cas9-VirD2). This chimeric protein combines the functions of Cas9, which produces targeted and specific DNA double-strand breaks (DSBs), and the VirD2 relaxase, which brings the repair template in close proximity to the DSBs, to facilitate HDR. We successfully employed our Cas9-VirD2 system for precise ACETOLACTATE SYNTHASE (OsALS) allele modification to generate herbicide-resistant rice (Oryza sativa) plants, CAROTENOID CLEAVAGE DIOXYGENASE-7 (OsCCD7) to engineer plant architecture, and generate in-frame fusions with the HA epitope at HISTONE DEACETYLASE (OsHDT) locus. The Cas9-VirD2 system expands our ability to improve agriculturally important traits in crops and opens new possibilities for precision genome engineering across diverse eukaryotic species.

Fusion of the Cas9 endonuclease and the VirD2 relaxase facilitates homology-directed repair for precise genome engineering in rice

Precise genome editing by systems such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) requires high-efficiency homology-directed repair (HDR). Different technologies have been developed to improve HDR but with limited success. Here, we generated a fusion between the Cas9 endonuclease and the Agrobacterium VirD2 relaxase (Cas9-VirD2). This chimeric protein combines the functions of Cas9, which produces targeted and specific DNA double-strand breaks (DSBs), and the VirD2 relaxase, which brings the repair template in close proximity to the DSBs, to facilitate HDR. We successfully employed our Cas9-VirD2 system for precise ACETOLACTATE SYNTHASE (OsALS) allele modification to generate herbicide-resistant rice (Oryza sativa) plants, CAROTENOID CLEAVAGE DIOXYGENASE-7 (OsCCD7) to engineer plant architecture, and generate in-frame fusions with the HA epitope at HISTONE DEACETYLASE (OsHDT) locus. The Cas9-VirD2 system expands our ability to improve agriculturally important traits in crops and opens new possibilities for precision genome engineering across diverse eukaryotic species.

Ali, Shami, Sedeek et al. generate a fusion between Cas9 and the VirD2 relaxase (Cas9-VirD2), which combines the functions of both proteins in producing targeted and specific double strand breaks and promoting homology-directed repair. They show the utility of their method by producing herbicide resistant rice.

Integrating the dynamics of yield traits in rice in response to environmental changes

Reductions in crop yields as a consequence of global climate change threaten worldwide food security. It is therefore imperative to develop high-yielding crop plants that show sustainable production under stress conditions. In order to achieve this aim through breeding or genetic engineering, it is crucial to have a complete and comprehensive understanding of the molecular basis of plant architecture and the regulation of its sub-components that contribute to yield under stress. Rice is one of the most widely consumed crops and is adversely affected by abiotic stresses such as drought and salinity. Using it as a model system, in this review we present a summary of our current knowledge of the physiological and molecular mechanisms that determine yield traits in rice under optimal growth conditions and under conditions of environmental stress. Based on physiological functioning, we also consider the best possible combination of genes that may improve grain yield under optimal as well as environmentally stressed conditions. The principles that we present here for rice will also be useful for similar studies in other grain crops.

Alternative splicing of a barley gene results in an excess-tillering and semi-dwarf mutant

An excess-tillering semi-dwarf gene Hvhtd was identified from an EMS-induced mutant in barley and alternative splicing results in excess-tillering semi-dwarf traits. Tillering and plant height are important traits determining plant architecture and grain production in cereal crops. This study identified an excess-tillering semi-dwarf mutant (htd) from an EMS-treated barley population. Genetic analysis of the F₁, F₂, and F_2:3 populations showed that a single recessive gene controlled the excess-tillering semi-dwarf in htd. Using BSR-Seq and gene mapping, the Hvhtd gene was delimited within a 1.8 Mb interval on chromosome 2HL. Alignment of the RNA-Seq data with the functional genes in the interval identified a gene HORVU2Hr1G098820 with alternative splicing between exon2 and exon3 in the mutant, due to a G to A single-nucleotide substitution at the exon and intron junction. An independent mutant with a similar phenotype confirmed the result, with alternative splicing between exon3 and exon4. In both cases, the alternative splicing resulted in a non-functional protein. And the gene HORVU2Hr1G098820 encodes a trypsin family protein and may be involved in the IAA signaling pathway and differs from the mechanism of Green Revolution genes in the gibberellic acid metabolic pathway.

Regulation of Aegilops tauschii Coss Tiller Bud Growth by Plant Density: Transcriptomic, Physiological and Phytohormonal Responses

Aegilops tauschii Coss is one of the most hazardous weeds that severely infests wheat fields in China. The tillering ability of Ae. tauschii strongly affects the occurrence and spread by influencing its seed output. In this study, Ae. tauschii was sown at low plant density (LPD) and high plant density (HPD) to investigate the effect of plant density on tiller bud outgrowth and its potential regulators using RNA-Seq. Additionally, the chlorophyll content and photosynthesis, soluble sugar and phytohormone levels were also determined at different plant densities. The results showed that an increased plant density significantly inhibited the elongation of tiller buds in the axil of the first leaf at 15 days after planting, with 7.69 mm at LPD and 1.69 mm at HPD. A total of seven putative tiller-related genes were selected and validated using quantitative real-time PCR. Furthermore, chlorophyll levels, photosynthetic efficiency, and soluble sugar contents were distinctly inhibited by HPD in Ae. tauschii, which may be responsible for the restriction of tiller bud growth. In addition, differentially expressed genes (DEGs) were markedly enriched in indole-3-acetic acid (IAA), abscisic acid (ABA), and gibberellin metabolism and signaling. Accordingly, the levels of ABA and gibberellin A3 in Ae. tauschii were strikingly higher at HPD compared with those at LPD, yet the reverse tendency was observed for IAA. Undoubtedly, such results will be highly beneficial for illuminating the underlying regulators of the Ae. tauschii tillering response to plant density and may provide new ideas for the control of this weed in the future.

Sugar availability suppresses the auxin-induced strigolactone pathway to promote bud outgrowth

Apical dominance occurs when the growing shoot tip inhibits the outgrowth of axillary buds. Apically-derived auxin in the nodal stem indirectly inhibits bud outgrowth via cytokinins and strigolactones. Recently, sugar deprivation was found to contribute to this phenomenon. Using rose and pea, we investigated whether sugar availability interacts with auxin in bud outgrowth control, and the role of cytokinins and strigolactones, in vitro and in planta. We show that sucrose antagonises auxin's effect on bud outgrowth, in a dose-dependent and coupled manner. Sucrose also suppresses strigolactone inhibition of outgrowth and the rms3 strigolactone-perception mutant is less affected by reducing sucrose supply. However, sucrose does not interfere with the regulation of cytokinin levels by auxin and stimulates outgrowth even with optimal cytokinin supply. These observations were assembled into a computational model in which sucrose represses bud response to strigolactones, largely independently of cytokinin levels. It quantitatively captures our observed dose-dependent sucrose-hormones effects on bud outgrowth and allows us to express outgrowth response to various combinations of auxin and sucrose levels as a simple quantitative law. This study places sugars in the bud outgrowth regulatory network and paves the way for a better understanding of branching plasticity in response to environmental and genotypic factors.

Chromatin Interacting Factor OsVIL2 Is Required for Outgrowth of Axillary Buds in Rice

Shoot branching is an essential agronomic trait that impacts on plant architecture and yield. Shoot branching is determined by two independent steps: axillary meristem formation and axillary bud outgrowth. Although several genes and regulatory mechanism have been studied with respect to shoot branching, the roles of chromatin-remodeling factors in the developmental process have not been reported in rice. We previously identified a chromatin-remodeling factor OsVIL2 that controls the trimethylation of histone H3 lysine 27 (H3K27me3) at target genes. In this study, we report that loss-of-function mutants in OsVIL2 showed a phenotype of reduced tiller number in rice. The reduction was due to a defect in axillary bud (tiller) outgrowth rather than axillary meristem initiation. Analysis of the expression patterns of the tiller-related genes revealed that expression of OsTB1, which is a negative regulator of bud outgrowth, was increased in osvil2 mutants. Chromatin immunoprecipitation assays showed that OsVIL2 binds to the promoter region of OsTB1 chromatin in wild-type rice, but the binding was not observed in osvil2 mutants. Tiller number of double mutant osvil2 ostb1 was similar to that of ostb1, suggesting that osvil2 is epistatic to ostb1. These observations indicate that OsVIL2 suppresses OsTB1 expression by chromatin modification, thereby inducing bud outgrowth.

Comparing and Contrasting the Multiple Roles of Butenolide Plant Growth Regulators: Strigolactones and Karrikins in Plant Development and Adaptation to Abiotic Stresses

Strigolactones (SLs) and karrikins (KARs) are both butenolide molecules that play essential roles in plant growth and development. SLs are phytohormones, with SLs having known functions within the plant they are produced in, while KARs are found in smoke emitted from burning plant matter and affect seeds and seedlings in areas of wildfire. It has been suggested that SL and KAR signaling may share similar mechanisms. The α/β hydrolases DWARF14 (D14) and KARRIKIN INSENSITIVE 2 (KAI2), which act as receptors of SL and KAR, respectively, both interact with the F-box protein MORE AXILLARY GROWTH 2 (MAX2) in order to target SUPPRESSOR OF MAX2 1 (SMAX1)-LIKE/D53 family members for degradation via the 26S proteasome. Recent reports suggest that SLs and/or KARs are also involved in regulating plant responses and adaptation to various abiotic stresses, particularly nutrient deficiency, drought, salinity, and chilling. There is also crosstalk with other hormone signaling pathways, including auxin, gibberellic acid (GA), abscisic acid (ABA), cytokinin (CK), and ethylene (ET), under normal and abiotic stress conditions. This review briefly covers the biosynthetic and signaling pathways of SLs and KARs, compares their functions in plant growth and development, and reviews the effects of any crosstalk between SLs or KARs and other plant hormones at various stages of plant development. We also focus on the distinct responses, adaptations, and regulatory mechanisms related to SLs and/or KARs in response to various abiotic stresses. The review closes with discussion on ways to gain additional insights into the SL and KAR pathways and the crosstalk between these related phytohormones.

Strigolactones and their crosstalk with other phytohormones

BACKGROUND

Strigolactones (SLs) are a diverse class of butenolide-bearing phytohormones derived from the catabolism of carotenoids. They are associated with an increasing number of emerging regulatory roles in plant growth and development, including seed germination, root and shoot architecture patterning, nutrient acquisition, symbiotic and parasitic interactions, as well as mediation of plant responses to abiotic and biotic cues.

SCOPE

Here, we provide a concise overview of SL biosynthesis, signal transduction pathways and SL-mediated plant responses with a detailed discourse on the crosstalk(s) that exist between SLs/components of SL signalling and other phytohormones such as auxins, cytokinins, gibberellins, abscisic acid, ethylene, jasmonates and salicylic acid.

CONCLUSION

SLs elicit their control on physiological and morphological processes via a direct or indirect influence on the activities of other hormones and/or integrants of signalling cascades of other growth regulators. These, among many others, include modulation of hormone content, transport and distribution within plant tissues, interference with or complete dependence on downstream signal components of other phytohormones, as well as acting synergistically or antagonistically with other hormones to elicit plant responses. Although much has been done to evince the effects of SL interactions with other hormones at the cell and whole plant levels, research attention must be channelled towards elucidating the precise molecular events that underlie these processes. More especially in the case of abscisic acid, cytokinins, gibberellin, jasmonates and salicylic acid for which very little has been reported about their hormonal crosstalk with SLs.

Light Regulation of Axillary Bud Outgrowth Along Plant Axes: An Overview of the Roles of Sugars and Hormones

Apical dominance, the process by which the growing apical zone of the shoot inhibits bud outgrowth, involves an intricate network of several signals in the shoot. Auxin originating from plant apical region inhibits bud outgrowth indirectly. This inhibition is in particular mediated by cytokinins and strigolactones, which move from the stem to the bud and that respectively stimulate and repress bud outgrowth. The action of this hormonal network is itself modulated by sugar levels as competition for sugars, caused by the growing apical sugar sink, may deprive buds from sugars and prevents bud outgrowth partly by their signaling role. In this review, we analyze recent findings on the interaction between light, in terms of quantity and quality, and apical dominance regulation. Depending on growth conditions, light may trigger different pathways of the apical dominance regulatory network. Studies pinpoint to the key role of shoot-located cytokinin synthesis for light intensity and abscisic acid synthesis in the bud for R:FR in the regulation of bud outgrowth by light. Our analysis provides three major research lines to get a more comprehensive understanding of light effects on bud outgrowth. This would undoubtedly benefit from the use of computer modeling associated with experimental observations to deal with a regulatory system that involves several interacting signals, feedbacks, and quantitative effects.

OsATG8c-Mediated Increased Autophagy Regulates the Yield and Nitrogen Use Efficiency in Rice

Autophagy, a conserved pathway in eukaryotes, degrades and recycles cellular components, thus playing an important role in nitrogen (N) remobilization. N plays an important role in the growth and development of plants, which also affects plant yield and quality. In this research, it was found that the transcriptional level of a core autophagy gene of rice (Oryza sativa), OsATG8c, was increased during N starvation conditions. It was found that the overexpression of OsATG8c significantly enhanced the activity of autophagy and that the number of autophagosomes, dwarfed the plant height and increased the effective tillers’ number and yield. The nitrogen uptake efficiency (NUpE) and nitrogen use efficiency (NUE) significantly increased in the transgenic rice under both optimal and suboptimal N conditions. Based on our results, OsATG8c is considered to be a good candidate gene for increasing NUE, especially under suboptimal field conditions.

Effect of D-ring C-3' methylation of strigolactone analogs on their transcription regulating activity in rice

Strigolactones (SLs) are a well-known class of plant hormones, which are involved in a number of developmental and adaptation processes and mediate different interspecific interactions. In spite of the growing knowledge on SL biosynthesis and signal transduction, effects of structural modifications on the activity and efficiency of SLs and their analogs remain largely elusive. SLs are characterized by the presence of a lactone ring (D-ring) that is connected by an enol ether bridge to a second moiety. In this study, we investigated the effect of additional D-ring methylation of SL analogs on their transcription regulating activity. For this purpose, we compared the SL analogs MP13 and AR8, which differ only by the presence of a methyl group at the C-3' atom in the latter. Transcription regulating activity was determined by quantitative real-time PCR measurement of transcript levels of SL-dependent, feed-back regulated genes in treated wild type and ccd7 mutant rice seedlings. Results obtained indicate that C-3' methylation reduces the transcription regulating activity, as shown by the more pronounced suppression of the SL biosynthesis genes DWARF27 (D27) and CAROTENOID CLEAVAGE DIOXYGENASES (CCD7 and CCD8) and higher induction of the SL signaling repressor gene DWARF53 (D53) in MP13 treated seedlings. These results are consistent with a recent study on the biological activities of MP13 and AR8.

Architecture of Wheat Inflorescence: Insights from Rice

The inflorescence architecture of grass crops affects the number of kernels and final grain yield. Great progress has been made in genetic analysis of rice inflorescence development in the past decades. However, the advances in wheat largely lag behind those in rice due to the repetitive and polyploid genomes of wheat. In view of the similar branching patterns and developmental characteristics between rice and wheat, the studies on inflorescence architecture in rice will facilitate related studies in wheat in the future. Here, we review the developmental regulation of inflorescences in rice and wheat and highlight several pathways that potentially regulate the inflorescence architecture of wheat.

Strigolactones shape the rhizomicrobiome in rice (Oryza sativa)

The rhizomicrobiome helps the host plant to better adapt to environmental stresses. In contrast, plant-derived metabolic substances, including phytohormones, play an active role in structuring rhizomicrobiome. Although strigolactones (SLs), a group of phytohormones, serve as potential rhizosphere signaling molecules, their contributions in shaping the rice (Oryza sativa) rhizomicrobiome remain elusive. To address this issue, we compared the rhizomicrobiome of rice mutants defective in either SL biosynthesis or signaling and wild-type (WT) plants. To understand whether SL-regulated metabolic pathways shape the rhizomicrobiome, a correlation network analysis was conducted among the metabolic pathway-related genes and the rhizomicrobiome of rice. Compared to WT, higher bacterial richness (evidenced by the operational taxonomic unit richness) and lower fungal diversity (evidenced by the Shannon index) were observed in both SL deficient dwarf17 (d17) and signaling (d14) mutants. Additionally, remarkable differences were observed in the composition of a large number of bacterial communities than the fungal communities in the d17 and d14 mutants with respect to the WT. The abundance of certain beneficial bacterial taxa, including Nitrosomonadaceae and Rhodanobacter, were significantly decreased in both mutants relative to the WT. Correlation network analysis between SL-regulated metabolic pathway-associated genes and rhizomicrobiome proposed a role for SL-dependent metabolic pathways in shaping rhizomicrobiome composition. Taken together, our study suggests that SL biosynthesis and signaling play a key role in determining the rice rhizomicrobiome, directly or indirectly, through the mediation of distinct metabolic pathways. Based on our findings, the genetic modulation of rice SL biosynthesis and/or signaling pathways may help to recruit/increase the abundance of the desired rhizomicrobiome, which may assist in the stress resilience of rice.

Novel OsGRAS19 mutant, D26, positively regulates grain shape in rice (Oryza sativa)

Grain size is an important factor in rice yield. Several genes related to grain size have been reported, but most of them are determined by quantitative trail loci (QTL) traits. Gene D26 is a novel site mutation of OsGRAS19 and involved in the brassinosteroid (BR) signalling pathway. However, whether D26 is involved in the process of rice reproductive development remains unclear. Here, gene cloning and functional analysis revealed that D26 has an obvious regulatory effect on grain size. Overexpression or CRISP/Cas9 mutant of D26 also showed that grain size was positively influenced. Cellular analyses show that D26 modulates grain size by promoting cell division and regulating the cell number in the upper epidermis of the glume. The overexpression results further suggest that the level of D26 expression positively impacts grain length and leaf angles and that the expression of several known grain size genes is involved in the regulation. Based on our results, D26, as a transcription factor, effectively improves rice grain shape.

Genetic dissection of cell wall defects and the strigolactone pathway in Arabidopsis

Defects in the biosynthesis and/or deposition of secondary plant cell wall polymers result in the collapse of xylem vessels causing a dwarfed plant stature and an altered plant architecture termed irregular xylem (irx) syndrome. For example, reduced xylan O-acetylation causes strong developmental defects and increased freezing tolerance. Recently, we demonstrated that the irx syndrome in the trichome birefringence-like 29/eskimo1 (tbl29/esk1) mutant is dependent on MORE AXILLARY GROWTH 4 (MAX4), a key enzyme in the biosynthesis of the phytohormone strigolactone (SL). In this report, we show that other xylan- and cellulose-deficient secondary wall mutants exhibit increased freezing tolerance correlated with the irx syndrome. In addition, these phenotypes are also dependent on MAX4, suggesting a more general interaction between secondary wall defects and SL biosynthesis. In contrast, MAX4 does not play a role in developmental defects triggered by primary wall deficiencies, suggesting that the interaction is restricted to vascular tissue. Through a reverse genetics approach, the requirement of different components of the SL pathway impacting the irx syndrome in tbl29 was evaluated. Our results show that the tbl29-associated irx phenotypes are dependent on the MAX3 and MAX4 enzymes, involved in the early steps of SL biosynthesis. In contrast, this signaling is independent on downstream enzymes in the biosynthesis and perception of SL such as MAX1 and MAX2.

Strigolactones regulate shoot elongation by mediating gibberellin metabolism and signaling in rice (Oryza sativa L.)

Strigolactones (SLs) are plant hormones that regulate diverse physiological processes including shoot elongation. However, little is known about the regulatory mechanism of SLs in rice shoot elongation. Our results demonstrate that defects in SL biosynthesis or signaling led to dwarfism, and the dwarf statures of SL-deficient mutant (d17) and SL-insensitive mutant (d14) were restored to wild-type (WT) by gibberellin (GA) treatment, indicating that their dwarfism was associated with decreased GA content or weakened GA sensitivity. Our results indicate that the bioactive GA₁ contents in d17 and d14 were lower than those in WT, due to the downregulated transcription of GA biosynthesis genes and upregulated transcription of GA inactivation genes. Moreover, d17 and d14 exhibited weakened GA-responsive sensitivity compared with WT. Although the transcription levels of cell division- and cell elongation-related genes were upregulated by GA₃ treatment, the increase in transcription of d17 and d14 was lower than that in WT. These results suggest that SL is required for rice shoot elongation by mediating GA metabolism and signaling. Therefore, a deficiency in SL biosynthesis or signaling leads to decreased GA content and weakened GA response, which in turn reduces shoot length by downregulating transcription levels of cell division- and cell elongation-related genes.

Functional analysis of the GbDWARF14 gene associated with branching development in cotton

Plant architecture, including branching pattern, is an important agronomic trait of cotton crops. In recent years, strigolactones (SLs) have been considered important plant hormones that regulate branch development. In some species such as Arabidopsis, DWARF14 is an unconventional receptor that plays an important role in the SL signaling pathway. However, studies on SL receptors in cotton are still lacking. Here, we cloned and analysed the structure of the GbD14 gene in Gossypium barbadense and found that it contains the domains necessary for a SL receptor. The GbD14 gene was expressed primarily in the roots, leaves and vascular bundles, and the GbD14 protein was determined via GFP to localize to the cytoplasm and nucleus. Gene expression analysis revealed that the GbD14 gene not only responded to SL signals but also was differentially expressed between cotton plants whose types of branching differed. In particular, GbD14 was expressed mainly in the axillary buds of normal-branching cotton, while it was expressed the most in the leaves of nulliplex-branch cotton. In cotton, the GbD14 gene can be induced by SL and other plant hormones, such as indoleacetic acid, abscisic acid, and jasmonic acid. Compared with wild-type Arabidopsis, GbD14-overexpressing Arabidopsis responded more rapidly to SL signals. Moreover, we also found that GbD14 can rescue the multi-branched phenotype of Arabidopsis Atd14 mutants. Our results indicate that the function of GbD14 is similar to that of AtD14, and GbD14 may be a receptor for SL in cotton and involved in regulating branch development. This research provides a theoretical basis for a profound understanding of the molecular mechanism of branch development and ideal plant architecture for cotton breeding improvements.

Identification of an active miniature inverted-repeat transposable element mJing in rice

Miniature inverted-repeat transposable elements (MITEs) are structurally homogeneous non-autonomous DNA transposons with high copy numbers that play important roles in genome evolution and diversification. Here, we analyzed the rice high-tillering dwarf (htd) mutant in an advanced backcross population between cultivated and wild rice, and identified an active MITE named miniature Jing (mJing). The mJing element belongs to the PIF/Harbinger superfamily. japonica rice var. Nipponbare and indica var. 93-11 harbor 72 and 79 mJing family members, respectively, have undergone multiple rounds of amplification bursts during the evolution of Asian cultivated rice (Oryza sativa L.). A heterologous transposition experiment in Arabidopsis thaliana indicated that the autonomous element Jing is likely to have provides the transposase needed for mJing mobilization. We identified 297 mJing insertion sites and their presence/absence polymorphism among 71 rice samples through targeted high-throughput sequencing. The results showed that the copy number of mJing varies dramatically among Asian cultivated rice (O. sativa), its wild ancestor (O. rufipogon), and African cultivated rice (O. glaberrima) and that some mJing insertions are subject to directional selection. These findings suggest that the amplification and removal of mJing elements have played an important role in rice genome evolution and species diversification.

Developmental analysis of the early steps in strigolactone-mediated axillary bud dormancy in rice

By contrast with rapid progress in understanding the mechanisms of biosynthesis and signaling of strigolactone (SL), mechanisms by which SL inhibits axillary bud outgrowth are less well understood. We established a rice (Oryza sativa L.) hydroponic culture system to observe axillary buds at the critical point when the buds enter the dormant state. In situ hybridization analysis indicated that cell division stops in the leaf primordia of the buds entering dormancy. We compared transcriptomes in the axillary buds isolated by laser capture microdissection before and after entering the dormant state and identified genes that are specifically upregulated or downregulated in dormant buds respectively, in SL-mediated axillary bud dormancy. Typically, cell cycle genes and ribosomal genes are included among the active genes while abscisic acid (ABA)-inducible genes are among the dormant genes. Application of ABA to the hydroponic culture suppressed the growth of axillary buds of SL mutants to the same level as wild-type (WT) buds. Tiller number was decreased in the transgenic lines overexpressing OsNCED1, the gene that encodes ABA biosynthesis enzyme. These results indicated that the main site of SL function is the leaf primordia in the axillary bud and that ABA is involved in SL-mediated axillary bud dormancy.

Genetics of barley tiller and leaf development

In cereals, tillering and leaf development are key factors in the concept of crop ideotype, introduced in the 1960s to enhance crop yield, via manipulation of plant architecture. In the present review, we discuss advances in genetic analysis of barley shoot architecture, focusing on tillering, leaf size and angle. We also discuss novel phenotyping techniques, such as 2D and 3D imaging, that have been introduced in the era of phenomics, facilitating reliable trait measurement. We discuss the identification of genes and pathways that are involved in barley tillering and leaf development, highlighting key hormones involved in the control of plant architecture in barley and rice. Knowledge on genetic control of traits related to plant architecture provides useful resources for designing ideotypes for enhanced barley yield and performance.

Identification and expression analysis of strigolactone biosynthetic and signaling genes reveal strigolactones are involved in fruit development of the woodland strawberry (Fragaria vesca)

BACKGROUND

The development and ripening of fresh fruits is an important trait for agricultural production and fundamental research. Almost all plant hormones participate in this process. Strigolactones (SLs) are a new class of plant hormones that regulate plant organ development and stress tolerance, but little is known about their roles in fruit development.

RESULTS

In this study, we identified SL biosynthetic and signaling genes in woodland strawberry, a typical non-climacteric fruit, and analyzed the expression patterns of these genes in different plant tissues and developing fruits. One D27, two MAX1, and one LBO gene were identified as involved in SL biosynthesis, and one D14, one D3, and two D53 genes as related to SL signaling. The proteins encoded by these genes had similar motifs as SL biosynthetic and signaling proteins in rice and Arabidopsis. The genes had different expression levels in the root, stem, leaf, and petiole of woodland strawberry. In addition, the expression of most SL biosynthetic genes was high in developing carpel, anther, and style, while that of SL signaling genes was high in carpel and style, but low in anther, suggesting active SL biosynthesis and signaling in the developing carpel and style. Notably, the expression of SL biosynthetic and signaling genes was significantly increased in the receptacle after pollination and decreased during receptacle development. Moreover, low or no expression of these genes was detected in ripening fruits.

CONCLUSIONS

Our results suggest that SLs play a role in the early stages of woodland strawberry fruit development. Our findings provide insight into the function of SLs and will facilitate further study of the regulation by SLs of fresh fruit development.

BRANCHED1: A Key Hub of Shoot Branching

Shoot branching is a key process for plant growth and fitness. Newly produced axes result from axillary bud outgrowth, which is at least partly mediated through the regulation of BRANCHED1 gene expression (BRC1/TB1/FC1). BRC1 encodes a pivotal bud-outgrowth-inhibiting transcription factor belonging to the TCP family. As the regulation of BRC1 expression is a hub for many shoot-branching-related mechanisms, it is influenced by endogenous (phytohormones and nutrients) and exogenous (light) inputs, which involve so-far only partly identified molecular networks. This review highlights the central role of BRC1 in shoot branching and its responsiveness to different stimuli, and emphasizes the different knowledge gaps that should be addressed in the near future.

Genetic improvement of the shoot architecture and yield in soya bean plants via the manipulation of GmmiR156b

The optimization of plant architecture in order to breed high-yielding soya bean cultivars is a goal of researchers. Tall plants bearing many long branches are desired, but only modest success in reaching these goals has been achieved. MicroRNA156 (miR156)-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene modules play pivotal roles in controlling shoot architecture and other traits in crops like rice and wheat. However, the effects of miR156-SPL modules on soya bean architecture and yield, and the molecular mechanisms underlying these effects, remain largely unknown. In this study, we achieved substantial improvements in soya bean architecture and yield by overexpressing GmmiR156b. Transgenic plants produced significantly increased numbers of long branches, nodes and pods, and they exhibited an increased 100-seed weight, resulting in a 46%-63% increase in yield per plant. Intriguingly, GmmiR156b overexpression had no significant impact on plant height in a growth room or under field conditions; however, it increased stem thickness significantly. Our data indicate that GmmiR156b modulates these traits mainly via the direct cleavage of SPL transcripts. Moreover, we found that GmSPL9d is expressed in the shoot apical meristem and axillary meristems (AMs) of soya bean, and that GmSPL9d may regulate axillary bud formation and branching by physically interacting with the homeobox gene WUSCHEL (WUS), a central regulator of AM formation. Together, our results identify GmmiR156b as a promising target for the improvement of soya bean plant architecture and yields, and they reveal a new and conserved regulatory cascade involving miR156-SPL-WUS that will help researchers decipher the genetic basis of plant architecture.

Identification and Characterization of a Novel Strigolactone-Insensitive Mutant, Dwarfism with High Tillering Ability 34 (dhta-34) in Rice (Oryza sativa L.)

Rice tillering ability and plant height are two of the important traits determining the grain yield. A novel rice (Oryza sativa L.) mutant dhta-34 from an Indica cultivar Zhenong 34 treated by ethyl methy1 sulfonate (EMS) was investigated in this study. The dhta-34 mutant significantly revealed thrifty tillers with reduced plant height, smaller panicles and lighter grains. It also exhibited late-maturing (19.80 days later than the wild type) and withered leaf tip during the mature stage. The length of each internode was reduced compared to the wild type, belonging to the dn type (each internode of the plant stem decreased in the same ratio). The longitudinal section of dhta-34 internodes showed that the length of cells was reduced leading to the dwarfism of the mutant. The F₂ population derived from a cross between dhta-34 and an Japonica cultivar Zhenongda 104 were used for gene mapping by using the map-based cloning strategy. The gene DHTA-34 was fine mapped in 183.8kb region flanked by markers 3R-7 and 3R-10. The cloning and sequencing of the target region from the mutant revealed that there was a substitution of G to A in the second exon of LOC_Os03g10620, which resulted in an amino acid substitution arginine to histidine. DHTA-34 encoded a protein of the α/β-fold hydrolase superfamily, which could suppress the tillering ability of rice. DHTA-34 was a strong loss-of-function allele of the Arabidopsis thaliana D14 gene, which was involved in part of strigolactones (SLs) perception and signaling. Moreover, the relative expression of DHTA-34 gene in leaf was higher than that in bud, internode, root or sheath. This study revealed that DHTA-34 played an important role in inhabiting tiller development in rice and further identifying the function of D14.

Systems model-guided rice yield improvements based on genes controlling source, sink, and flow

A large number of genes related to source, sink, and flow have been identified after decades of research in plant genetics. Unfortunately, these genes have not been effectively utilized in modern crop breeding. This perspective paper aims to examine the reasons behind such a phenomenon and propose a strategy to resolve this situation. Specifically, we first systematically survey the currently cloned genes related to source, sink, and flow; then we discuss three factors hindering effective application of these identified genes, which include the lack of effective methods to identify limiting or critical steps in a signaling network, the misplacement of emphasis on properties, at the leaf, instead of the whole canopy level, and the non-linear complex interaction between source, sink, and flow. Finally, we propose the development of systems models of source, sink and flow, together with a detailed simulation of interactions between them and their surrounding environments, to guide effective use of the identified elements in modern rice breeding. These systems models will contribute directly to the definition of crop ideotype and also identification of critical features and parameters that limit the yield potential in current cultivars.

Transcriptome Profiles Reveal the Crucial Roles of Auxin and Cytokinin in the "Shoot Branching" of Cremastra appendiculata

Cremastra appendiculata has become endangered due to reproductive difficulties. Specifically, vegetative reproduction is almost its only way to reproduce, and, under natural conditions, it cannot grow branches, resulting in an extremely low reproductive coefficient (reproductive percentage). Here, we performed RNA-Seq and a differentially expressed gene (DEG) analysis of the three stages of lateral bud development in C. appendiculata after decapitation-dormancy (D2), transition (TD2), and emergence (TG2)-and the annual axillary bud natural break (G1) to gain insight into the molecular regulatory network of shoot branching in this plant. Additionally, we applied the auxin transport inhibitors N-1-naphthylphthalamic acid (NPA) and 2,3,5-triiodibenzoic acid (TIBA) to a treated pseudobulb string of C. appendiculata to verify the conclusions obtained by the transcriptome. RNA-Seq provided a wealth of valuable information. Successive pairwise comparative transcriptome analyses revealed 5988 genes as DEGs. GO (Gene Ontology) and KEGG (Kyoto encyclopedia of genes and genomes) analyses of DEGs showed significant enrichments in phytohormone biosynthesis and metabolism, regulation of hormone levels, and a hormone-mediated signaling pathway. qRT-PCR validation showed a highly significant correlation (p < 0.01) with the RNA-Seq generated data. High-performance liquid chromatography (HPLC) and qRT-PCR results showed that, after decapitation, the NPA- and TIBA-induced lateral buds germinated due to rapidly decreasing auxin levels, caused by upregulation of the dioxygenase for auxin oxidation gene (DAO). Decreased auxin levels promoted the expression of isopentenyl transferase (IPT) and cytochrome P450 monooxygenase, family 735, subfamily A (CYP735A) genes and inhibited two carotenoid cleavage dioxygenases (CCD7 and CCD8). Zeatin levels significantly increased after the treatments. The increased cytokinin levels promoted the expression of WUSCHEL (WUS) and inhibited expression of BRANCHED1 (BRC1) in the cytokinin signal transduction pathway and initiated lateral bud outgrowth. Our data suggest that our theories concerning the regulation of shoot branching and apical dominance is really similar to those observed in annual plants. Auxin inhibits bud outgrowth and tends to inhibit cytokinin levels. The pseudobulb in the plant behaves in a similar manner to that of a shoot above the ground.

Non-dormant Axillary Bud 1 regulates axillary bud outgrowth in sorghum

Tillering contributes to grain yield and plant architecture and therefore is an agronomically important trait in sorghum (Sorghum bicolor). Here, we identified and functionally characterized a mutant of the Non-dormant Axillary Bud 1 (NAB1) gene from an ethyl methanesulfonate-mutagenized sorghum population. The nab1 mutants have increased tillering and reduced plant height. Map-based cloning revealed that NAB1 encodes a carotenoid-cleavage dioxygenase 7 (CCD7) orthologous to rice (Oryza sativa) HIGH-TILLERING DWARF1/DWARF17 and Arabidopsis thaliana MORE AXILLARY BRANCHING 3. NAB1 is primarily expressed in axillary nodes and tiller bases and NAB1 localizes to chloroplasts. The nab1 mutation causes outgrowth of basal axillary buds; removing these non-dormant basal axillary buds restored the wild-type phenotype. The tillering of nab1 plants was completely suppressed by exogenous application of the synthetic strigolactone analog GR24. Moreover, the nab1 plants had no detectable strigolactones and displayed stronger polar auxin transport than wild-type plants. Finally, RNA-seq showed that the expression of genes involved in multiple processes, including auxin-related genes, was significantly altered in nab1. These results suggest that NAB1 functions in strigolactone biosynthesis and the regulation of shoot branching via an interaction with auxin transport.

Engineering plant architecture via CRISPR/Cas9-mediated alteration of strigolactone biosynthesis

BACKGROUND

Precision plant genome engineering holds much promise for targeted improvement of crop traits via unprecedented single-base level control over the genetic material. Strigolactones (SLs) are a key determinant of plant architecture, known for their role in inhibiting shoot branching (tillering).

RESULTS

We used CRISPR/Cas9 in rice (Oryza sativa) for targeted disruption of CAROTENOID CLEAVAGE DIOXYGENASE 7 (CCD7), which controls a key step in SL biosynthesis. The ccd7 mutants exhibited a striking increase in tillering, combined with a reduced height, which could be rescued by application of the synthetic SL analog GR24. Striga germination assays and liquid chromatography-mass spectrometry analysis showed that root exudates of ccd7 mutants were also SL deficient.

CONCLUSIONS

Taken together, our results show the potential and feasibility of the use of the CRISPR/Cas9 system for targeted engineering of plant architecture and for elucidating the molecular underpinnings of architecture-related traits.

Abscisic acid influences tillering by modulation of strigolactones in barley

Strigolactones (SLs) represent a class of plant hormones that are involved in inhibiting shoot branching and in promoting abiotic stress responses. There is evidence that the biosynthetic pathways of SLs and abscisic acid (ABA) are functionally connected. However, little is known about the mechanisms underlying the interaction of SLs and ABA, and the relevance of this interaction for shoot architecture. Based on sequence homology, four genes (HvD27, HvMAX1, HvCCD7, and HvCCD8) involved in SL biosynthesis were identified in barley and functionally verified by complementation of Arabidopsis mutants or by virus-induced gene silencing. To investigate the influence of ABA on SLs, two transgenic lines accumulating ABA as a result of RNAi-mediated down-regulation of HvABA 8'-hydroxylase 1 and 3 were employed. LC-MS/MS analysis confirmed higher ABA levels in root and stem base tissues in these transgenic lines. Both lines showed enhanced tiller formation and lower concentrations of 5-deoxystrigol in root exudates, which was detected for the first time as a naturally occurring SL in barley. Lower expression levels of HvD27, HvMAX1, HvCCD7, and HvCCD8 indicated that ABA suppresses SL biosynthesis, leading to enhanced tiller formation in barley.

The tomato MAX1 homolog, SlMAX1, is involved in the biosynthesis of tomato strigolactones from carlactone

Strigolactones (SLs) are rhizosphere signalling molecules exuded by plants that induce seed germination of root parasitic weeds and hyphal branching of arbuscular mycorrhiza. They are also phytohormones regulating plant architecture. MORE AXILLARY GROWTH 1 (MAX1) and its homologs encode cytochrome P450 (CYP) enzymes that catalyse the conversion of the strigolactone precursor carlactone to canonical strigolactones in rice (Oryza sativa), and to an SL-like compound in Arabidopsis. Here, we characterized the tomato (Solanum lycopersicum) MAX1 homolog, SlMAX1. The targeting induced local lesions in genomes method was used to obtain Slmax1 mutants that exhibit strongly reduced production of orobanchol, solanacol and didehydro-orobanchol (DDH) isomers. This results in a severe strigolactone mutant phenotype in vegetative and reproductive development. Transient expression of SlMAX1 - together with SlD27, SlCCD7 and SlCCD8 - in Nicotiana benthamiana showed that SlMAX1 catalyses the formation of carlactonoic acid from carlactone. Plant feeding assays showed that carlactone, but not 4-deoxy-orobanchol, is the precursor of orobanchol, which in turn is the precursor of solanacol and two of the three DDH isomers. Inhibitor studies suggest that a 2-oxoglutarate-dependent dioxygenase is involved in orobanchol biosynthesis from carlactone and that the formation of solanacol and DDH isomers from orobanchol is catalysed by CYPs.